Contacts of the strand formed by residues 92 - 100 (chain A) in PDB entry 2VSC
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 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A PHE* 4.0 4.7 - - - -
43A LYS* 5.7 2.0 - - - -
90A HIS 4.0 0.2 + - - -
91A THR* 1.3 74.9 - - - +
93A ASN* 1.3 64.2 + - - -
94A TYR* 3.5 7.6 - - - -
1119A NAG 3.8 22.7 - - - -
110B GLU* 3.8 10.5 - - - -
111B LEU 2.9 31.9 + - - -
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Residues in contact with ASN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS 4.1 0.2 - - - +
42A PHE* 3.7 22.0 - - - -
43A LYS* 4.3 5.4 + - - +
92A GLY* 1.3 68.6 - - - -
94A TYR* 1.3 62.4 + - - +
95A THR* 5.1 1.3 + - - +
1119A NAG 1.5 64.1 + - - +
108B ILE* 4.0 20.6 - - + +
109B ILE 3.7 2.5 - - - -
110B GLU* 3.4 20.1 + - - +
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Residues in contact with TYR 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.6 29.8 - - + -
40A TRP* 3.9 24.7 - + + -
41A LYS 3.3 12.6 - - - -
42A PHE* 3.6 24.2 - + + -
47A ILE* 4.1 15.3 - - + -
63A PHE* 3.5 7.8 - + - -
80A LEU* 4.5 0.2 - - + -
82A MET* 4.0 13.9 - - + +
90A HIS* 2.7 42.0 + - - +
92A GLY 3.5 11.4 - - - -
93A ASN* 1.3 74.4 - - - +
95A THR* 1.3 60.8 + - - +
96A CYS 4.1 0.2 - - - -
107B THR 3.9 0.3 - - - +
108B ILE* 3.2 6.3 - - - +
109B ILE* 2.8 39.0 + - - +
111B LEU* 3.8 23.0 - - + +
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Residues in contact with THR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LYS 3.6 1.2 - - - +
40A TRP* 3.2 9.3 - - - -
41A LYS* 2.8 60.3 + - + +
93A ASN* 4.2 1.6 + - - +
94A TYR* 1.3 73.7 - - - +
96A CYS* 1.3 62.9 + - - +
97A GLU* 4.0 1.1 - - + +
106B GLU* 3.9 34.3 - - + +
107B THR 3.4 9.0 - - - +
108B ILE* 3.6 20.5 - - + +
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Residues in contact with CYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PHE* 4.3 1.2 - - - -
23A CYS* 2.0 48.5 - - + -
38A VAL* 5.0 0.7 - - - -
39A LYS 3.7 2.9 - - - -
40A TRP* 3.6 33.8 - - + -
78A ALA* 3.9 12.3 - - - -
94A TYR 4.1 0.4 - - - -
95A THR* 1.3 72.3 - - - +
97A GLU* 1.3 62.0 + - - +
98A VAL* 4.0 7.5 + - - -
106B GLU* 3.0 6.5 - - - +
107B THR* 2.8 40.5 + - + +
109B ILE* 4.5 0.2 - - + -
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TYR* 3.9 4.9 - - - +
38A VAL* 3.3 5.7 - - - +
39A LYS* 2.8 71.2 + - + +
41A LYS* 3.8 28.4 + - - -
95A THR* 5.0 0.9 - - + -
96A CYS* 1.3 74.0 - - - +
98A VAL* 1.3 67.3 + - - +
99A THR* 4.3 10.3 + - - +
104B GLU* 4.2 15.4 - - - +
105B GLY 3.4 10.1 - - - +
106B GLU* 3.8 24.0 - - + +
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 3.3 22.7 - - + +
4A PHE* 4.3 4.3 - - + -
25A VAL* 3.9 24.9 - - + -
28A MET* 4.3 10.1 - - + -
36A VAL* 4.1 18.6 - - + -
37A TYR 3.4 7.4 - - - +
38A VAL* 4.5 4.3 - - + -
73A LEU* 4.9 2.5 - - + -
78A ALA* 3.9 24.9 - - + -
96A CYS* 4.0 9.9 - - - -
97A GLU* 1.3 78.3 - - - +
99A THR* 1.3 67.7 + - - +
100A GLU* 5.5 0.2 - - + -
104B GLU* 3.4 1.7 - - - +
105B GLY 3.1 30.8 + - - +
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Residues in contact with THR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU 3.6 0.5 - - - +
36A VAL* 3.2 8.3 - - - +
37A TYR* 2.8 48.4 + - - +
97A GLU* 4.3 14.4 + - - +
98A VAL* 1.3 78.2 + - - +
100A GLU* 1.3 68.6 + - - +
101A LEU* 3.9 12.1 - - + +
102B THR* 3.5 28.3 - - + -
103B ARG 3.4 7.0 - - - +
104B GLU* 3.9 12.3 + - + +
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 4.2 12.3 - - + +
28A MET* 3.5 21.2 - - + +
29A GLU* 2.7 29.9 + - - +
30A ALA* 2.8 27.8 + - + +
35A GLU* 3.3 6.5 - - + +
36A VAL* 4.6 2.2 - - + -
99A THR* 1.3 75.1 - - - +
101A LEU* 1.3 65.0 + - - +
1120A MG 4.3 10.6 - - - -
29B GLU* 5.8 0.4 - - - -
101B LEU 4.5 0.5 - - - +
102B THR* 3.3 3.6 - - - +
103B ARG* 2.7 68.7 + - + +
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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