Contacts of the helix formed by residues 382 - 429 (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 ASP 382 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381I LEU* 3.8 28.5 - - - +
383I ALA* 3.8 29.2 - - - +
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Residues in contact with ALA 383 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382I ASP* 3.8 29.4 - - - +
384I ALA* 3.8 27.4 - - - +
386I ILE* 4.4 18.4 - - - +
----------------------------------------------------------
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Residues in contact with ALA 384 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383I ALA* 3.8 26.7 - - - +
385I GLY* 3.8 29.4 - - - +
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Residues in contact with GLY 385 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384I ALA* 3.8 29.6 - - - +
386I ILE* 3.8 25.8 - - - +
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Residues in contact with ILE 386 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383I ALA* 4.4 16.2 - - - +
385I GLY* 3.8 26.5 - - - +
387I GLU* 3.8 28.9 - - - +
389I ALA* 4.5 16.4 - - - +
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Residues in contact with GLU 387 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386I ILE* 3.8 24.9 - - - +
388I GLU* 3.7 29.4 - - - +
----------------------------------------------------------
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Residues in contact with GLU 388 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387I GLU* 3.7 30.1 - - - +
389I ALA* 3.8 26.5 - - - +
----------------------------------------------------------
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Residues in contact with ALA 389 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386I ILE* 4.5 13.9 - - - +
388I GLU* 3.8 23.8 - - - +
390I ILE* 3.8 29.6 - - - +
----------------------------------------------------------
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Residues in contact with ILE 390 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389I ALA* 3.8 28.9 - - - +
391I THR* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with THR 391 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390I ILE* 3.8 24.9 - - - +
392I ALA* 3.8 29.6 - - - +
----------------------------------------------------------
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Residues in contact with ALA 392 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391I THR* 3.8 26.2 - - - +
393I VAL* 3.8 29.4 - - - +
----------------------------------------------------------
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Residues in contact with VAL 393 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392I ALA* 3.8 29.8 - - - +
394I GLY* 3.8 27.8 - - - +
----------------------------------------------------------
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Residues in contact with GLY 394 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393I VAL* 3.8 27.4 - - - +
395I SER* 3.7 28.9 - - - +
----------------------------------------------------------
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Residues in contact with SER 395 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394I GLY* 3.7 29.8 - - - +
396I PHE* 3.8 25.4 - - - +
----------------------------------------------------------
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Residues in contact with PHE 396 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395I SER* 3.8 29.4 - - - +
397I ILE* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with ILE 397 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396I PHE* 3.8 26.7 - - - +
398I LEU* 3.7 30.1 - - - +
----------------------------------------------------------
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Residues in contact with LEU 398 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397I ILE* 3.7 29.8 - - - +
399I LYS* 3.8 26.9 - - - +
401I ASN* 4.6 15.9 - - - +
----------------------------------------------------------
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Residues in contact with LYS 399 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398I LEU* 3.8 25.1 - - - +
400I ALA* 3.8 30.1 - - - +
402I GLU* 4.4 15.3 - - - +
----------------------------------------------------------
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Residues in contact with ALA 400 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399I LYS* 3.8 25.8 - - - +
401I ASN* 3.8 29.8 - - - +
----------------------------------------------------------
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Residues in contact with ASN 401 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398I LEU* 4.6 13.7 - - - +
400I ALA* 3.8 25.4 - - - +
402I GLU* 3.8 28.9 - - - +
404I LEU* 4.2 18.2 - - - +
----------------------------------------------------------
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Residues in contact with GLU 402 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399I LYS* 4.4 17.7 - - - +
401I ASN* 3.8 28.7 - - - +
403I LEU* 3.8 26.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 403 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402I GLU* 3.8 29.2 - - - +
404I LEU* 3.8 25.1 - - - +
----------------------------------------------------------
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Residues in contact with LEU 404 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401I ASN* 4.2 19.7 - - - +
403I LEU* 3.8 26.9 - - - +
405I GLN* 3.8 28.9 - - - +
407I ILE* 4.5 15.3 - - - +
----------------------------------------------------------
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Residues in contact with GLN 405 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404I LEU* 3.8 29.4 - - - +
406I VAL* 3.8 26.5 - - - +
