Contacts of the strand formed by residues 31 - 37 (chain E) in PDB entry 3VXR
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 31 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A THR* 4.3 0.2 + - - -
5C THR* 3.0 28.3 + - - -
6C PHE* 3.5 27.0 - - - +
98D TYR* 3.4 30.0 - - - -
29E HIS* 4.6 0.3 - - - +
30E ASN* 1.3 106.9 - - - +
32E LEU* 1.3 61.2 + - - +
33E TYR* 3.5 24.5 - - + +
48E TYR* 4.1 12.1 - - + -
49E PHE 3.2 14.4 - - - +
50E GLN* 3.1 36.4 + - + +
69E ARG* 4.2 2.2 - - - -
94E SER* 2.9 9.4 - - - -
95E SER* 2.9 40.3 + - - +
96E SER 4.9 0.2 + - - -
97E TRP 4.8 1.8 + - - -
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Residues in contact with LEU 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E CYS* 4.0 9.6 - - - -
25E PRO* 3.8 24.7 - - + -
31E ARG* 1.3 75.1 - - - +
33E TYR* 1.3 64.7 + - - +
34E TRP* 3.7 21.5 - - + +
48E TYR* 3.3 4.2 - - - +
49E PHE* 2.9 38.8 + - + -
69E ARG* 3.8 17.4 - - - +
73E SER 3.7 18.8 - - - +
75E SER* 3.4 36.8 - - - +
92E CYS* 3.8 8.1 - - - -
93E ALA 3.2 10.1 - - - +
94E SER* 4.2 1.3 - - - +
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Residues in contact with TYR 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C PHE* 4.0 1.0 - - - -
93D ARG* 3.2 14.9 + - - -
98D TYR* 3.6 22.5 + - + -
99D LYS* 4.3 9.2 - - - -
31E ARG* 3.5 28.1 - - + -
32E LEU* 1.3 76.1 - - - +
34E TRP* 1.3 62.8 + - - +
35E TYR* 3.8 19.0 - + + -
45E PHE* 4.6 3.4 - + + -
47E THR 3.7 4.3 - - - +
48E TYR* 3.7 26.5 - + + -
91E LEU 3.7 0.5 - - - +
92E CYS* 3.4 8.7 - - - -
93E ALA* 2.7 44.2 + - + +
95E SER* 2.9 32.3 + - - -
102E LEU* 3.6 37.0 - - + -
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Residues in contact with TRP 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E GLN* 3.9 21.3 - - - -
21E PHE* 4.2 16.4 - - + -
22E ARG 4.3 4.7 - - - -
23E CYS* 3.7 29.2 - - + -
32E LEU* 3.7 17.5 - - + +
33E TYR* 1.3 72.7 - - - +
35E TYR* 1.3 69.8 + - - +
45E PHE* 3.8 2.1 - - - -
46E LEU* 2.9 37.6 + - + -
47E THR* 2.8 36.3 + - + +
49E PHE* 4.3 4.3 - + - -
67E ALA* 4.4 4.3 - - + -
75E SER* 3.0 33.8 + - - -
76E THR 4.4 0.8 + - - -
77E LEU* 3.9 44.1 - - + +
90E TYR* 4.5 9.0 - - + -
91E LEU 3.5 19.5 - - - -
92E CYS* 4.0 3.4 - - + -
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Residues in contact with TYR 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LYS* 3.8 1.9 - - - +
100D LEU* 2.7 50.1 + - + +
102D PHE* 3.7 16.6 - + - -
33E TYR* 3.8 24.6 - - + -
34E TRP* 1.3 78.9 - - - +
36E ARG* 1.3 60.0 - - - +
43E PRO* 3.8 23.1 - - + -
44E GLU 3.2 22.9 - - - -
45E PHE* 3.5 23.8 - + - -
46E LEU* 3.5 10.5 - - - +
90E TYR* 3.4 5.5 - - - +
91E LEU* 2.8 46.2 + - + +
102E LEU* 4.3 10.9 - - + +
104E PHE* 3.9 16.6 - + - -
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Residues in contact with ARG 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E TYR* 1.3 74.4 - - - +
37E GLN* 1.3 62.9 + - - +
38E THR* 3.9 24.5 - - - +
43E PRO* 3.5 0.8 - - - +
44E GLU* 2.6 69.6 + - + +
46E LEU* 3.8 26.0 - - + +
65E PHE* 5.1 4.7 - - - -
85E GLY 3.2 26.1 + - - -
86E ASP* 4.3 3.4 + - - +
88E ALA* 3.7 15.2 - - + +
89E MET 3.5 3.8 - - - -
90E TYR* 3.7 28.4 + - + -
91E LEU* 5.2 0.2 - - - -
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Residues in contact with GLN 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLN* 2.7 44.1 + - - -
89D LEU* 4.5 2.2 - - - +
36E ARG* 1.3 77.4 - - - +
38E THR* 1.3 68.6 + - - +
40E GLY 6.0 0.2 - - - +
41E GLN 2.7 29.9 + - - +
42E GLY* 4.0 3.1 - - - -
43E PRO* 3.5 30.7 - - + +
44E GLU* 5.9 0.2 - - - -
88E ALA* 3.6 1.5 - - - +
89E MET* 2.8 52.2 + - + +
91E LEU* 4.0 13.3 - - + +
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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