Contacts of the helix formed by residues 70 - 83 (chain B) in PDB entry 1NKV
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 LEU 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B THR* 6.1 2.2 - - - +
67B MSE 3.4 47.1 - - + +
71B PHE* 1.3 65.4 + - - +
72B THR* 3.1 15.3 - - + -
73B ALA* 3.3 38.5 + - + +
74B GLN* 4.3 0.9 + - - +
76B LYS* 4.9 5.4 - - - +
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Residues in contact with PHE 71 (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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7B PHE* 4.6 22.0 - + - -
8B THR* 5.1 15.3 - - + -
11B GLU* 4.2 14.1 - - + -
12B SER* 5.5 2.5 - - - -
17B HIS* 3.0 44.2 - + - -
46B GLY* 3.8 25.5 - - - +
66B ASP* 4.9 8.5 - - - +
67B MSE 4.4 4.0 - - - +
70B LEU* 1.3 75.3 - - - +
72B THR* 1.3 64.6 + - - +
73B ALA 3.0 2.9 - - - -
74B GLN* 3.0 29.3 + - + +
75B ALA* 2.9 23.2 + - - +
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Residues in contact with THR 72 (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 GLY 5.1 1.1 - - - -
66B ASP* 3.9 7.0 - - - +
67B MSE 2.8 39.6 + - - +
70B LEU* 3.1 12.7 - - + -
71B PHE* 1.3 78.5 - - - +
73B ALA* 1.3 57.7 + - - +
75B ALA* 3.5 7.9 + - - +
76B LYS* 2.8 48.1 + - - +
90B PHE* 4.0 7.2 - - + +
91B ILE* 3.2 33.2 + - - +
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Residues in contact with ALA 73 (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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70B LEU* 3.3 24.4 - - + +
71B PHE 3.0 0.2 - - - -
72B THR* 1.3 77.7 - - - +
74B GLN* 1.3 65.1 + - - +
76B LYS* 3.0 35.0 + - + +
77B ARG* 3.4 21.0 + - - +
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Residues in contact with GLN 74 (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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11B GLU 5.2 0.2 - - - +
12B SER 4.7 8.7 - - - +
13B GLU* 5.6 0.7 - - - -
14B HIS 3.8 10.8 + - - +
15B ARG* 5.2 0.2 - - - +
17B HIS* 2.9 20.5 + - - -
47B SER* 2.7 38.8 + - - +
70B LEU 4.3 0.8 + - - +
71B PHE* 3.0 32.6 + - + +
73B ALA* 1.3 79.5 - - - +
75B ALA* 1.3 60.5 + - - +
77B ARG* 3.3 41.5 + - - +
78B ARG* 3.9 7.9 + - + +
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Residues in contact with ALA 75 (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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45B SER* 4.4 0.2 - - - +
46B GLY 3.7 9.6 - - - +
47B SER 3.1 22.8 + - - +
48B GLY* 3.8 11.4 - - - -
52B CYS* 4.0 4.5 - - - -
71B PHE 2.9 14.1 + - - +
72B THR* 3.7 9.0 - - - +
73B ALA 3.2 0.2 - - - -
74B GLN* 1.3 76.5 - - - +
76B LYS* 1.3 62.2 + - - +
78B ARG* 3.8 3.7 + - - +
79B ALA 3.8 10.2 + - - -
90B PHE* 3.3 33.9 - - + -
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Residues in contact with LYS 76 (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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70B LEU* 4.9 4.9 - - - +
72B THR* 2.8 43.4 - - - +
73B ALA* 3.0 23.4 + - + +
75B ALA* 1.3 76.6 - - - +
77B ARG* 1.3 65.9 + - - +
79B ALA* 3.2 17.8 + - - +
80B GLU* 3.5 7.1 + - - +
90B PHE* 4.4 20.9 - - + -
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Residues in contact with ARG 77 (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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73B ALA* 3.4 14.8 + - - +
74B GLN* 3.3 41.9 + - - +
76B LYS* 1.3 77.3 - - - +
78B ARG* 1.3 67.1 + - + +
80B GLU* 2.9 19.1 + - - +
81B GLU* 3.0 21.7 + - + +
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Residues in contact with ARG 78 (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 ARG* 2.8 46.2 - - - +
22B GLU* 4.8 2.2 + - - -
47B SER 5.1 7.6 - - - +
49B GLU* 2.6 40.7 + - + +
52B CYS* 3.6 21.9 - - - +
53B THR* 5.0 4.0 + - - +
56B ARG* 5.2 3.2 - - - +
74B GLN* 4.4 10.8 - - + +
75B ALA 3.8 3.1 + - - +
76B LYS 3.5 0.2 - - - -
77B ARG* 1.3 79.5 - - + +
79B ALA* 1.3 57.6 + - - +
81B GLU* 3.8 18.7 + - - -
82B LEU* 2.7 66.1 + - + +
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Residues in contact with ALA 79 (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 CYS* 4.0 9.5 - - - -
75B ALA 3.8 8.2 + - - +
76B LYS* 3.2 13.6 + - - +
77B ARG 3.0 0.8 + - - -
78B ARG* 1.3 80.2 - - - +
80B GLU* 1.3 62.1 + - - +
82B LEU 3.7 1.6 + - - -
84B VAL* 2.9 34.7 + - + +
85B SER* 3.0 15.5 + - - +
86B GLU* 5.1 3.6 - - - +
88B VAL* 4.8 13.7 - - + +
90B PHE* 4.8 7.9 - - + -
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Residues in contact with GLU 80 (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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76B LYS 3.5 5.5 + - - +
77B ARG* 2.9 9.4 + - - +
79B ALA* 1.3 79.8 - - - +
81B GLU* 1.3 60.8 + - - +
82B LEU 3.6 0.3 + - - -
83B GLY* 3.9 7.8 + - - -
85B SER* 3.9 25.7 + - - -
86B GLU* 6.1 0.7 - - - +
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Residues in contact with GLU 81 (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 ARG* 4.6 5.9 + - - -
77B ARG* 3.0 22.7 + - + +
78B ARG* 3.8 33.3 + - - +
80B GLU* 1.3 78.8 - - - +
82B LEU* 1.3 63.7 + - + +
83B GLY 3.4 0.4 + - - -
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Residues in contact with LEU 82 (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 CYS* 4.6 11.9 - - + +
56B ARG* 3.1 55.5 - - - +
78B ARG* 2.7 73.4 + - + +
80B GLU 3.4 0.4 - - - -
81B GLU* 1.3 81.3 - - + +
83B GLY* 1.3 57.1 + - - +
84B VAL* 3.3 20.6 - - + +
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Residues in contact with GLY 83 (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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79B ALA 3.8 3.2 + - - -
80B GLU 3.9 6.3 + - - -
81B GLU 3.4 3.8 + - - -
82B LEU* 1.3 78.8 - - - +
84B VAL* 1.3 66.2 + - - +
85B SER* 3.7 4.2 - - - -
87B ARG* 5.0 1.6 + - - -
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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