Contacts of the strand formed by residues 33 - 39 (chain E) in PDB entry 2VLR
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 ALA 33 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E HIS* 3.6 0.7 - - - +
32E ASP* 1.3 77.7 - - - +
34E MET* 1.3 66.6 + - - +
35E TYR* 3.6 27.8 - - + +
51E SER 3.2 11.4 - - - +
52E GLN* 4.0 7.6 - - - +
95E SER* 3.1 6.9 - - - -
96E SER* 2.9 34.9 + - - +
99E ALA* 3.8 22.0 - - - +
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Residues in contact with MET 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ILE* 5.6 0.2 - - - -
25E CYS* 4.9 10.8 - - - -
27E GLN* 3.7 23.8 - - - +
32E ASP 4.2 0.2 + - - -
33E ALA* 1.3 79.2 - - - +
35E TYR* 1.3 65.9 + - - +
50E TYR* 3.5 2.9 - - - +
51E SER 3.0 31.8 + - - +
70E ARG* 2.9 30.7 - - - +
73E LYS 2.7 33.2 - - - +
74E GLU 4.2 4.7 - - - +
75E SER 3.8 12.1 - - - +
76E PHE* 3.5 33.8 - - + -
93E CYS* 5.1 2.0 - - - -
94E ALA 3.3 7.6 - - - +
95E SER* 4.0 11.2 - - - -
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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
----------------------------------------------------------
97D GLY 2.7 29.3 + - - -
98D ASN* 3.8 12.1 - - + -
33E ALA* 3.6 25.1 - - + +
34E MET* 1.3 79.5 - - - +
36E TRP* 1.3 60.7 + - - +
37E TYR* 3.8 14.4 - - + -
47E LEU* 4.3 10.3 - - + -
49E TYR 3.8 4.9 - - - -
50E TYR* 3.4 30.3 - + + -
51E SER 5.3 0.7 - - - -
52E GLN* 5.1 0.2 - - - +
76E PHE* 3.9 2.6 - - - -
93E CYS* 3.4 10.9 - - - -
94E ALA* 3.1 32.1 + - + +
96E SER* 3.7 11.2 - - - -
99E ALA* 3.3 20.6 - - - +
100E SER 3.7 3.7 + - - -
103E GLN* 3.5 42.8 - - + +
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Residues in contact with TRP 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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8E GLN* 3.4 29.8 - - - -
23E LEU* 3.9 26.2 - - + -
24E SER 3.7 13.2 - - - -
25E CYS* 3.7 18.6 - - + -
35E TYR* 1.3 71.7 - - - +
37E TYR* 1.3 62.3 + - - +
47E LEU* 3.5 9.9 - - - +
48E ILE* 3.1 34.7 + - + +
49E TYR 3.1 13.4 + - - +
68E VAL* 4.4 7.6 - - + -
76E PHE* 2.9 50.8 + + - -
78E LEU* 3.6 37.6 - - + +
91E TYR* 3.9 18.6 - - + -
92E LEU 3.5 23.8 - - - -
93E CYS* 4.0 9.3 - - + -
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Residues in contact with TYR 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ASN* 6.0 0.2 - - - +
99D LEU* 4.8 5.1 + - - +
101D PHE* 3.5 30.4 - + - -
35E TYR* 3.8 16.7 - - + +
36E TRP* 1.3 75.5 - - - +
38E ARG* 1.3 60.8 + - - +
45E LEU* 4.1 22.7 - - + -
46E ARG 3.2 20.9 - - - +
47E LEU* 3.8 29.9 - - + +
48E ILE* 3.9 4.9 - - - -
91E TYR* 3.6 9.4 - - - +
92E LEU* 3.0 43.9 + - + +
94E ALA* 4.3 2.5 - - + -
103E GLN* 2.7 39.1 + - - -
105E PHE* 3.7 24.9 - + - -
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Residues in contact with ARG 38 (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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37E TYR* 1.3 76.2 - - - +
39E GLN* 1.3 61.4 + - - +
40E ASP* 3.0 29.1 + - - -
44E GLY 4.0 0.7 - - - +
45E LEU* 3.8 1.0 - - - -
46E ARG* 2.9 67.1 + - + +
48E ILE* 3.8 17.3 - - + +
62E ILE* 4.5 14.2 - - + +
66E TYR* 2.8 38.5 + - - -
86E ASN* 2.8 50.6 + - - +
88E THR 3.8 8.9 + - - -
89E ALA* 4.0 9.6 - - + +
90E PHE 3.5 5.4 - - - +
91E TYR* 4.0 14.1 + - + -
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Residues in contact with GLN 39 (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* 3.0 41.7 + - - -
41D GLY 5.7 0.7 + - - -
87D LEU* 4.3 8.5 - - - +
38E ARG* 1.3 76.1 - - - +
40E ASP* 1.3 78.8 + - - +
41E PRO* 4.7 0.5 - - - +
42E GLY 6.1 0.4 - - - +
43E GLN 3.2 17.7 + - - +
44E GLY 3.7 15.1 - - - +
45E LEU* 4.2 18.3 - - + +
89E ALA* 4.1 0.9 - - - +
90E PHE* 2.9 53.4 + - + +
92E LEU* 4.2 4.3 - - + +
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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