Contacts of the strand formed by residues 34 - 40 (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 SER 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A HIS* 4.7 7.0 - - - -
17B ILE 3.8 0.4 - - - +
18B SER* 3.4 2.3 - - - -
19B LEU* 2.8 48.0 + - - +
32B CYS* 3.4 8.5 - - - -
33B LEU* 1.3 82.0 - - - +
35B GLN* 1.3 62.5 + - - +
36B ARG* 6.0 2.8 - - - +
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Residues in contact with GLN 35 (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* 6.1 0.6 - - - +
96A SER* 3.0 30.7 + - - -
97A SER* 4.1 3.9 + - - +
98A CYS* 3.9 6.7 + - - -
111A VAL 3.7 18.7 - - - +
113A HIS* 3.9 37.6 + - + +
16B VAL* 4.0 17.2 - - + +
17B ILE 3.0 7.0 - - - +
18B SER* 3.1 23.2 + - - +
32B CYS* 3.9 11.2 - - - -
34B SER* 1.3 78.0 - - - +
36B ARG* 1.3 69.1 + - - +
37B TRP* 4.0 15.2 - - + +
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Residues in contact with ARG 36 (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 3.4 1.7 - - - +
16B VAL* 3.4 3.8 - - - -
17B ILE* 2.7 47.9 + - + +
34B SER* 6.0 2.7 - - - +
35B GLN* 1.3 78.7 - - - +
37B TRP* 1.3 67.2 + - - +
38B GLN* 3.7 27.9 + - + +
292B GLN* 3.5 37.4 + - - +
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Residues in contact with TRP 37 (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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14A LEU* 3.6 21.5 - - + -
16A VAL* 4.0 14.7 - - + +
37A TRP* 3.4 40.4 - + - -
68A VAL* 4.6 12.6 - - + -
96A SER* 4.4 9.1 + - - -
14B LEU* 3.8 23.3 - - + -
15B ASP 3.5 3.4 - - - -
16B VAL* 3.9 25.7 - - + +
35B GLN* 4.0 14.3 - - + +
36B ARG* 1.3 81.6 - - - +
38B GLN* 1.3 62.9 + - - +
71B PHE* 3.6 44.8 - + + -
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Residues in contact with GLN 38 (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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14B LEU* 3.6 5.6 - - - +
15B ASP* 2.8 45.5 + - + +
17B ILE* 3.6 25.9 - - + +
36B ARG* 3.7 36.6 - - + +
37B TRP* 1.3 78.3 - - - +
39B ARG* 1.3 67.0 + - - +
71B PHE* 4.2 7.0 - - - -
75B ASP* 5.9 0.2 - - - -
254B LEU* 6.1 1.2 - - - +
292B GLN* 4.7 7.3 + - - -
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Residues in contact with ARG 39 (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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12B VAL* 3.8 10.8 - - + -
13B VAL 3.7 3.4 - - - -
38B GLN* 1.3 77.8 - - - +
40B GLY* 1.3 57.9 + - - +
44B SER* 2.8 50.4 + - - +
45B ASN* 3.9 9.9 + - - +
48B THR* 2.9 31.0 + - - +
71B PHE* 4.3 3.2 - - + -
72B LEU* 3.9 22.0 - - + -
75B ASP* 2.7 45.9 + - - +
76B PHE* 3.4 46.9 - - - +
79B ARG* 3.3 23.6 - - - +
81B VAL* 4.8 0.6 - - - +
294B PHE* 5.8 1.0 - - - -
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Residues in contact with GLY 40 (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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12B VAL* 3.6 0.7 - - - +
13B VAL* 2.8 32.5 + - - -
15B ASP* 3.5 19.1 - - - -
38B GLN* 3.7 1.8 + - - -
39B ARG* 1.3 73.5 - - - +
41B GLY* 1.3 62.1 + - - -
44B SER* 3.3 17.3 + - - -
45B ASN* 4.0 7.9 - - - -
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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