Contacts of the strand formed by residues 73 - 79 (chain B) in PDB entry 1NUE
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 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ALA* 4.3 8.1 - - + -
11B ILE 3.5 16.8 - - - +
12B LYS* 4.2 2.5 - - - -
13B PRO* 4.0 20.2 - - + -
39B LYS 3.7 0.7 - - - +
40B PHE* 3.3 7.1 - - - -
41B LEU* 2.7 35.7 + - + +
43B ALA* 5.4 3.8 - - + +
48B LEU* 5.8 0.9 - - + -
68B MET* 4.3 22.9 - - + +
71B GLY 4.7 0.4 - - - +
72B PRO* 1.3 78.0 - - - +
74B VAL* 1.3 74.5 + - - +
75B ALA 4.0 2.0 - - - +
133B TRP* 3.9 32.3 - - + -
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Residues in contact with VAL 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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9B ILE 3.8 0.9 - - - +
10B ALA* 3.2 5.2 - - - -
11B ILE* 3.0 41.7 + - + -
16B VAL* 4.1 15.3 - - + -
21B VAL* 4.1 23.1 - - + -
38B MET* 4.1 7.2 - - - -
39B LYS 3.5 6.5 - - - +
40B PHE* 3.7 21.3 - - + -
73B VAL* 1.3 73.0 - - - +
75B ALA* 1.3 60.7 + - - +
76B MET* 3.9 25.7 + - + +
35E LEU* 5.2 0.4 - - + -
38E MET* 3.9 21.5 - - + -
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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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8B PHE* 3.8 20.9 - - + -
9B ILE 3.9 3.6 - - - -
10B ALA* 4.5 1.1 - - - +
38B MET* 3.2 5.4 - - - +
39B LYS* 2.8 39.4 + - + +
41B LEU* 4.1 9.2 - - + -
73B VAL* 3.8 2.3 - - + -
74B VAL* 1.3 72.4 - - - +
76B MET* 1.3 61.1 + - - +
133B TRP* 3.9 22.9 - - + -
134B PHE* 3.5 13.1 - - + -
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Residues in contact with MET 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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8B PHE* 3.4 10.0 - - - -
9B ILE* 2.9 62.2 + - + +
11B ILE* 3.8 29.6 - - + -
24B ILE* 5.0 4.0 - - + -
25B ILE* 4.0 24.0 - - + -
28B PHE* 5.8 1.1 - - + -
35B LEU* 4.2 2.0 - - + -
37B ALA 3.3 7.6 - - - +
38B MET* 3.9 24.0 - - + +
74B VAL* 4.0 9.0 - - + +
75B ALA* 1.3 79.2 - - - +
77B VAL* 1.3 64.9 + - - +
78B TRP* 3.5 29.4 - - + +
134B PHE* 4.0 1.7 - - - -
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Residues in contact with VAL 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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6B ARG* 3.9 24.7 - - + +
7B THR 3.4 10.1 - - - +
8B PHE* 4.6 1.1 - - + -
35B LEU* 3.7 4.9 - - - +
36B VAL* 2.8 41.9 + - + -
37B ALA* 3.0 19.7 + - + +
76B MET* 1.3 79.1 - - - +
78B TRP* 1.3 64.5 + - - +
130B ILE* 4.0 23.1 - - + -
134B PHE* 3.6 28.5 - - + -
139B LEU* 4.0 14.1 - - + -
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Residues in contact with TRP 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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6B ARG* 3.3 3.8 - - - +
7B THR* 3.0 35.9 + - + -
9B ILE* 3.7 24.4 - - + +
25B ILE* 4.0 20.4 - - + -
28B PHE* 3.7 41.8 - + + -
29B GLU* 3.9 23.3 - - + -
33B PHE* 3.6 27.1 - - + -
34B ARG 3.3 7.4 - - - -
35B LEU* 3.5 50.7 - - + -
36B VAL* 4.3 2.0 - - - -
76B MET* 3.5 31.6 - - + +
77B VAL* 1.3 75.8 - - - +
79B GLU* 1.3 59.7 + - - +
83B VAL* 3.9 17.4 - - + +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B ASN* 5.3 0.3 - - - +
4B LEU* 3.5 40.2 + - + +
5B GLU 3.4 8.7 - - - +
6B ARG* 2.6 31.2 + - - +
33B PHE* 3.5 12.1 - - - -
34B ARG* 2.8 65.4 + - + +
36B VAL* 3.5 15.5 - - + -
78B TRP* 1.3 74.2 - - - +
80B GLY* 1.3 62.5 + - - +
83B VAL* 4.3 0.9 - - - -
151B TYR* 4.8 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