Contacts of the helix formed by residues 430 - 438 (chain A) in PDB entry 2WSC
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 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A GLY* 2.6 39.2 - - - +
345A GLY 5.2 4.7 - - - -
346A LEU* 4.4 8.7 - - - +
347A TYR* 4.4 15.1 - - - -
427A ARG 2.7 26.8 - - - +
428A TYR 2.7 2.7 + - - +
429A ASN* 1.3 73.1 - - - +
431A LEU* 1.3 66.9 + - - +
432A LEU* 2.5 10.5 + - - +
433A ASP* 2.6 24.8 + - - +
434A ARG* 2.5 52.3 + - - +
1779A CLA 5.5 0.2 - - - +
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Residues in contact with LEU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A GLY* 3.7 18.6 - - - +
342A GLY* 3.6 3.8 - - - -
343A HIS* 3.6 39.5 - - + +
346A LEU* 3.7 6.7 - - + -
430A ASP* 1.3 82.3 + - - +
432A LEU* 1.3 50.4 + - - +
434A ARG* 3.5 10.7 - - - +
435A VAL* 2.5 33.1 + - - +
1779A CLA 3.5 62.8 - - + +
1786A CLA 3.9 20.0 - - + +
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Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A TYR* 3.3 33.0 - - + +
417A PHE* 4.9 5.2 - - + -
418A MET* 4.6 24.7 - - + -
427A ARG* 6.4 0.2 - - + -
430A ASP* 2.5 11.9 + - - +
431A LEU* 1.3 72.8 - - + +
433A ASP* 1.3 64.7 + - - +
434A ARG 2.5 5.8 + - - -
435A VAL* 2.5 36.6 + - + -
436A LEU* 2.8 28.7 + - + +
1776A CLA 4.3 12.3 - - + -
1779A CLA 4.2 19.7 - - + -
1805A BCR 4.4 11.2 - - + -
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Residues in contact with ASP 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ARG* 4.2 19.0 + - - +
428A TYR* 3.1 20.8 - - - -
429A ASN* 3.2 10.6 + - - +
430A ASP* 2.6 50.0 + - - +
432A LEU* 1.3 75.9 - - - +
434A ARG* 1.3 62.5 + - - +
436A LEU* 4.4 10.2 - - - +
437A ARG* 3.2 36.1 + - - +
64D GLY* 4.3 18.4 - - - +
65D ALA* 5.3 1.8 - - + +
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Residues in contact with ARG 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A PHE 5.1 0.2 - - - -
339A THR 4.0 19.0 + - - -
340A GLY* 4.5 2.5 - - - -
341A GLN* 3.2 39.2 - - - +
342A GLY 4.1 0.6 - - - +
429A ASN* 2.7 37.4 + - - +
430A ASP* 2.5 41.6 + - - +
431A LEU* 3.5 12.1 - - - +
432A LEU 2.5 5.7 + - - -
433A ASP* 1.3 66.3 - - - +
435A VAL* 1.3 56.3 + - - +
437A ARG* 2.5 55.2 + - + +
438A HIS* 3.6 4.1 + - - -
1786A CLA 3.9 23.6 - - + +
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Residues in contact with VAL 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A LEU 2.5 31.4 - - - +
432A LEU* 2.5 19.0 + - + -
434A ARG* 1.3 70.6 - - - +
436A LEU* 1.3 54.4 - - + +
438A HIS* 1.7 57.5 + - + +
442A ILE* 3.8 21.7 - - + +
561A LEU* 3.9 22.4 - - + -
1776A CLA 3.8 33.2 - - + -
1779A CLA 3.9 11.0 - - + -
1786A CLA 4.7 7.8 - - + +
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Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A MET* 4.5 14.8 - - + -
427A ARG* 6.1 2.7 - - - +
432A LEU* 2.8 39.4 + - + +
433A ASP* 4.3 12.8 - - - +
435A VAL* 1.3 72.7 - - + +
437A ARG* 1.4 61.0 + - - +
438A HIS 2.4 22.4 - - - +
439A ARG* 2.8 26.1 - - + +
561A LEU* 3.7 28.5 - - + +
564A ARG* 5.7 9.4 - - + +
1776A CLA 6.5 0.2 - - + -
63D GLY* 4.1 19.7 - - - +
64D GLY 4.6 13.2 - - - +
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Residues in contact with ARG 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A ASN* 3.8 22.8 - - - +
433A ASP* 3.2 28.6 + - - +
434A ARG* 2.5 44.0 + - - +
436A LEU* 1.4 70.0 - - - +
438A HIS* 1.3 55.7 + - - +
440A ASP* 4.7 0.3 - - - +
1786A CLA 5.6 7.9 - - - -
29D PHE* 2.9 30.6 + - + -
30D ALA* 3.9 12.7 - - - +
31D GLY* 4.6 10.4 - - - +
32D SER* 3.4 22.9 + - - -
33D THR* 2.9 27.4 + - - -
34D GLY 4.3 1.4 + - - -
62D THR 5.3 0.3 - - - +
63D GLY 4.1 8.2 + - - +
64D GLY* 3.9 5.8 - - - -
65D ALA 3.8 26.7 + - - +
23L LEU* 4.2 6.5 - - + -
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Residues in contact with HIS 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A ARG 3.8 2.1 + - - -
435A VAL* 1.7 71.7 + - - +
436A LEU 2.4 14.6 - - - +
437A ARG* 1.3 74.4 - - - +
439A ARG* 1.3 56.3 + - - +
441A ALA* 3.4 17.3 - - + -
442A ILE* 3.2 30.6 - - + +
1786A CLA 2.7 84.8 + + + -
1787A CLA 5.6 0.9 - - - +
33D THR* 3.2 9.9 - - + +
23L LEU* 4.1 12.6 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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