Contacts of the strand formed by residues 85 - 91 (chain B) in PDB entry 1VGX
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 GLY 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU 3.3 13.0 - - - -
42B ARG* 4.3 1.3 - - - -
43B PHE* 3.9 8.7 - - - -
51B ILE* 4.4 2.8 - - - +
56B ILE* 3.7 10.3 - - - +
80B MET* 3.0 33.2 + - - +
82B CSD 3.8 2.6 + - - -
83B ARG 3.4 1.4 - - - -
84B THR* 1.3 83.7 + - - +
86B MET* 1.3 65.8 + - - -
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Residues in contact with MET 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 2.9 42.9 + - + +
43B PHE* 3.7 21.3 - - + -
51B ILE* 5.7 0.2 - - - -
56B ILE* 3.6 27.8 - - - +
59B LEU* 4.1 11.9 - - - +
60B GLU* 3.6 37.2 - - + +
63B LEU* 3.9 11.9 - - + -
77B VAL* 4.1 19.5 - - + -
78B SER 3.3 9.0 - - - +
79B PRO* 3.7 21.1 - - + -
80B MET* 3.3 8.4 - - - +
85B GLY* 1.3 77.3 - - - +
87B TYR* 1.3 59.4 + - - +
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Residues in contact with TYR 87 (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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75A VAL* 3.6 13.7 - - + +
76A ASP* 3.0 40.2 + - + +
78A SER* 3.7 23.6 - - - +
25B ALA* 5.7 4.0 - - + -
38B LYS* 3.6 31.7 - - + +
39B TYR 3.5 10.3 - - - -
40B ASP* 6.0 0.2 - - - -
76B ASP 5.3 2.0 - - - -
77B VAL* 3.4 3.5 - - - +
78B SER* 2.7 45.7 + - - +
79B PRO 5.1 1.6 - - - +
80B MET* 4.0 18.7 - - + +
86B MET* 1.3 73.9 - - - +
88B MET* 1.3 66.0 + - - +
89B ALA* 3.8 18.6 - - + +
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Residues in contact with MET 88 (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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37B SER 3.8 1.0 - - - +
38B LYS* 3.6 0.7 - - - -
39B TYR* 2.8 48.4 + - + +
41B LEU* 4.0 16.6 - - + -
67B MET* 3.7 28.7 - - + -
71B LEU* 3.6 21.5 - - + -
74B VAL* 4.2 10.8 - - + -
76B ASP 3.3 14.1 - - - +
77B VAL* 4.0 19.3 - - + -
87B TYR* 1.3 80.5 - - - +
89B ALA* 1.3 68.8 - - - +
90B VAL* 3.6 20.0 - - + -
99B VAL* 3.9 18.6 - - + -
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Residues in contact with ALA 89 (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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75A VAL* 4.4 5.6 - - + -
36B ILE* 4.1 17.7 - - + -
37B SER 3.4 5.4 - - - +
38B LYS* 4.4 2.0 - - + +
74B VAL 3.8 0.5 - - - -
75B VAL* 2.7 46.9 + - + +
76B ASP 3.2 8.8 + - - +
87B TYR* 3.8 24.0 - - + +
88B MET* 1.3 76.7 - - - +
90B VAL* 1.3 59.1 + - - +
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 3.4 3.4 - - - +
37B SER* 2.8 36.0 + - - +
39B TYR* 3.8 19.7 - - + -
71B LEU* 4.0 17.0 - - + -
72B GLU 3.6 23.3 - - - +
73B GLY 3.4 7.2 - - - +
74B VAL* 4.5 2.0 - - - +
75B VAL* 4.3 2.5 - - - -
88B MET* 3.6 32.1 - - + -
89B ALA* 1.3 80.1 - - - +
91B ILE* 1.3 73.8 + - - +
92B GLY* 3.4 2.7 + - - +
99B VAL* 5.7 0.7 - - + -
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Residues in contact with ILE 91 (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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28A LYS* 3.4 35.0 - - + -
29A THR 4.3 1.3 - - - +
30A THR* 4.2 15.7 - - + -
31A PRO* 3.5 30.3 - - + -
36A ILE* 3.6 32.3 - - + -
34B ASP* 4.4 12.3 - - + -
35B GLN 3.6 9.2 - - - +
36B ILE* 3.7 7.0 - - + -
72B GLU 4.5 1.4 - - - +
73B GLY* 2.7 25.9 + - - +
75B VAL* 3.9 3.1 - - + -
90B VAL* 1.3 80.5 - - - +
92B GLY* 1.3 59.0 + - - +
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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