Contacts of the strand formed by residues 2 - 10 (chain A) in PDB entry 2VWK
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 72.8 - - - +
3A LEU* 1.3 61.4 + - - +
4A ASP* 3.9 20.4 - - - +
18A ILE* 4.1 17.0 - - + -
19A PHE 3.7 5.8 - - - +
20A LYS* 4.5 13.7 - - + +
22A GLU* 6.0 0.2 - - - +
121A LEU* 4.4 15.9 - - + -
126A LEU* 3.8 44.6 - - + -
127A ILE 4.2 14.6 + - - +
128A PRO* 3.3 19.9 - - + +
129A MET* 3.1 25.9 + - - +
130A GLU* 6.1 0.2 - - - +
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Residues in contact with LEU 3 (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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1A MET* 4.6 5.4 - - + -
2A ILE* 1.3 76.5 - - - +
4A ASP* 1.3 63.4 + - + +
19A PHE* 2.8 22.6 + - + +
20A LYS 4.6 4.3 - - - -
21A LYS* 4.3 24.2 - - + +
26A PHE* 4.7 4.5 - - + -
128A PRO* 4.7 2.2 - - - +
129A MET* 4.5 10.6 - - - +
135A LEU* 3.9 28.5 - - + -
204A ASP* 4.7 9.9 - - + +
234A ARG* 4.2 11.0 - - - +
254A GLY 4.1 19.5 - - - +
255A ARG 6.4 0.2 - - - -
256A ILE* 3.8 38.3 - - + +
340A SER* 4.0 13.7 - - - -
341A LEU 4.5 4.0 + - - -
342A TRP 5.7 0.2 + - - -
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Residues in contact with ASP 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ILE* 3.7 5.4 - - - +
3A LEU* 1.3 81.3 - - + +
5A THR* 1.3 92.8 + - - +
19A PHE* 3.1 41.4 + - + +
121A LEU* 5.8 1.3 - - - +
128A PRO* 5.9 0.7 - - - -
251A GLU* 3.7 21.9 - - - +
253A LYS* 6.0 1.5 - - - -
255A ARG 5.3 5.2 - - - +
256A ILE* 5.8 4.7 - - + +
340A SER* 3.3 29.4 + - - -
342A TRP* 4.3 7.3 - - - +
343A ASP* 4.7 1.9 - - - +
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Residues in contact with THR 5 (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 ILE* 4.5 1.3 - - + -
4A ASP* 1.3 94.8 + - - +
6A ASP* 1.3 66.3 + - - +
16A ILE* 4.8 4.9 - - - -
17A ARG 3.2 13.7 - - - +
18A ILE* 4.1 21.1 - - + -
19A PHE* 4.4 4.0 - - - -
117A ALA* 3.0 33.5 + - - +
120A TYR* 4.6 5.8 - - + -
121A LEU* 3.7 33.4 - - + +
340A SER* 5.2 0.2 - - - -
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Residues in contact with ASP 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A THR* 1.3 75.2 - - - +
7A TYR* 1.3 72.4 + - - +
8A ILE* 5.1 0.2 - - - +
16A ILE* 3.5 8.3 - - - +
17A ARG* 2.9 69.8 + - - +
19A PHE* 3.9 8.9 - - + -
117A ALA* 3.6 14.1 - - - -
253A LYS* 3.1 37.0 + - - +
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Residues in contact with TYR 7 (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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6A ASP* 1.3 86.9 - - - +
8A ILE* 1.3 78.7 + - - +
9A THR* 3.7 17.0 - - - -
14A PRO* 4.2 9.2 - - + -
15A VAL 3.2 17.7 - - - +
16A ILE* 4.1 1.3 - - + -
89A HIS* 3.7 11.9 - + - -
90A PRO* 3.7 12.3 - - + +
91A GLN* 3.5 23.1 + - - -
116A PHE* 3.6 33.0 - + + -
117A ALA* 4.5 6.5 - - + -
1777A SO4 2.5 40.3 + - - -
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Residues in contact with ILE 8 (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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6A ASP* 5.1 0.2 - - - +
7A TYR* 1.3 82.6 - - - +
9A THR* 1.3 64.3 + - - +
10A GLU* 4.3 20.2 - - + +
14A PRO* 3.5 4.2 - - - +
15A VAL* 2.8 61.2 + - + +
17A ARG* 3.7 46.4 - - + +
30A TYR* 5.1 5.8 - - + -
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Residues in contact with THR 9 (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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7A TYR* 3.7 9.2 - - - -
8A ILE* 1.3 81.7 + - - +
10A GLU* 1.3 63.6 + - - +
11A ASP 4.1 0.4 + - - -
12A GLY* 3.7 28.3 - - - +
13A LYS 3.4 3.1 - - - +
89A HIS* 2.8 36.1 + - + +
91A GLN* 4.7 2.1 + - - +
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Residues in contact with GLU 10 (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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8A ILE* 4.3 18.3 - - + +
9A THR* 1.3 74.0 - - - +
11A ASP* 1.3 83.1 + - - +
13A LYS* 2.9 29.6 + - - +
15A VAL* 4.6 1.1 - - + -
32A ARG* 3.1 33.6 + - - +
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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