Contacts of the helix formed by residues 315 - 377 (chain I) in PDB entry 5KHU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 315 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314I SER* 3.8 24.5 - - - +
316I GLU* 3.8 29.4 - - - +
318I GLN* 4.6 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 316 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315I ALA* 3.8 26.2 - - - +
317I LEU* 3.8 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 317 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316I GLU* 3.8 29.2 - - - +
318I GLN* 3.8 25.4 - - - +
320I LEU* 4.3 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 318 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315I ALA* 4.6 16.8 - - - +
317I LEU* 3.8 26.2 - - - +
319I THR* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 319 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318I GLN* 3.8 29.4 - - - +
320I LEU* 3.8 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317I LEU* 4.3 16.6 - - - +
319I THR* 3.8 27.1 - - - +
321I LEU* 3.8 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320I LEU* 3.8 28.9 - - - +
322I MET* 3.8 26.9 - - - +
324I GLN* 4.1 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 322 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321I LEU* 3.8 25.1 - - - +
323I ASN* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 323 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322I MET* 3.8 28.9 - - - +
324I GLN* 3.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 324 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321I LEU* 4.1 17.3 - - - +
323I ASN* 3.8 28.7 - - - +
325I LEU* 3.8 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324I GLN* 3.8 28.7 - - - +
326I THR* 3.8 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 326 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325I LEU* 3.8 29.2 - - - +
327I VAL* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 327 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326I THR* 3.8 29.6 - - - +
328I LYS* 3.8 25.4 - - - +
330I LEU* 4.6 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 328 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327I VAL* 3.8 26.5 - - - +
329I GLY* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 329 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328I LYS* 3.8 25.8 - - - +
330I LEU* 3.8 29.2 - - - +
332I LYS* 4.3 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327I VAL* 4.6 15.5 - - - +
329I GLY* 3.8 29.2 - - - +
331I LYS* 3.8 24.9 - - - +
333I LEU* 4.5 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 331 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330I LEU* 3.8 25.1 - - - +
332I LYS* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 332 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329I GLY* 4.3 17.3 - - - +
331I LYS* 3.8 28.7 - - - +
333I LEU* 3.8 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330I LEU* 4.5 14.8 - - - +
332I LYS* 3.8 27.8 - - - +
334I GLY* 3.8 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 334 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333I LEU* 3.8 30.1 - - - +
335I GLN* 3.8 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 335 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334I GLY* 3.8 25.6 - - - +
336I SER* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 336 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335I GLN* 3.8 28.9 - - - +
337I ILE* 3.8 25.8 - - - +
339I SER* 4.5 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 337 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336I SER* 3.8 25.8 - - - +
338I GLU* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 338 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337I ILE* 3.8 29.6 - - - +
339I SER* 3.8 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 339 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336I SER* 4.5 18.2 - - - +
338I GLU* 3.8 27.8 - - - +
340I SER* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 340 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339I SER* 3.8 28.9 - - - +
341I TYR* 3.8 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 341 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340I SER* 3.8 25.4 - - - +
342I SER* 3.8 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 342 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341I TYR* 3.8 28.9 - - - +
343I SER* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 343 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342I SER* 3.8 29.4 - - - +
344I ILE* 3.8 26.5 - - - +
346I LYS* 4.4 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 344 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343I SER* 3.8 26.7 - - - +
345I GLN* 3.8 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 345 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344I ILE* 3.8 29.8 - - - +
346I LYS* 3.8 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 346 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343I SER* 4.4 15.7 - - - +
345I GLN* 3.8 28.9 - - - +
347I LEU* 3.8 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 347 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346I LYS* 3.8 28.7 - - - +
348I VAL* 3.8 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 348 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347I LEU* 3.8 27.6 - - - +
349I ILE* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 349 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348I VAL* 3.8 28.0 - - - +
350I SER* 3.8 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 350 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349I ILE* 3.8 28.9 - - - +
351I HIS* 3.8 26.9 - - - +
353I GLN* 4.3 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 351 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350I SER* 3.8 28.9 - - - +
352I LEU* 3.8 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351I HIS* 3.8 25.1 - - - +
353I GLN* 3.8 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350I SER* 4.3 17.9 - - - +
352I LEU* 3.8 29.2 - - - +
354I SER* 3.8 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 354 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353I GLN* 3.8 29.2 - - - +
355I GLY* 3.8 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 355 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354I SER* 3.8 25.8 - - - +
356I SER* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 356 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355I GLY* 3.8 30.3 - - - +
357I GLU* 3.8 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 357 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356I SER* 3.8 26.7 - - - +
358I SER* 3.8 29.8 - - - +
360I LEU* 4.6 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 358 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357I GLU* 3.8 25.6 - - - +
359I LEU* 3.8 29.6 - - - +
361I TYR* 4.6 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 359 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358I SER* 3.8 26.0 - - - +
360I LEU* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357I GLU* 4.6 15.0 - - - +
359I LEU* 3.8 29.4 - - - +
361I TYR* 3.8 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 361 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358I SER* 4.6 16.4 - - - +
360I LEU* 3.8 26.0 - - - +
362I HIS* 3.7 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 362 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361I TYR* 3.7 29.8 - - - +
363I LEU* 3.8 25.8 - - - +
365I GLU* 4.1 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 363 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362I HIS* 3.8 24.9 - - - +
364I SER* 3.7 29.6 - - - +
366I LEU* 4.5 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 364 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363I LEU* 3.7 29.6 - - - +
365I GLU* 3.8 25.1 - - - +
367I LYS* 4.3 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 365 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362I HIS* 4.1 18.2 - - - +
364I SER* 3.8 29.2 - - - +
366I LEU* 3.8 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363I LEU* 4.5 13.9 - - - +
365I GLU* 3.8 30.1 - - - +
367I LYS* 3.8 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 367 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364I SER* 4.3 19.5 - - - +
366I LEU* 3.8 26.0 - - - +
368I GLY* 3.8 29.4 - - - +
370I ALA* 4.5 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 368 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367I LYS* 3.8 28.9 - - - +
369I MET* 3.8 26.0 - - - +
371I SER* 4.5 15.7 - - - +
653O ALA* 4.1 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 369 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368I GLY* 3.8 28.9 - - - +
370I ALA* 3.8 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 370 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367I LYS* 4.5 15.0 - - - +
369I MET* 3.8 30.3 - - - +
371I SER* 3.8 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 371 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368I GLY* 4.5 18.4 - - - +
370I ALA* 3.8 26.7 - - - +
372I TRP* 3.8 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 372 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371I SER* 3.8 28.9 - - - +
373I LYS* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 373 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372I TRP* 3.8 29.4 - - - +
374I GLN* 3.8 29.4 - - - +
377I GLU* 4.4 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 374 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373I LYS* 3.8 28.0 - - - +
375I LYS* 3.8 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 375 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374I GLN* 3.8 28.3 - - - +
376I TYR* 3.8 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 376 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375I LYS* 3.8 29.4 - - - +
377I GLU* 3.8 28.5 - - - +
379I LEU* 4.6 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 377 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373I LYS* 4.4 17.7 - - - +
376I TYR* 3.8 28.9 - - - +
378I PRO* 3.8 25.6 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il