Contacts of the strand formed by residues 10 - 18 (chain B) in PDB entry 4JVS
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 TYR 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B TYR* 3.2 17.5 - - - +
9B ASP* 1.3 91.1 - - + +
11B LEU* 1.3 61.8 + - - +
12B PHE* 3.6 28.0 - + + -
58B LYS* 4.1 24.6 - - + +
59B THR 3.2 2.4 + - - -
60B ILE* 3.8 26.9 - - + -
61B LYS 3.0 20.4 + - - -
173B LYS* 4.3 25.4 + - + +
176B MET* 5.6 14.9 - - - +
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Residues in contact with LEU 11 (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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493A LEU* 4.5 11.4 - - + -
8B TYR* 3.8 25.5 - - + +
10B TYR* 1.3 75.3 - - - +
12B PHE* 1.3 64.4 + - - +
13B LYS* 4.2 29.6 - - + -
61B LYS* 3.5 37.7 - - + +
63B GLN* 4.0 24.2 - - + +
85B HIS* 3.0 26.8 - - + -
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Residues in contact with PHE 12 (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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10B TYR* 3.6 34.3 - + + -
11B LEU* 1.3 79.7 - - - +
13B LYS* 1.3 62.3 + - - +
14B LEU* 3.5 13.2 + - + +
60B ILE* 3.7 25.1 - - + -
61B LYS 2.8 9.7 + - - -
62B LEU* 3.6 20.3 - - + -
63B GLN 2.9 25.3 + - - -
85B HIS* 3.3 11.7 - + + +
169B ALA* 3.3 29.6 - - - -
172B ILE* 3.8 31.6 - - + -
173B LYS* 3.8 18.6 - - + -
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Residues in contact with LYS 13 (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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493A LEU* 3.4 34.2 - - - +
11B LEU* 3.9 14.5 + - + -
12B PHE* 1.3 70.9 - - - +
14B LEU* 1.3 63.0 + - - +
15B LEU* 5.7 0.4 - - + -
63B GLN* 3.3 26.7 - - + +
65B TRP* 4.8 9.0 - - + +
80B TYR 6.0 0.7 - - - +
82B ARG 5.5 0.4 - - - +
83B GLY* 3.1 36.4 + - - +
84B ALA* 3.9 6.4 - - + -
85B HIS* 3.0 32.6 + - + +
86B GLY 3.3 7.3 + - - +
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Residues in contact with LEU 14 (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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12B PHE* 3.8 17.5 - - + +
13B LYS* 1.3 81.9 - - - +
15B LEU* 1.3 67.6 + - - +
62B LEU* 4.4 15.9 - - + -
63B GLN 2.7 7.4 + - - +
64B ILE* 3.8 28.0 - - + -
65B TRP* 2.7 30.3 + - - +
86B GLY 3.3 6.1 - - - +
88B ILE* 5.1 4.0 - - + -
165B PHE* 3.9 31.6 - - + +
168B MET* 4.2 20.9 - - + -
169B ALA* 5.7 0.9 - - - +
172B ILE* 3.8 25.8 - - + -
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Residues in contact with LEU 15 (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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13B LYS* 5.4 0.9 - - + -
14B LEU* 1.3 87.2 - - - +
16B LEU* 1.3 61.4 + - - +
17B ILE* 3.7 22.9 - - + -
65B TRP* 3.5 21.3 - - + -
67B THR* 3.7 17.5 - - + -
80B TYR* 3.4 31.4 - - + +
81B TYR* 3.8 22.9 - - + -
84B ALA* 4.2 11.2 - - + -
86B GLY 3.0 6.2 + - - +
87B ILE* 3.7 22.6 - - + +
88B ILE* 2.7 33.6 + - - +
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Residues in contact with LEU 16 (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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15B LEU* 1.3 73.1 - - - +
17B ILE* 1.3 52.1 + - - +
24B LYS* 3.9 32.2 - - + +
27B LEU* 4.4 10.8 - - + -
28B LEU* 4.2 17.0 - - + -
64B ILE* 3.8 17.0 - - + -
65B TRP 2.6 16.1 + - - +
66B ASP* 4.2 6.5 - - - -
67B THR* 2.5 37.2 + - - +
88B ILE* 3.8 13.7 - - + -
90B VAL* 3.7 27.1 - - + -
165B PHE* 3.7 34.1 - - + -
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Residues in contact with ILE 17 (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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15B LEU* 3.7 22.4 - - + -
16B LEU* 1.3 79.3 - - - +
18B GLY* 1.3 60.9 + - - +
24B LYS* 3.4 6.5 - - - -
67B THR* 3.4 13.2 - - - +
81B TYR* 3.3 31.6 - - + +
87B ILE* 3.7 20.9 - - + -
88B ILE 3.0 17.2 + - - +
89B VAL* 4.0 12.3 - - + -
90B VAL* 2.8 26.9 + - - +
105B TRP* 4.0 22.2 - - + +
109B ILE* 4.0 18.8 - - + -
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Residues in contact with GLY 18 (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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17B ILE* 1.3 78.7 - - - +
19B ASP* 1.3 70.4 + - - +
22B VAL* 4.4 0.4 - - - -
24B LYS* 3.3 9.6 - - - -
67B THR* 4.7 0.2 + - - -
69B GLY* 3.2 18.4 - - - -
90B VAL 3.5 15.0 - - - -
105B TRP* 3.3 26.7 - - - -
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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