Contacts of the strand formed by residues 13 - 20 (chain B) in PDB entry 3NBV
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 VAL 13 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 4.3 13.2 - - + -
12B VAL* 1.3 76.2 - - - +
14B LEU* 1.3 74.9 + - - +
15B ASP* 3.9 14.4 - - - +
40B GLY* 2.8 47.6 + - - -
41B GLY* 3.7 7.9 - - - +
72B LEU* 3.7 10.7 - - - +
95B PRO* 3.5 29.2 - - + +
96B SER 3.7 2.5 - - - +
97B SER* 3.7 18.4 - - - +
113B HIS* 4.5 3.8 - - + -
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 6.3 0.7 - - + -
37A TRP* 4.6 4.3 - - + +
13B VAL* 1.3 69.5 - - - +
15B ASP* 1.3 62.5 + - - +
16B VAL* 4.4 7.2 - - + -
37B TRP* 3.8 43.1 - - + -
38B GLN 3.6 10.8 - - - +
68B VAL* 3.9 41.5 - - + -
71B PHE* 3.7 25.8 - - + -
72B LEU* 3.8 9.0 - - + +
95B PRO 2.9 12.5 + - - +
96B SER* 3.0 14.1 + - - +
97B SER 2.7 32.2 + - - +
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Residues in contact with ASP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B VAL* 3.7 14.7 + - - +
14B LEU* 1.3 74.7 - - - +
16B VAL* 1.3 62.0 + - - +
17B ILE* 3.9 19.1 + - + +
36B ARG 3.4 2.6 - - - +
37B TRP* 3.5 2.1 - - - -
38B GLN* 2.8 46.8 + - + +
39B ARG 4.7 0.3 - - - -
40B GLY* 3.5 22.5 - - - -
41B GLY 4.7 0.3 + - - -
97B SER* 3.4 24.8 - - - +
99B CYS* 6.0 2.7 - - + -
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 4.4 17.5 - - + -
98A CYS* 3.3 29.8 - - - -
14B LEU* 4.4 11.0 - - + -
15B ASP* 1.3 74.0 - - - +
17B ILE* 1.3 63.2 + - - +
18B SER* 4.2 0.4 - - - +
35B GLN* 4.0 14.6 - - + +
36B ARG 3.4 2.2 - - - -
37B TRP* 3.9 33.4 - - + +
96B SER* 4.3 12.6 - - - +
97B SER 2.8 15.8 + - - +
98B CYS* 3.6 2.5 - - + +
99B CYS* 2.8 29.1 + - - +
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Residues in contact with ILE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASP* 4.3 16.2 - - + +
16B VAL* 1.3 78.7 - - - +
18B SER* 1.3 64.8 + - - +
19B LEU* 4.3 0.8 + - + +
34B SER 3.8 0.5 - - - +
35B GLN* 3.0 4.6 - - - -
36B ARG* 2.7 48.1 + - + +
38B GLN* 3.6 38.6 - - + +
99B CYS* 3.5 16.2 - - + +
101B ILE* 3.4 33.9 - - + -
254B LEU* 5.8 9.0 - - + -
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Residues in contact with SER 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A CYS* 4.3 10.5 - - - +
111A VAL* 3.8 24.6 - - - +
17B ILE* 1.3 73.9 - - - +
19B LEU* 1.3 60.5 + - - +
20B VAL* 3.9 2.6 + - - -
32B CYS* 4.3 3.1 - - - -
34B SER 3.4 6.7 - - - -
35B GLN* 3.1 28.8 + - - +
98B CYS* 6.2 0.2 - - - -
99B CYS 2.9 12.0 + - - -
100B ILE* 3.5 9.3 - - - +
101B ILE* 2.8 31.1 + - - +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ILE* 4.3 0.6 - - + +
18B SER* 1.3 74.0 - - - +
20B VAL* 1.3 54.9 + - - +
32B CYS* 3.2 5.2 - - - +
33B LEU* 2.7 45.2 + - + -
34B SER* 2.8 31.6 + - - +
101B ILE* 3.5 37.9 - - + +
103B ASN* 3.4 42.4 - - + +
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 4.1 8.3 - - + -
18B SER 4.6 2.0 - - - +
19B LEU* 1.3 79.9 - - - +
21B ASP* 1.3 63.1 + - - +
22B LYS 3.5 26.2 - - - +
23B TYR* 4.4 2.2 - - - +
30B ILE* 3.5 26.0 - - + -
31B ARG 4.7 0.7 - - - +
32B CYS* 3.9 17.3 - - + +
33B LEU* 4.3 4.9 - - - +
100B ILE* 3.7 25.4 - - + -
101B ILE 2.9 19.2 + - - +
102B ASN* 4.4 2.2 - - - -
103B ASN* 2.8 31.3 + - - +
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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