Contacts of the helix formed by residues 53 - 65 (chain B) in PDB entry 2NBV
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 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B SER* 1.3 79.3 - - - +
54B VAL* 1.3 66.6 + - - +
55B GLN* 3.3 13.0 - - - -
56B GLN* 3.3 24.7 + - - +
57B PHE* 3.5 5.7 + - - +
86B THR* 5.5 2.9 - - - -
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Residues in contact with VAL 54 (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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53B SER* 1.3 71.2 - - - +
55B GLN* 1.3 60.9 + - - +
57B PHE* 2.9 13.3 + - + +
58B LYS* 2.8 38.2 + - + +
74B LEU* 5.2 8.3 - - + -
81B LEU* 5.3 1.3 - - + -
82B LYS* 3.3 39.0 - - - +
83B ASP* 3.9 8.5 - - - +
85B ASP* 3.5 18.2 - - - +
86B THR* 3.7 4.3 - - + -
87B LEU* 3.6 31.0 - - + +
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Residues in contact with GLN 55 (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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53B SER* 3.3 9.2 - - - -
54B VAL* 1.3 77.3 - - - +
56B GLN* 1.3 61.9 + - - +
58B LYS* 3.3 13.6 + - + +
59B GLU* 3.1 34.5 + - - +
83B ASP* 3.7 28.1 + - + +
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Residues in contact with GLN 56 (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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52B SER* 5.1 9.4 - - - -
53B SER* 3.3 21.5 + - - +
54B VAL 3.1 0.4 - - - -
55B GLN* 1.3 78.5 - - - +
57B PHE* 1.3 61.0 + - - +
59B GLU* 3.8 11.9 + - - +
60B ALA* 3.4 19.2 + - - +
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Residues in contact with PHE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 4.1 30.5 - - + -
37B VAL* 4.2 12.8 - - + -
46B PHE* 4.0 24.7 - + + -
48B VAL* 3.6 33.2 - - + -
53B SER 3.5 4.6 + - - +
54B VAL* 2.9 16.2 + - + +
56B GLN* 1.3 77.8 - - - +
58B LYS* 1.3 65.4 + - - +
60B ALA* 3.0 18.5 + - + +
61B ILE* 3.0 48.5 + - + +
74B LEU* 4.7 16.4 - - + -
87B LEU* 4.7 22.2 - - + -
98B VAL* 6.0 0.4 - - + -
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Residues in contact with LYS 58 (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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54B VAL* 2.8 33.6 + - + +
55B GLN* 3.3 18.0 + - + +
57B PHE* 1.3 78.0 - - + +
59B GLU* 1.3 60.1 + - + +
60B ALA 3.2 0.3 + - - -
61B ILE* 3.2 11.1 + - - +
62B SER* 2.9 25.6 + - - -
69B THR* 3.1 43.3 + - + +
70B ASP* 4.5 12.1 + - - +
72B LEU* 4.1 16.9 - - + +
74B LEU* 4.9 11.4 - - + -
82B LYS* 5.1 6.5 - - - +
83B ASP* 2.7 33.4 + - + +
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Residues in contact with GLU 59 (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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55B GLN* 3.1 19.7 + - - +
56B GLN* 4.2 13.4 + - - +
58B LYS* 1.3 78.6 - - + +
60B ALA* 1.3 60.1 + - - +
62B SER* 3.1 17.0 + - - +
63B LYS* 3.4 17.2 + - - +
69B THR* 4.0 15.5 - - + -
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Residues in contact with ALA 60 (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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46B PHE* 5.0 5.2 - - + -
48B VAL* 6.2 0.7 - - + -
56B GLN* 3.4 14.0 + - - +
57B PHE* 3.0 22.3 + - + +
59B GLU* 1.3 77.9 - - - +
61B ILE* 1.3 59.9 + - - +
63B LYS* 3.2 5.0 + - - +
64B ARG* 2.9 42.4 + - + +
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Residues in contact with ILE 61 (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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37B VAL* 5.1 6.3 - - + -
46B PHE* 4.7 7.6 - - + -
57B PHE* 3.0 54.5 + - + +
58B LYS* 3.8 2.2 - - - +
60B ALA* 1.3 75.3 - - - +
62B SER* 1.3 55.9 + - - +
64B ARG* 4.5 4.7 - - - +
65B PHE* 2.8 59.9 + - + +
67B SER* 4.9 0.8 + - - -
72B LEU* 3.7 27.6 - - + -
74B LEU* 4.2 21.8 - - + -
100B LEU* 4.1 10.5 - - + -
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Residues in contact with SER 62 (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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58B LYS 2.9 17.2 + - - -
59B GLU* 3.1 16.8 + - - -
61B ILE* 1.3 75.3 - - - +
63B LYS* 1.3 55.2 + - - +
66B LYS* 2.9 25.5 - - - +
67B SER* 3.6 7.9 + - - +
68B GLN* 3.1 30.2 + - - -
69B THR* 3.1 19.6 + - - -
72B LEU* 4.9 0.4 - - - -
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Residues in contact with LYS 63 (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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59B GLU 3.4 16.4 + - - +
60B ALA* 3.2 5.5 + - - +
61B ILE 3.1 0.4 - - - -
62B SER* 1.3 79.1 - - - +
64B ARG* 1.3 92.5 + - - +
66B LYS* 4.0 7.3 + - - +
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Residues in contact with ARG 64 (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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46B PHE* 4.0 31.6 - - + -
60B ALA* 2.9 25.4 + - + +
61B ILE 4.1 0.7 - - - +
63B LYS* 1.3 115.0 + - - +
65B PHE* 1.3 63.6 + - + +
66B LYS* 3.7 1.4 + - - +
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Residues in contact with PHE 65 (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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37B VAL* 4.2 11.9 - - + -
39B THR* 4.0 29.6 - - + -
41B LYS* 5.7 13.7 - - + -
42B GLU* 6.2 3.6 - - + -
44B GLU* 3.9 28.5 - - + -
46B PHE* 3.7 26.9 - + - -
61B ILE* 2.8 36.4 + - + +
64B ARG* 1.3 76.0 - - - +
66B LYS* 1.3 74.6 + - - +
67B SER* 3.8 13.5 + - - +
100B LEU* 5.7 0.2 - - + -
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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