Contacts of the strand formed by residues 73 - 79 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ALA* 4.3 8.5 - - + -
11C ILE 3.5 15.5 - - - +
12C LYS* 4.2 2.7 - - - -
13C PRO* 3.9 21.1 - - + -
16C VAL* 4.7 0.2 - - - -
39C LYS 3.8 0.7 - - - +
40C PHE* 3.3 7.1 - - - -
41C LEU* 2.7 35.3 + - + +
43C ALA* 5.3 4.9 - - + +
48C LEU* 6.0 0.2 - - + -
68C MET* 4.3 22.2 - - + +
71C GLY 4.7 0.4 - - - +
72C PRO* 1.3 78.5 - - - +
74C VAL* 1.3 73.5 + - - +
75C ALA 4.0 2.2 - - - +
133C TRP* 3.9 31.9 - - + -
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Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE 3.8 0.9 - - - +
10C ALA* 3.2 4.5 - - - -
11C ILE* 2.9 44.9 + - + -
16C VAL* 4.1 7.4 - - + +
21C VAL* 4.0 32.1 - - + -
25C ILE* 5.0 0.2 - - + -
38C MET* 4.1 9.6 - - + -
39C LYS 3.6 3.6 - - - +
40C PHE* 3.7 21.8 - - + -
73C VAL* 1.3 72.1 - - - +
75C ALA* 1.3 59.9 + - - +
76C MET* 4.0 24.2 - - + +
35F LEU* 5.1 0.4 - - + -
38F MET* 3.8 21.8 - - + -
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Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C PHE* 3.8 14.1 - - + -
9C ILE 3.9 3.1 - - - -
10C ALA* 4.4 1.3 - - - +
38C MET* 3.2 4.5 - - - +
39C LYS* 2.9 38.2 + - + +
41C LEU* 4.1 9.2 - - + -
73C VAL* 3.8 1.8 - - + -
74C VAL* 1.3 72.5 - - - +
76C MET* 1.3 61.6 + - - +
133C TRP* 3.8 30.1 - - + -
134C PHE* 3.4 14.1 - - + -
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Residues in contact with MET 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C PHE* 3.3 10.8 - - - -
9C ILE* 2.8 67.7 + - + +
11C ILE* 3.8 29.4 - - + -
24C ILE* 5.0 4.5 - - + -
25C ILE* 4.0 23.3 - - + -
28C PHE* 5.8 1.1 - - + -
35C LEU* 4.2 2.2 - - + -
37C ALA 3.2 9.0 - - - +
38C MET* 3.9 23.6 - - + +
74C VAL* 4.0 7.9 - - + +
75C ALA* 1.3 78.0 - - - +
77C VAL* 1.3 64.4 + - - +
78C TRP* 3.5 28.7 - - + +
134C PHE* 4.0 3.0 - - - -
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Residues in contact with VAL 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ARG* 4.0 24.0 - - + +
7C THR 3.3 10.3 - - - +
8C PHE* 4.7 0.9 - - + -
35C LEU* 3.7 6.8 - - - +
36C VAL* 2.8 44.3 + - + -
37C ALA* 3.0 23.7 + - + +
76C MET* 1.3 77.9 - - - +
78C TRP* 1.3 59.6 + - - +
130C ILE* 4.0 24.0 - - + -
134C PHE* 3.7 27.8 - - + -
139C LEU* 4.1 9.9 - - + -
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Residues in contact with TRP 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ARG* 3.2 4.0 - - - +
7C THR* 2.9 36.3 + - + -
9C ILE* 3.7 23.5 - - + +
25C ILE* 3.9 19.7 - - + -
28C PHE* 3.6 41.8 - + + -
29C GLU* 3.9 22.9 - - + -
33C PHE* 3.6 31.2 - - + -
34C ARG 3.3 20.4 - - - -
35C LEU* 3.6 32.5 - - + -
36C VAL* 4.4 1.6 - - - -
76C MET* 3.5 32.2 - - + +
77C VAL* 1.3 77.1 - - - +
79C GLU* 1.3 61.1 + - - +
83C VAL* 3.8 18.5 - - + +
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Residues in contact with GLU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ASN* 2.9 32.1 + - - +
4C LEU* 3.7 28.4 - - + +
5C GLU 3.3 12.3 - - - +
6C ARG* 2.9 19.8 + - - -
33C PHE* 3.6 9.7 - - - -
34C ARG* 2.8 63.7 + - + +
36C VAL* 3.5 15.0 - - + -
78C TRP* 1.3 76.9 - - - +
80C GLY* 1.3 63.1 + - - +
83C VAL* 4.3 0.9 - - - -
151C 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