Contacts of the strand formed by residues 31 - 35 (chain B) in PDB entry 2Q2U
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 ILE 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLY* 1.3 77.6 - - - +
32B ARG* 1.3 74.9 + - - +
33B SER 3.6 0.3 + - - -
41B SER* 5.7 0.7 - - - -
47B ILE* 5.5 4.5 - - + -
67B GLU* 3.4 3.5 + - - -
68B ILE* 2.7 46.6 + - + +
75B PHE* 4.7 3.8 - - + -
78B THR* 4.2 3.8 - - + +
79B THR* 3.9 23.8 - - - +
82B VAL* 3.8 39.3 - - + -
83B MET* 4.6 6.1 - - + -
30H OMC 3.4 49.1 - - - +
31H C 4.3 2.2 - - - -
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Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PRO* 3.7 8.7 - - + +
7B LEU* 2.8 43.8 + - - +
8B LEU* 3.7 15.8 - - - +
31B ILE* 1.3 85.6 - - - +
33B SER* 1.3 63.3 + - - +
34B VAL* 4.4 3.1 - - + +
41B SER* 3.8 4.2 - - - -
42B ARG* 3.7 34.0 + - + +
47B ILE* 4.7 0.5 - - - +
65B ASP* 2.6 41.0 + - - -
66B GLY 3.3 16.4 - - - -
67B GLU* 3.6 18.0 + - - +
98B PHE* 3.5 15.5 - - - -
172B TYR* 3.5 1.4 + - - -
31H C 3.4 16.7 + - - +
32H C 5.8 1.8 - - - +
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Residues in contact with SER 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG* 1.3 79.2 - - - +
34B VAL* 1.3 59.2 + - - +
39B MET* 3.2 19.9 - - - +
40B LEU 2.9 17.3 + - - -
41B SER* 4.6 0.4 - - - +
47B ILE* 3.5 16.2 - - - +
66B GLY 2.9 16.2 + - - +
68B ILE* 3.8 28.4 - - - +
95B TYR* 2.8 29.6 + - - -
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 3.7 29.4 - - + -
6B PRO* 4.3 22.2 - - + -
32B ARG* 4.4 4.0 - - + +
33B SER* 1.3 75.4 - - - +
35B LYS* 1.3 64.2 + - - +
36B GLN* 3.6 11.9 + - + +
39B MET* 3.7 3.2 - - - -
40B LEU* 2.8 38.3 + - + +
41B SER 5.2 3.3 + - - +
44B PHE* 4.4 18.8 - - + -
64B SER 3.2 13.5 - - - +
65B ASP* 3.3 24.9 - - - +
172B TYR* 4.5 2.0 - - - +
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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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34B VAL* 1.3 70.0 - - - +
36B GLN* 1.3 75.5 + - - +
37B THR 3.9 7.9 - - - +
38B GLN 3.3 11.7 - - - +
39B MET* 3.5 19.9 - - - +
57B THR* 3.3 35.3 + - - +
60B LEU* 2.6 33.1 + - + +
61B PRO* 3.4 14.2 - - - +
62B GLU* 3.3 24.5 + - - +
63B GLY* 2.8 23.4 + - - -
64B SER* 2.7 27.4 + - - +
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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
------------------------------------------------------------
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