Contacts of the strand formed by residues 110 - 122 (chain R) in PDB entry 1VQN
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 110 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37R GLY* 3.5 26.1 + - - +
38R LYS 3.7 3.6 - - - -
39R THR* 4.4 5.9 + - - +
108R ALA 3.7 2.7 + - - -
109R MET* 1.3 73.7 - - - +
111R ILE* 1.3 72.6 + - - +
112R LYS* 2.9 10.1 + - - +
147R LEU* 3.3 3.8 - - - -
148R GLU* 2.8 46.5 + - - -
149R GLU 5.5 0.4 - - - -
150R PRO* 4.6 13.3 - - - +
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Residues in contact with ILE 111 (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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35R ILE* 3.4 31.2 - - + +
36R LYS* 4.0 3.4 - - - +
37R GLY* 2.9 24.3 + - - -
38R LYS 2.8 20.6 + - - +
39R THR 4.3 1.1 - - - +
40R ALA 4.4 4.7 - - - +
43R ALA* 3.5 29.2 - - + -
92R LEU* 4.2 9.2 - - + -
110R THR* 1.3 68.7 - - - +
112R LYS* 1.3 61.6 + - - +
113R HIS 4.1 1.3 - - - +
114R VAL* 3.6 24.0 - - + -
145R LEU* 3.2 26.2 - - + -
146R ILE 3.9 4.3 - - - -
147R LEU* 3.9 18.6 - - + -
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Residues in contact with LYS 112 (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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6R VAL* 4.4 12.1 - - + +
7R GLU 3.5 23.4 + - - -
8R ALA* 4.8 5.7 - - - +
9R ASP 5.5 1.4 - - - +
13R THR* 4.9 3.3 + - - +
36R LYS* 3.6 21.5 - - - -
110R THR* 2.9 12.4 + - + +
111R ILE* 1.3 73.1 - - - +
113R HIS* 1.3 61.1 + - + +
146R ILE* 2.9 23.2 + - + +
148R GLU* 3.9 47.6 + - + +
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Residues in contact with HIS 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5250 G 3.5 23.1 + - - -
5R SER* 3.6 6.2 + - - -
6R VAL* 3.3 32.1 - - + +
36R LYS* 5.1 6.3 - - - +
111R ILE 3.4 0.2 - - - -
112R LYS* 1.3 86.4 - - + +
114R VAL* 1.3 68.3 + - - +
115R ALA* 4.2 8.2 - - + +
144R GLU* 3.0 46.3 + - + +
145R LEU* 3.1 8.6 - - - +
146R ILE* 2.7 57.7 + - + +
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Residues in contact with VAL 114 (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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5250 G 4.8 6.6 - - - +
32R ALA* 3.7 22.4 - - + +
35R ILE* 4.5 7.4 - - + -
36R LYS* 3.7 31.3 - - + +
88R PHE* 4.1 26.5 - - + -
91R LEU* 5.0 0.7 - - + -
111R ILE* 3.6 17.9 - - + -
113R HIS* 1.3 81.4 + - - +
115R ALA* 1.3 64.4 + - - +
143R VAL* 4.4 3.8 - - + -
144R GLU 3.0 13.0 - - - +
145R LEU* 3.6 17.7 - - + -
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Residues in contact with ALA 115 (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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5240 A 3.3 17.0 - - - +
5250 G 3.7 22.0 - - - +
32R ALA* 4.3 6.1 - - - -
113R HIS* 4.2 5.2 - - + -
114R VAL* 1.3 77.3 - - - +
116R ALA* 1.3 60.6 + - - +
117R HIS* 3.6 14.4 + - + +
143R VAL* 3.3 6.2 - - - +
144R GLU* 3.0 42.1 + - - +
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Residues in contact with ALA 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5240 A 2.6 36.0 + - - +
25R PHE* 3.6 11.8 - - + -
28R SER* 3.7 39.5 - - - +
29R LYS* 4.3 4.0 - - + +
32R ALA* 4.5 3.8 - - - +
88R PHE* 5.0 1.1 - - + -
115R ALA* 1.3 73.9 - - - +
117R HIS* 1.3 63.4 + - - +
141R VAL* 4.1 4.5 - - + -
142R ASP 3.5 8.1 - - - +
143R VAL* 4.1 7.4 - - + -
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Residues in contact with HIS 117 (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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200 G 3.2 34.5 + - - +
210 G 4.3 6.5 - - - +
5230 C 5.8 0.2 - - - -
5240 A 3.3 31.4 + - - -
5250 G 5.8 0.2 - - - -
2R ILE* 3.6 40.4 - - + +
5R SER* 4.7 2.8 + - - -
25R PHE* 3.7 6.1 - - - -
115R ALA* 3.6 21.3 + - + +
116R ALA* 1.3 72.3 - - - +
118R LYS* 1.3 63.0 + - - +
119R VAL* 3.3 1.6 + - + +
141R VAL* 3.6 2.4 - - - -
142R ASP* 2.8 35.1 + - - +
144R GLU* 3.0 31.9 + - - -
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Residues in contact with LYS 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210 G 4.0 16.5 + - - +
220 U 4.1 9.2 - - - +
5230 C 5.0 4.8 + - - +
13660 C 4.4 19.4 + - - +
25R PHE* 3.5 35.1 - - + -
117R HIS* 1.3 70.7 - - - +
119R VAL* 1.3 61.1 + - - +
120R GLY* 3.8 15.7 - - - +
121R GLU* 3.2 42.3 + - - +
139R PRO* 4.3 11.5 - - - +
140R GLN 3.5 7.4 - - - +
9306R CL 3.6 28.4 - - + +
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Residues in contact with VAL 119 (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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210 G 3.9 14.8 - - - +
220 U 3.3 39.0 - - - +
230 G 5.1 0.7 + - - -
1R GLY* 4.2 12.6 - - - +
2R ILE* 4.4 2.9 - - + -
20R GLU* 4.7 15.9 - - + +
117R HIS 3.3 2.0 + - - +
118R LYS* 1.3 74.3 - - - +
120R GLY* 1.3 57.6 + - - +
140R GLN* 2.8 14.7 + - + +
142R ASP* 3.2 44.2 - - + +
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Residues in contact with GLY 120 (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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220 U 5.2 4.5 - - - -
230 G 5.8 1.6 - - - -
118R LYS* 3.4 11.6 + - - +
119R VAL* 1.3 81.6 - - - +
121R GLU* 1.3 63.1 + - - +
139R PRO* 3.6 1.9 - - - +
140R GLN* 2.7 44.3 + - - +
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Residues in contact with GLU 121 (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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13660 C 5.6 3.4 + - - -
20540 A 5.2 4.0 + - - -
118R LYS* 3.2 29.6 + - - -
120R GLY* 1.3 79.6 - - - +
122R GLN* 1.3 61.7 + - - +
123R GLN* 3.3 15.7 + - + +
137R ASN* 2.9 38.6 + - + +
138R SER 3.0 10.0 - - - +
139R PRO* 4.8 2.1 - - + +
140R GLN* 3.4 7.7 + - - +
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Residues in contact with GLN 122 (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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14270 A 4.6 0.2 - - - +
14280 C 3.0 28.4 + - - +
14290 U 4.3 14.2 + - - +
22R GLN* 3.0 39.8 + - - +
121R GLU* 1.3 71.0 - - - +
123R GLN* 1.3 68.7 + - - +
137R ASN* 3.3 2.6 - - - +
138R SER* 2.7 52.9 + - - +
140R GLN* 3.8 18.9 + - - +
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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