Contacts of the strand formed by residues 13 - 22 (chain A) in PDB entry 2VWJ
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 LYS 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A THR* 4.3 1.8 - - - -
10A GLU 2.8 37.8 + - - +
11A ASP* 3.1 14.7 - - + +
12A GLY* 1.3 80.6 - - - +
14A PRO* 1.4 72.0 - - + +
15A VAL* 3.7 5.4 - - + +
88A THR* 4.8 10.1 - - + -
89A HIS* 4.4 0.4 - - - -
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Residues in contact with PRO 14 (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* 4.3 4.9 - - + -
8A ILE 3.8 4.0 - - - +
9A THR* 4.5 0.2 - - - -
12A GLY 4.2 0.2 - - - +
13A LYS* 1.4 89.2 - - + +
15A VAL* 1.3 64.0 + - - +
31A ASP 4.4 2.9 - - - +
32A ARG* 4.5 11.6 - - - +
34A PHE 4.7 13.3 - - - +
36A PRO* 4.8 0.7 - - + -
88A THR 3.1 30.1 - - - +
89A HIS* 3.9 15.9 - - + -
90A PRO* 3.5 30.1 - - + -
116A PHE* 4.2 10.8 - - + -
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Residues in contact with VAL 15 (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* 2.9 8.0 - - - +
8A ILE* 2.7 57.0 + - + +
10A GLU* 3.9 26.5 - - + +
13A LYS* 3.7 9.9 - - + +
14A PRO* 1.3 80.2 - - - +
16A ILE* 1.3 67.6 + - - +
17A ARG 3.6 0.7 + - - -
30A TYR* 4.4 10.8 - - + -
31A ASP 3.4 24.0 - - - +
32A ARG* 4.0 27.4 - - + +
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Residues in contact with ILE 16 (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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5A THR* 5.2 2.0 - - - -
6A ASP 3.4 9.9 - - - +
7A TYR* 4.1 2.2 - - + -
15A VAL* 1.3 72.0 - - - +
17A ARG* 1.3 65.6 + - - +
18A ILE* 3.6 26.0 - - + +
29A ASP 3.6 0.3 - - - +
30A TYR* 3.3 7.8 - - - +
31A ASP* 2.9 43.5 + - + +
34A PHE* 4.3 4.7 - - + -
116A PHE* 3.4 42.2 - - + +
117A ALA* 4.4 5.6 - - - -
120A TYR* 3.8 48.2 - - + -
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Residues in contact with ARG 17 (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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5A THR* 3.3 8.3 - - - -
6A ASP* 2.8 66.0 + - - +
8A ILE* 4.1 40.6 - - + +
15A VAL 3.6 0.6 + - - +
16A ILE* 1.3 74.5 - - - +
18A ILE* 1.3 62.1 + - - +
19A PHE* 3.7 22.2 + - + -
28A ILE* 3.9 16.9 - - + +
29A ASP 3.3 3.4 - - - -
30A TYR* 3.7 33.5 + - + -
235A GLU* 3.5 32.1 + - - +
253A LYS* 4.1 8.5 - - - +
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Residues in contact with ILE 18 (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* 3.9 39.5 - - + -
4A ASP 3.8 2.9 - - - -
5A THR* 4.0 7.9 - - + -
16A ILE* 3.6 16.4 - - + +
17A ARG* 1.3 73.7 - - - +
19A PHE* 1.3 62.2 + - - +
20A LYS* 3.7 18.9 + - + +
27A LYS 3.7 0.3 - - - +
28A ILE* 3.6 3.0 - - - -
29A ASP* 2.9 51.6 + - + +
30A TYR 4.8 0.9 - - - +
31A ASP* 4.7 4.9 - - + -
120A TYR* 3.5 39.0 - - + +
126A LEU* 5.0 3.8 - - + -
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Residues in contact with PHE 19 (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* 3.6 3.3 - - - +
3A LEU* 2.7 37.2 + - + -
4A ASP* 2.9 39.6 + - + +
5A THR 4.7 0.4 - - - -
6A ASP* 3.4 27.4 - - - -
17A ARG* 3.7 40.4 - - + -
18A ILE* 1.3 71.2 - - - +
20A LYS* 1.3 56.1 + - - +
26A PHE* 3.7 19.7 - + + -
27A LYS 3.8 2.7 - - - -
28A ILE* 3.8 24.2 - - + -
235A GLU* 5.3 4.3 - - + -
253A LYS* 4.4 13.2 - - + -
254A GLY* 3.6 30.3 - - - +
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Residues in contact with LYS 20 (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 3.2 12.8 - - - +
2A ILE* 4.4 14.1 - - + +
3A LEU* 4.2 4.6 - - - +
18A ILE* 4.0 26.9 - - + +
19A PHE* 1.3 78.1 - - - +
21A LYS* 1.3 61.7 + - - +
22A GLU* 3.2 30.3 + - + +
26A PHE* 3.2 13.9 - - - -
27A LYS* 2.9 42.3 + - + +
29A ASP* 3.1 29.5 + - - +
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Residues in contact with LYS 21 (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 2.6 34.0 + - - +
3A LEU* 4.1 8.5 - - + -
20A LYS* 1.3 74.4 - - - +
22A GLU* 1.3 57.1 + - - +
24A GLY* 3.4 31.1 - - - +
25A GLU 3.6 4.7 - - - -
26A PHE* 3.9 20.6 - - + +
133A GLU* 3.2 21.9 + - - +
134A GLU 3.9 14.1 + - - -
135A LEU* 4.3 11.7 - - + -
136A LYS* 5.3 4.2 - - - +
202A ASP 5.7 0.9 - - - -
204A ASP* 3.2 41.2 + - - +
234A ARG* 4.5 6.1 - - - +
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Residues in contact with GLU 22 (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 4.1 10.8 - - - +
20A LYS* 3.2 40.7 + - + +
21A LYS* 1.3 76.3 - - - +
23A ASN* 1.3 80.1 + - - +
24A GLY 3.5 1.1 - - - -
25A GLU* 3.1 23.8 + - - +
27A LYS* 4.7 14.4 - - + +
133A GLU* 3.2 4.5 - - - +
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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