Contacts of the strand formed by residues 76 - 84 (chain E) in PDB entry 1NVI
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 76 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E ALA* 4.4 4.2 + - - +
25E ARG* 4.9 0.3 + - - -
67E VAL* 5.8 0.2 - - + -
70E ALA* 4.0 25.4 - - + +
71E ARG* 3.2 31.8 + - + +
74E TRP* 3.1 30.6 + - + +
75E PRO* 1.3 76.8 - - - +
77E GLY* 1.3 61.0 + - - +
79E VAL* 4.0 15.5 - - + -
99E VAL* 3.5 28.0 - - + -
100E THR 3.4 6.3 - - - +
101E SER* 4.5 4.7 - - - +
106E SER 4.1 5.4 - - - +
110E ALA* 3.8 22.2 - - + -
114E ILE* 5.1 0.9 - - + -
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Residues in contact with GLY 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E ALA* 3.2 9.5 - - - +
25E ARG* 3.2 25.6 - - - -
28E ASP* 3.8 5.1 + - - -
71E ARG* 2.8 32.1 + - - -
75E PRO 4.2 0.4 + - - -
76E LEU* 1.3 69.8 - - - +
78E ARG* 1.3 62.7 + - - -
79E VAL* 4.1 0.3 - - - +
100E THR* 2.9 19.3 + - - -
101E SER* 4.5 0.8 - - - +
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Residues in contact with ARG 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ALA* 4.8 0.7 - - + -
3E GLU* 3.4 24.5 + - - +
21E TRP* 2.8 73.8 + - + +
22E LEU* 3.7 16.4 - - + +
24E GLU* 2.9 34.2 + - - +
25E ARG* 4.0 32.1 - - - +
28E ASP* 4.0 2.0 + - - +
77E GLY* 1.3 73.4 - - - -
79E VAL* 1.3 62.1 + - - +
99E VAL* 3.7 1.0 - - - -
100E THR* 2.8 38.4 + - - +
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Residues in contact with VAL 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E GLU 3.2 6.5 + - - +
4E THR* 3.3 5.2 - - + -
5E LYS 2.8 25.0 + - - +
21E TRP* 3.9 2.0 - - - -
22E LEU* 4.2 1.1 - - - -
67E VAL* 3.9 34.1 - - + -
71E ARG* 3.7 20.6 - - - +
76E LEU* 4.0 28.9 - - + -
77E GLY 4.1 1.8 - - - +
78E ARG* 1.3 80.3 - - - +
80E THR* 1.3 73.9 + - - +
81E VAL* 4.3 1.3 - - + -
98E GLY 3.2 11.2 - - - +
99E VAL* 4.3 6.3 - - + -
114E ILE* 4.2 12.8 - - + -
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Residues in contact with THR 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LYS* 3.3 22.7 - - + +
18E GLU* 4.1 6.5 + - - +
21E TRP* 3.3 29.5 - - - -
22E LEU* 3.6 9.5 - - - +
79E VAL* 1.3 70.5 - - - +
81E VAL* 1.3 68.6 + - - +
82E ILE* 3.9 26.5 - - + -
96E PHE* 3.8 22.4 - - + +
97E VAL* 3.3 3.6 - - - -
98E GLY 2.8 34.2 + - - +
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Residues in contact with VAL 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LYS 2.9 7.6 + - - +
6E ILE* 3.3 16.5 - - + +
7E VAL 3.0 23.2 + - - +
63E LEU* 4.2 21.3 - - + +
67E VAL* 3.8 28.7 - - + -
79E VAL* 4.3 4.0 - - + -
80E THR* 1.3 79.0 - - - +
82E ILE* 1.3 68.3 + - - +
83E HIS 4.3 0.2 - - - -
95E VAL* 5.3 0.2 - - + -
96E PHE 3.3 7.6 - - - +
97E VAL* 4.3 6.5 - - + -
114E ILE* 4.0 17.7 - - + -
118E LEU* 4.1 25.1 - - + -
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Residues in contact with ILE 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LYS* 4.6 3.8 - - - -
7E VAL* 3.3 31.9 - - + +
9E GLY 6.1 0.4 - - - +
11E GLN 5.7 1.6 - - - +
13E PHE* 3.5 36.3 - - + -
18E GLU* 3.5 42.6 - - + +
80E THR* 3.9 15.0 - - + -
81E VAL* 1.3 81.0 - - - +
83E HIS* 1.3 66.7 + - - +
84E ARG* 5.0 2.7 - - + +
94E ILE 4.6 0.2 - - - -
95E VAL* 3.3 6.9 - - - +
96E PHE* 2.9 41.5 + - + +
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Residues in contact with HIS 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D GLY 3.9 1.0 - - - -
81D GLY* 2.9 28.2 + - - -
7E VAL 2.9 7.6 + - - +
8E VAL* 3.3 26.9 - - - +
9E GLY 3.4 2.8 + - - -
52E LEU* 3.6 15.3 - - + -
63E LEU* 4.6 9.6 - - + +
81E VAL* 5.2 0.4 - - - +
82E ILE* 1.3 76.3 - - - +
84E ARG* 1.3 86.2 + - - +
94E ILE* 3.5 28.7 - - + +
95E VAL* 3.8 21.5 - - + -
118E LEU* 3.9 11.2 - - + -
124E PHE* 3.5 37.9 - + + -
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Residues in contact with ARG 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E GLY 3.1 7.4 - - - +
10E PRO 3.0 23.8 + - - -
11E GLN 3.3 17.3 + - - +
12E PRO* 3.6 35.3 - - - +
13E PHE* 4.2 13.9 - - + +
52E LEU* 3.5 8.8 - - - +
82E ILE* 5.2 2.0 - - + -
83E HIS* 1.3 93.5 + - - +
85E ILE* 1.3 65.2 + - - +
87E GLU 4.9 2.8 + - - -
88E LEU* 3.4 33.9 - - + +
92E ASP* 4.0 18.4 + - - +
93E GLU* 3.1 29.7 + - - +
94E ILE 3.0 16.2 + - - +
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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