Contacts of the strand formed by residues 2 - 9 (chain S) in PDB entry 2VGL
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 2 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1S MET* 1.3 92.2 - - - +
3S ARG* 1.3 62.4 + - - +
4S PHE 3.6 14.1 - - - +
5S ILE* 3.9 6.3 - - + -
20S TYR* 3.5 20.2 - - + +
69S ILE* 3.5 27.1 - - + -
70S CYS 3.6 3.6 - - - -
71S VAL* 4.3 2.2 - - - -
80S TYR* 3.8 26.0 - - + +
118S PHE* 3.4 41.3 - - + -
121S GLY* 2.9 33.5 + - - +
122S GLU 4.4 2.2 - - - +
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Residues in contact with ARG 3 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1S MET* 3.8 21.8 - - - +
2S ILE* 1.3 78.3 - - - +
4S PHE* 1.3 57.3 + - + +
19S TRP* 4.0 0.9 - - - -
20S TYR* 2.8 35.4 + - - +
21S MET* 3.0 56.6 + - + +
55S PHE* 3.8 31.8 - - + -
70S CYS* 2.7 28.5 + - - +
71S VAL 4.7 2.2 - - - -
72S ASP* 3.1 35.7 + - - -
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Residues in contact with PHE 4 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2S ILE* 3.6 6.5 - - - +
3S ARG* 1.3 82.8 - - + +
5S ILE* 1.3 65.9 + - - +
6S LEU* 3.7 37.9 - - + -
18S LYS 3.1 17.3 - - - +
19S TRP* 3.5 33.9 - + + -
20S TYR* 4.0 3.4 - - - -
21S MET* 5.6 0.2 - - + -
23S PHE* 5.0 6.7 - + - -
31S LEU* 4.5 13.0 - - + -
35S VAL* 3.8 22.9 - - + -
52S PHE* 4.0 10.8 - + - -
55S PHE* 5.8 1.3 - + - -
57S ILE* 5.5 1.1 - - + -
68S CYS* 5.4 3.6 - - + -
69S ILE* 3.6 0.6 - - - -
70S CYS* 3.0 61.6 + - + -
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Residues in contact with ILE 5 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2S ILE* 3.9 16.2 - - + -
4S PHE* 1.3 77.1 - - - +
6S LEU* 1.3 72.2 + - - +
7S ILE* 5.0 2.5 - - + -
16S LEU* 4.4 14.6 - - + +
17S ALA* 3.5 3.5 + - - -
18S LYS* 3.0 35.6 + - + +
20S TYR* 3.7 27.6 - - + +
67S PHE* 6.3 2.0 - - + -
68S CYS 3.3 12.1 - - - +
69S ILE* 4.2 13.7 - - + -
87S PHE* 5.2 10.3 - - + -
114S VAL* 4.4 7.6 - - + -
118S PHE* 4.0 30.1 - - + -
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Residues in contact with LEU 6 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4S PHE* 3.7 31.6 - - + -
5S ILE* 1.3 78.9 - - - +
7S ILE* 1.3 70.3 + - - +
8S GLN* 4.1 11.7 - - + +
14S THR* 5.0 1.1 - - + -
16S LEU 3.5 3.4 - - - +
17S ALA* 3.7 27.8 - - + -
18S LYS 4.8 0.4 - - - +
19S TRP* 4.3 7.4 - - + -
32S ILE* 3.8 33.0 - - + -
35S VAL* 3.9 26.9 - - + -
66S TYR 3.9 0.7 - - - +
68S CYS* 2.9 39.9 + - + +
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Residues in contact with ILE 7 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5S ILE* 5.0 2.2 - - + -
6S LEU* 1.3 76.5 - - - +
8S GLN* 1.3 69.7 + - - +
14S THR* 3.7 0.9 - - - +
15S ARG* 3.0 25.2 + - + -
16S LEU* 3.0 49.6 + - + +
65S LEU* 4.0 20.6 - - + -
66S TYR 3.4 5.8 - - - +
67S PHE* 3.3 50.3 - - + -
87S PHE* 4.2 9.6 - - + -
91S LEU* 4.7 6.7 - - + -
103S LEU* 4.5 15.0 - - + -
110S VAL* 5.1 0.4 - - + -
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Residues in contact with GLN 8 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6S LEU* 4.1 16.6 - - + +
7S ILE* 1.3 80.5 - - - +
9S ASN* 1.3 63.7 + - - +
12S GLY 4.2 7.8 - - - +
13S LYS 3.3 13.7 - - - +
14S THR* 4.2 9.2 - - - +
15S ARG 4.6 0.7 - - - +
32S ILE* 2.9 39.2 - - - +
35S VAL* 4.5 6.0 - - - +
36S HIS* 3.5 36.7 + - - +
39S VAL* 5.6 3.0 - - - +
40S THR* 5.7 1.2 - - - +
65S LEU* 3.9 4.3 - - - -
66S TYR* 2.7 48.1 + - + +
68S CYS* 5.4 2.7 - - - -
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Residues in contact with ASN 9 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LYS* 4.8 14.9 - - - +
8S GLN* 1.3 78.6 + - - +
10S ARG* 1.3 66.6 + - - +
11S ALA* 3.1 18.7 + - - +
12S GLY* 3.0 10.4 + - - -
13S LYS* 2.8 52.0 + - - +
15S ARG* 3.8 7.6 - - - +
36S HIS* 4.4 2.8 + - - -
64S GLY 3.1 13.9 - - - +
65S LEU* 3.9 7.6 - - + +
66S TYR* 4.5 3.5 - - - -
100S GLU* 3.4 29.3 + - - +
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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