Contacts of the helix formed by residues 334 - 364 (chain K) 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 GLY 334 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333K TYR* 3.8 29.4 - - - +
335K PRO* 3.8 29.6 - - - -
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Residues in contact with PRO 335 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334K GLY* 3.8 30.1 - - - -
336K ALA* 3.8 27.6 - - - -
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Residues in contact with ALA 336 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335K PRO* 3.8 25.8 - - - -
337K TRP* 3.8 29.4 - - - +
339K ALA* 4.4 16.8 - - - +
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Residues in contact with TRP 337 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336K ALA* 3.8 25.1 - - - +
338K ILE* 3.8 29.2 - - - +
340K TYR* 4.7 14.6 - - - +
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Residues in contact with ILE 338 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337K TRP* 3.8 24.9 - - - +
339K ALA* 3.8 29.6 - - - +
341K GLY* 4.5 14.6 - - - +
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Residues in contact with ALA 339 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336K ALA* 4.4 16.8 - - - +
338K ILE* 3.8 29.2 - - - +
340K TYR* 3.8 25.8 - - - +
342K HIS* 4.7 15.9 - - - +
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Residues in contact with TYR 340 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337K TRP* 4.7 14.1 - - - +
339K ALA* 3.8 23.8 - - - +
341K GLY* 3.8 29.2 - - - +
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Residues in contact with GLY 341 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338K ILE* 4.5 17.7 - - - +
340K TYR* 3.8 29.4 - - - +
342K HIS* 3.8 25.6 - - - +
353K ALA* 4.1 25.1 - - - +
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Residues in contact with HIS 342 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339K ALA* 4.7 14.8 - - - +
341K GLY* 3.8 28.5 - - - +
343K SER* 3.8 24.5 - - - +
345K ALA* 4.3 17.7 - - - +
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Residues in contact with SER 343 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342K HIS* 3.8 26.9 - - - +
344K PHE* 3.7 29.6 - - - +
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Residues in contact with PHE 344 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343K SER* 3.7 29.4 - - - +
345K ALA* 3.8 25.8 - - - +
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Residues in contact with ALA 345 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342K HIS* 4.3 20.6 - - - +
344K PHE* 3.8 24.5 - - - +
346K VAL* 3.8 29.4 - - - +
348K SER* 4.2 19.1 - - - +
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Residues in contact with VAL 346 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345K ALA* 3.8 29.6 - - - +
347K GLU* 3.8 26.7 - - - +
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Residues in contact with GLU 347 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346K VAL* 3.8 28.7 - - - +
348K SER* 3.8 24.7 - - - +
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Residues in contact with SER 348 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345K ALA* 4.2 22.7 - - - +
347K GLU* 3.8 28.3 - - - +
349K GLU* 3.8 29.2 - - - +
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Residues in contact with GLU 349 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348K SER* 3.8 24.0 - - - +
350K HIS* 3.7 30.7 - - - +
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Residues in contact with HIS 350 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349K GLU* 3.7 30.3 - - - +
351K ASP* 3.8 29.4 - - - +
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Residues in contact with ASP 351 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350K HIS* 3.8 29.6 - - - +
352K GLN* 3.8 28.0 - - - +
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Residues in contact with GLN 352 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351K ASP* 3.8 26.9 - - - +
353K ALA* 3.8 29.2 - - - +
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Residues in contact with ALA 353 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341K GLY* 4.1 25.4 - - - +
352K GLN* 3.8 28.7 - - - +
354K MET* 3.8 26.7 - - - +
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Residues in contact with MET 354 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353K ALA* 3.8 26.5 - - - +
355K ALA* 3.8 29.4 - - - +
357K TYR* 4.6 13.5 - - - +
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Residues in contact with ALA 355 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354K MET* 3.8 29.4 - - - +
356K ALA* 3.8 26.7 - - - +
358K PHE* 4.5 16.6 - - - +
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Residues in contact with ALA 356 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355K ALA* 3.8 25.6 - - - +
357K TYR* 3.8 30.1 - - - +
359K THR* 4.3 16.2 - - - +
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Residues in contact with TYR 357 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354K MET* 4.6 16.4 - - - +
356K ALA* 3.8 29.4 - - - +
358K PHE* 3.8 25.1 - - - +
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Residues in contact with PHE 358 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355K ALA* 4.5 14.6 - - - +
357K TYR* 3.8 29.2 - - - +
359K THR* 3.8 24.7 - - - +
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Residues in contact with THR 359 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356K ALA* 4.3 19.7 - - - +
358K PHE* 3.8 27.8 - - - +
360K ALA* 3.8 29.4 - - - +
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Residues in contact with ALA 360 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359K THR* 3.8 29.2 - - - +
361K ALA* 3.8 26.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA 361 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360K ALA* 3.8 26.5 - - - +
362K GLN* 3.8 28.7 - - - +
----------------------------------------------------------
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Residues in contact with GLN 362 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361K ALA* 3.8 26.5 - - - +
363K LEU* 3.7 30.1 - - - +
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Residues in contact with LEU 363 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362K GLN* 3.7 29.4 - - - +
364K MET* 3.8 27.4 - - - +
----------------------------------------------------------
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Residues in contact with MET 364 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174K HIS* 4.6 16.4 - - - +
363K LEU* 3.8 28.3 - - - +
365K LYS* 3.8 29.8 - - - +
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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) + - + + + + + -
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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