Contacts of the strand formed by residues 73 - 79 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E ALA* 4.5 7.9 - - + -
11E ILE 3.4 14.8 - - - +
12E LYS* 4.1 2.5 - - - -
13E PRO* 3.9 21.1 - - + -
39E LYS 3.8 0.7 - - - +
40E PHE* 3.4 7.6 - - - -
41E LEU* 2.8 35.9 + - + +
43E ALA* 5.4 4.3 - - + +
48E LEU* 6.0 0.2 - - + -
68E MET* 4.2 21.3 - - + +
71E GLY 4.8 0.7 - - - +
72E PRO* 1.3 77.8 - - - +
74E VAL* 1.3 75.1 + - - +
75E ALA* 4.0 3.1 - - + +
133E TRP* 3.9 32.5 - - + -
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Residues in contact with VAL 74 (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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35B LEU* 5.1 0.2 - - + -
38B MET* 3.9 22.2 - - + -
9E ILE 3.9 0.7 - - - +
10E ALA* 3.2 5.0 - - - -
11E ILE* 2.9 41.0 + - + -
16E VAL* 4.1 7.0 - - + -
21E VAL* 4.1 33.2 - - + -
25E ILE* 5.0 0.2 - - + -
38E MET* 4.1 8.3 - - + -
39E LYS 3.6 3.1 - - - +
40E PHE* 3.7 21.3 - - + -
73E VAL* 1.3 73.8 - - - +
75E ALA* 1.3 60.2 + - - +
76E MET* 4.0 26.1 + - + +
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Residues in contact with ALA 75 (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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8E PHE* 3.8 20.9 - - + -
9E ILE 3.9 3.6 - - - -
38E MET* 3.1 5.2 - - - +
39E LYS* 2.9 39.4 + - + +
41E LEU* 4.2 9.2 - - + -
73E VAL* 3.8 2.9 - - + -
74E VAL* 1.3 72.6 - - - +
76E MET* 1.3 60.5 + - - +
133E TRP* 3.9 22.0 - - + -
134E PHE* 3.4 13.7 - - + -
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Residues in contact with MET 76 (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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8E PHE* 3.4 10.2 - - - -
9E ILE* 2.9 59.3 + - + +
11E ILE* 3.7 33.9 - - + -
24E ILE* 5.1 3.6 - - + -
25E ILE* 4.0 23.6 - - + -
28E PHE* 5.9 1.1 - - + -
35E LEU* 4.1 2.0 - - + -
37E ALA 3.1 9.0 - - - +
38E MET* 3.9 24.5 - - + +
74E VAL* 4.0 8.5 - - + +
75E ALA* 1.3 78.8 - - - +
77E VAL* 1.3 65.7 + - - +
78E TRP* 3.5 29.2 - - + +
134E PHE* 4.0 2.9 - - - -
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Residues in contact with VAL 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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6E ARG* 3.9 30.1 - - + -
7E THR 3.3 9.6 - - - +
8E PHE* 4.7 1.3 - - + -
35E LEU* 3.6 5.9 - - - +
36E VAL* 2.8 36.1 + - + -
37E ALA* 2.9 23.4 + - + +
76E MET* 1.3 79.0 - - - +
78E TRP* 1.3 64.5 + - - +
130E ILE* 3.9 30.5 - - + -
134E PHE* 3.7 26.5 - - + -
139E LEU* 4.4 4.0 - - + -
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Residues in contact with TRP 78 (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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6E ARG* 3.2 4.2 - - - +
7E THR* 2.9 35.4 + - + -
9E ILE* 3.7 23.3 - - + +
25E ILE* 4.0 20.2 - - + -
28E PHE* 3.6 38.3 - + + -
29E GLU* 3.8 26.9 - - + -
33E PHE* 3.6 30.5 - - + -
34E ARG 3.3 20.9 - - - -
35E LEU* 3.6 32.3 - - + -
36E VAL* 4.4 1.6 - - - -
76E MET* 3.5 32.4 - - + +
77E VAL* 1.3 78.8 - - - +
79E GLU* 1.3 60.9 + - - +
83E VAL* 3.8 18.3 - - + +
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Residues in contact with GLU 79 (chain E).
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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2E ALA 5.3 0.5 - - - +
3E ASN* 4.5 3.0 - - - +
4E LEU* 3.6 39.2 + - + +
5E GLU 3.2 12.3 - - - +
6E ARG* 2.9 31.8 + - + +
33E PHE* 3.6 9.1 - - - -
34E ARG* 2.8 67.5 + - + +
36E VAL* 3.6 15.3 - - + -
78E TRP* 1.3 76.9 - - - +
80E GLY* 1.3 62.0 + - - +
83E VAL* 4.3 0.9 - - - -
151E TYR* 4.9 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