Contacts of the strand formed by residues 13 - 21 (chain R) in PDB entry 1VQ9
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 THR 13 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8R ALA* 3.5 26.6 - - + +
9R ASP 2.9 25.3 + - - +
10R PRO* 3.4 16.9 + - + +
12R THR* 1.3 83.0 + - - +
14R ALA* 1.3 67.2 + - - +
15R LYS* 4.3 7.4 - - + -
102R GLN* 3.5 12.0 - - - +
104R PHE* 3.6 7.3 - - - -
109R MET* 5.4 1.1 - - - -
112R LYS* 5.1 2.4 + - - +
146R ILE* 4.0 16.1 - - + +
147R LEU 3.3 11.0 + - - -
148R GLU* 4.2 8.7 + - - +
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Residues in contact with ALA 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13R THR* 1.3 75.4 - - - +
15R LYS* 1.3 63.1 + - - +
95R ALA 4.4 3.8 - - - +
98R ASN* 4.9 0.4 - - + -
99R ALA* 3.8 37.0 - - + +
102R GLN* 4.3 13.0 - - - +
104R PHE* 4.9 1.3 - - + -
109R MET* 4.2 9.8 - - + -
145R LEU 4.0 0.2 - - - +
146R ILE* 3.6 2.1 - - - -
147R LEU* 2.8 42.0 + - + +
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Residues in contact with LYS 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5010 G 3.6 16.7 + - - +
5020 A 4.1 18.6 + - - +
4R TYR* 3.3 55.5 - - + +
6R VAL 5.6 0.4 + - - -
8R ALA* 3.8 25.2 + - - +
13R THR* 4.3 11.0 - - + -
14R ALA* 1.3 77.3 - - - +
16R ALA* 1.3 65.3 + - - +
95R ALA* 4.2 3.3 - - - -
98R ASN* 3.0 25.3 - - - +
102R GLN* 5.1 3.0 - - - +
145R LEU 3.5 4.5 - - - -
146R ILE* 4.6 6.7 - - + -
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Residues in contact with ALA 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5000 G 3.4 9.0 - - - -
5010 G 4.2 0.2 - - - -
4R TYR* 3.1 10.4 + - - -
15R LYS* 1.3 80.6 - - - +
17R MET* 1.3 64.4 + - - +
91R LEU* 3.8 14.8 - - + -
94R ASN* 3.4 17.0 - - - +
95R ALA* 3.7 24.9 - - + +
145R LEU* 3.0 30.3 + - + +
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Residues in contact with MET 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4990 G 4.3 1.7 + - - -
5000 G 3.3 40.2 + - - +
5010 G 3.5 10.3 - - - +
2R ILE* 3.9 21.8 - - - +
3R SER* 4.6 1.6 - - - -
4R TYR* 3.3 44.9 - - + +
16R ALA* 1.3 83.2 - - - +
18R LEU* 1.3 63.9 + - - +
19R ARG* 3.1 44.0 - - - +
91R LEU* 3.5 8.8 - - - +
94R ASN* 5.2 1.0 + - - +
143R VAL 3.2 13.0 - - - +
144R GLU* 4.0 5.6 - - + -
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Residues in contact with LEU 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4990 G 4.8 1.1 - - - -
17R MET* 1.3 78.2 - - - +
19R ARG* 1.3 69.1 + - - +
21R ARG* 3.9 33.9 - - + +
23R MET* 4.6 4.7 - - + -
87R ALA* 3.6 42.4 - - + +
88R PHE* 4.4 2.9 - - + +
90R ASP* 4.7 2.9 - - + -
91R LEU* 3.8 26.9 - - + +
141R VAL 4.7 0.2 - - - +
142R ASP* 3.4 4.9 - - - +
143R VAL* 2.9 52.1 + - + +
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Residues in contact with ARG 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4990 G 3.4 41.2 + - - +
5000 G 3.0 24.7 + - - +
5010 G 5.2 2.0 + - - -
1R GLY* 3.8 5.0 - - - -
2R ILE* 2.9 28.3 + - - +
17R MET* 3.1 39.3 - - - +
18R LEU* 1.3 82.2 - - - +
20R GLU* 1.3 75.9 + - + +
21R ARG* 3.0 14.7 + - - +
142R ASP* 3.0 23.7 + - - -
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Residues in contact with GLU 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19R ARG* 1.3 75.7 - - + +
21R ARG* 1.3 65.4 + - - +
22R GLN* 3.4 10.9 + - - +
119R VAL* 4.6 15.6 - - + +
140R GLN* 3.4 33.4 + - + +
141R VAL 3.4 8.2 + - - +
142R ASP* 2.8 20.5 + - - +
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Residues in contact with ARG 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4960 G 5.9 0.8 + - - -
4980 A 5.8 9.1 + - - -
18R LEU* 3.9 47.3 - - + +
19R ARG 3.0 13.8 + - - +
20R GLU* 1.3 73.2 - - - +
22R GLN* 1.3 60.6 + - - +
23R MET* 3.3 24.3 + - + +
87R ALA* 3.6 22.9 - - - +
90R ASP* 3.3 27.7 + - - +
139R PRO 3.5 0.2 - - - +
140R GLN* 3.4 1.9 - - - -
141R VAL* 2.6 43.2 + - - +
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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