----------------------------------------------------------
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Residues in contact with VAL 406 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405I GLN* 3.8 25.1 - - - +
407I ILE* 3.8 30.1 - - - +
409I SER* 4.5 17.0 - - - +
----------------------------------------------------------
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Residues in contact with ILE 407 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404I LEU* 4.5 17.7 - - - +
406I VAL* 3.8 28.9 - - - +
408I ASP* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with ASP 408 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407I ILE* 3.8 28.9 - - - +
409I SER* 3.8 26.0 - - - +
----------------------------------------------------------
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Residues in contact with SER 409 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406I VAL* 4.5 17.3 - - - +
408I ASP* 3.8 28.9 - - - +
410I SER* 3.8 26.5 - - - +
----------------------------------------------------------
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Residues in contact with SER 410 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409I SER* 3.8 29.4 - - - +
411I MET* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with MET 411 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410I SER* 3.8 28.0 - - - +
412I LYS* 3.8 28.3 - - - +
----------------------------------------------------------
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Residues in contact with LYS 412 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411I MET* 3.8 28.7 - - - +
413I ASN* 3.8 26.0 - - - +
415I LYS* 4.4 18.4 - - - +
----------------------------------------------------------
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Residues in contact with ASN 413 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412I LYS* 3.8 27.4 - - - +
414I PHE* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with PHE 414 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413I ASN* 3.8 28.9 - - - +
415I LYS* 3.8 26.9 - - - +
417I PHE* 4.6 16.2 - - - +
----------------------------------------------------------
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Residues in contact with LYS 415 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412I LYS* 4.4 19.1 - - - +
414I PHE* 3.8 27.1 - - - +
416I ALA* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with ALA 416 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415I LYS* 3.8 25.6 - - - +
417I PHE* 3.8 28.9 - - - +
419I ARG* 4.2 20.4 - - - +
----------------------------------------------------------
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Residues in contact with PHE 417 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414I PHE* 4.6 16.8 - - - +
416I ALA* 3.8 24.2 - - - +
418I PHE* 3.8 29.8 - - - +
----------------------------------------------------------
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Residues in contact with PHE 418 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417I PHE* 3.8 29.2 - - - +
419I ARG* 3.8 25.8 - - - +
----------------------------------------------------------
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Residues in contact with ARG 419 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416I ALA* 4.2 17.5 - - - +
418I PHE* 3.8 29.6 - - - +
420I TRP* 3.8 27.1 - - - +
----------------------------------------------------------
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Residues in contact with TRP 420 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419I ARG* 3.8 26.0 - - - +
421I LEU* 3.8 28.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 421 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420I TRP* 3.8 28.9 - - - +
422I TYR* 3.8 27.1 - - - +
424I ALA* 4.5 15.9 - - - +
----------------------------------------------------------
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Residues in contact with TYR 422 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421I LEU* 3.8 28.5 - - - +
423I VAL* 3.8 25.1 - - - +
425I MET* 4.6 15.0 - - - +
----------------------------------------------------------
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Residues in contact with VAL 423 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422I TYR* 3.8 26.0 - - - +
424I ALA* 3.8 28.5 - - - +
426I LEU* 4.3 16.8 - - - +
----------------------------------------------------------
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Residues in contact with ALA 424 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421I LEU* 4.5 16.4 - - - +
423I VAL* 3.8 24.9 - - - +
425I MET* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with MET 425 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422I TYR* 4.6 14.4 - - - +
424I ALA* 3.8 29.2 - - - +
426I LEU* 3.8 25.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 426 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423I VAL* 4.3 16.8 - - - +
425I MET* 3.8 29.2 - - - +
427I ARG* 3.8 26.9 - - - +
----------------------------------------------------------
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Residues in contact with ARG 427 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426I LEU* 3.8 29.4 - - - +
428I MET* 3.8 28.3 - - - +
----------------------------------------------------------
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Residues in contact with MET 428 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427I ARG* 3.8 28.9 - - - +
429I THR* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with THR 429 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428I MET* 3.8 27.1 - - - +
430I GLU* 3.8 29.2 - - - +
----------------------------------------------------------
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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