Contacts of the strand formed by residues 138 - 148 (chain R) in PDB entry 1VQM
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 SER 138 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20530 G 2.5 23.1 + - - -
22R GLN* 3.5 27.1 + - - -
121R GLU* 3.0 7.8 - - - -
122R GLN* 2.6 54.0 + - - -
136R TRP 5.2 0.5 + - - -
137R ASN* 1.3 72.7 - - - +
139R PRO* 1.3 69.7 - - - +
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Residues in contact with PRO 139 (chain R).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13700 G 3.4 29.8 - - + +
20530 G 4.2 10.5 - - - +
20540 A 5.7 1.8 - - - +
21R ARG 3.4 0.7 - - - +
22R GLN* 3.4 25.2 - - - +
23R MET* 3.5 22.6 + - - +
25R PHE* 4.3 14.4 - - + +
118R LYS* 4.2 22.7 - - + +
120R GLY 3.8 4.7 - - - +
121R GLU* 4.5 2.2 - - + +
137R ASN 4.3 2.7 - - - +
138R SER* 1.3 88.7 - - - +
140R GLN* 1.3 60.8 + - - +
141R VAL* 4.1 1.6 - - + -
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Residues in contact with GLN 140 (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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20R GLU* 4.0 37.6 + - + +
21R ARG 3.3 3.8 - - - -
22R GLN* 4.6 12.0 - - + +
118R LYS* 3.5 5.7 - - - +
119R VAL* 2.8 30.2 + - + +
120R GLY* 2.7 27.4 + - - +
121R GLU 3.5 16.9 + - - +
122R GLN* 3.9 32.1 + - + +
138R SER 4.1 0.2 - - - +
139R PRO* 1.3 77.0 - - - +
141R VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 141 (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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18R LEU* 4.2 1.7 - - - +
19R ARG 3.8 1.4 - - - -
20R GLU 3.3 2.4 + - - -
21R ARG* 2.7 43.3 + - - +
23R MET* 3.7 48.0 - - + +
25R PHE* 3.7 30.1 - - + -
28R SER* 4.2 2.0 - - - +
116R ALA* 4.1 17.3 - - + -
117R HIS 3.5 6.1 - - - +
139R PRO* 4.6 0.4 - - + -
140R GLN* 1.3 81.1 - - - +
142R ASP* 1.3 77.7 + - - +
143R VAL* 4.4 0.8 + - + -
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Residues in contact with ASP 142 (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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1R GLY* 3.2 5.1 - - - -
2R ILE* 3.2 37.2 + - + -
18R LEU 3.2 11.0 - - - +
19R ARG* 3.2 16.5 + - - -
20R GLU* 2.7 35.9 + - - +
117R HIS* 2.8 30.5 + - - +
119R VAL* 3.2 31.3 - - + +
141R VAL* 1.3 78.1 - - - +
143R VAL* 1.3 61.1 + - - +
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Residues in contact with VAL 143 (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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2R ILE* 4.3 4.0 - - - -
17R MET* 3.3 6.8 - - - +
18R LEU* 3.0 71.6 + - + -
23R MET* 4.7 7.4 - - + -
88R PHE* 3.9 24.9 - - + -
91R LEU* 3.8 19.6 - - + +
114R VAL* 4.3 1.8 - - + -
115R ALA 3.3 20.9 - - - +
116R ALA* 4.2 6.3 - - + -
141R VAL* 4.9 1.6 - - + -
142R ASP* 1.3 76.6 - - - +
144R GLU* 1.3 65.2 + - - +
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Residues in contact with GLU 144 (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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2R ILE* 3.9 12.7 - - + +
3R SER 4.6 0.7 - - - -
4R TYR* 3.3 24.7 - - + +
5R SER* 2.6 43.9 + - - -
6R VAL 4.6 0.3 + - - -
16R ALA 3.8 3.8 - - - -
17R MET* 4.0 2.9 - - + -
113R HIS* 2.9 28.3 + - + +
114R VAL* 3.1 26.9 - - - +
115R ALA* 3.0 14.5 + - - +
117R HIS* 3.0 24.1 - - + -
143R VAL* 1.3 75.2 - - - +
145R LEU* 1.3 62.7 + - - +
146R ILE* 4.9 0.3 - - - +
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Residues in contact with LEU 145 (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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4R TYR* 3.9 1.5 - - - -
14R ALA 4.0 0.3 - - - +
15R LYS* 3.4 4.7 - - - -
16R ALA* 3.0 37.0 + - + +
35R ILE* 5.6 1.6 - - + -
91R LEU* 3.7 26.7 - - + -
92R LEU* 3.5 29.2 - - + -
95R ALA* 3.8 23.3 - - + -
111R ILE* 3.3 32.3 - - + -
113R HIS 3.2 15.3 - - - +
114R VAL* 3.7 10.8 - - + -
144R GLU* 1.3 77.2 - - - +
146R ILE* 1.3 69.4 + - - +
147R LEU* 4.4 7.4 - - + -
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Residues in contact with ILE 146 (chain R).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4R TYR* 4.0 23.8 - - + -
6R VAL* 4.1 29.8 - - + +
7R GLU 4.8 0.2 - - - +
8R ALA* 4.2 11.4 - - + -
13R THR* 3.4 33.9 - - + +
14R ALA 3.5 2.7 - - - +
15R LYS* 4.4 4.3 - - + -
111R ILE* 3.8 1.9 - - - -
112R LYS* 2.9 40.2 + - + +
113R HIS* 2.8 42.6 + - + +
144R GLU* 4.9 0.2 - - - +
145R LEU* 1.3 79.4 - - - +
147R LEU* 1.3 61.6 + - - +
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Residues in contact with LEU 147 (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* 3.3 10.6 + - - -
14R ALA* 2.7 36.1 + - + +
40R ALA* 4.3 6.3 - - + -
92R LEU* 5.0 0.9 - - + -
95R ALA* 3.6 34.8 - - + +
96R VAL* 3.9 23.6 - - + +
99R ALA* 4.5 7.9 - - + -
106R GLY 4.5 7.0 - - - +
109R MET* 3.9 22.2 - - + +
110R THR 3.2 13.0 - - - +
111R ILE* 3.9 24.7 - - + -
145R LEU* 4.4 10.8 - - + -
146R ILE* 1.3 75.2 - - - +
148R GLU* 1.3 59.9 + - - +
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Residues in contact with GLU 148 (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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12R THR* 3.6 19.1 + - - +
13R THR* 4.0 7.3 + - - +
109R MET* 3.6 6.0 - - - +
110R THR* 2.8 38.4 + - - +
112R LYS* 3.7 46.2 + - + +
147R LEU* 1.3 77.5 - - - +
149R GLU* 1.3 78.7 + - + +
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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