Contacts of the helix formed by residues 30 - 40 (chain B) in PDB entry 2WWB
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 ARG 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B PRO 3.4 6.3 + - - -
29B ASP* 1.4 65.1 - - - +
31B LYS* 1.4 63.2 + - - +
32B GLU 3.2 0.9 - - - -
33B PHE* 3.3 34.2 + - + +
34B GLN* 3.6 11.3 + - - +
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Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ASP 2.8 9.1 + - - +
30B ARG* 1.4 73.0 - - - +
32B GLU* 1.4 82.6 + - - +
34B GLN* 3.5 6.9 + - - +
35B LYS* 3.0 45.0 + - - +
80D A 5.1 13.3 + - - -
81D U 5.3 6.7 + - - -
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B PRO* 3.5 11.2 - - + +
29B ASP* 3.3 21.9 + - - +
30B ARG 3.2 0.6 - - - -
31B LYS* 1.4 100.1 - - - +
33B PHE* 1.4 62.2 + - - +
35B LYS* 3.5 34.6 + - + +
36B ILE* 3.2 35.9 + - + +
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Residues in contact with PHE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ILE* 4.7 15.7 - - + -
257A TYR* 4.2 17.3 - + - -
27B LYS* 4.0 24.2 - - + -
28B PRO* 3.3 44.9 + - + +
29B ASP* 5.4 0.2 - - - -
30B ARG* 3.3 36.6 + - + +
32B GLU* 1.4 77.5 - - - +
34B GLN* 1.4 62.6 + - - +
36B ILE* 3.6 14.2 - - + +
37B ALA* 3.7 11.3 - - - +
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ARG 3.6 6.7 + - - +
31B LYS* 3.5 10.1 + - - +
33B PHE* 1.4 77.5 - - - +
35B LYS* 1.4 60.0 + - - +
37B ALA* 3.5 8.2 + - - +
38B MET* 3.0 47.5 + - + +
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Residues in contact with LYS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 3.0 42.0 + - + +
32B GLU* 3.5 33.5 + - + +
33B PHE 3.4 0.6 - - - -
34B GLN* 1.4 76.8 - - - +
36B ILE* 1.4 59.5 + - + +
38B MET* 3.4 21.8 + - + +
39B ALA* 3.1 29.8 + - + +
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ILE* 4.0 30.7 - - + +
259A GLN* 5.3 8.7 - - + +
455A TYR* 3.5 21.9 - - + -
459A GLU* 4.8 19.5 - - - +
28B PRO* 3.8 24.0 - - + -
32B GLU* 3.2 28.4 + - + +
33B PHE* 3.6 9.6 - - - +
35B LYS* 1.4 77.1 - - + +
37B ALA* 1.4 66.3 + - + +
39B ALA* 3.6 4.9 + - - +
40B THR* 3.4 18.7 + - - -
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A PHE* 5.8 8.3 - - + -
455A TYR* 4.4 12.1 - - - +
33B PHE 3.7 15.5 + - - +
34B GLN* 3.5 13.2 + - - +
35B LYS 3.4 0.4 - - - -
36B ILE* 1.4 83.1 - - + +
38B MET* 1.4 60.0 + - - +
40B THR 3.3 5.4 - - - -
41B ALA* 3.1 30.9 + - + +
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Residues in contact with MET 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLN* 3.0 34.6 + - + +
35B LYS* 3.6 26.7 - - + +
36B ILE 3.4 0.2 - - - -
37B ALA* 1.4 73.7 - - - +
39B ALA* 1.4 61.9 + - + +
40B THR 3.0 13.2 - - - +
41B ALA* 5.2 0.8 - - - +
42B ILE* 4.8 9.9 - - - +
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A PHE* 3.5 37.7 - - + -
459A GLU* 6.1 4.5 - - + -
470A SER* 5.2 9.6 - - - +
35B LYS* 3.1 21.0 + - + +
36B ILE* 4.0 6.1 - - - +
37B ALA 3.4 0.2 - - - -
38B MET* 1.4 75.1 - - + +
40B THR* 1.4 65.2 - - - +
42B ILE* 5.8 0.2 - - - +
43B GLY* 4.9 3.8 + - - -
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Residues in contact with THR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A ILE* 4.0 25.7 + - + +
455A TYR* 3.3 47.5 + - + -
458A PHE* 5.1 7.8 - - + +
36B ILE 3.4 5.0 + - - -
37B ALA 3.3 4.4 - - - +
38B MET 3.0 15.8 - - - +
39B ALA* 1.4 79.3 - - - +
41B ALA* 1.4 61.2 + - - +
42B ILE* 2.7 18.2 + - - +
43B GLY* 3.4 10.3 + - - +
44B PHE* 3.7 22.4 - - + +
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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