Contacts of the strand formed by residues 76 - 83 (chain E) in PDB entry 1NQ3
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 76 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62E ILE* 5.3 2.0 - - + -
66E LEU* 3.9 31.9 - - + -
73E PHE* 3.3 20.6 + - + +
74E THR 4.4 0.3 - - - +
75E ASN* 1.3 78.1 - - - +
77E VAL* 1.3 62.9 + - - +
78E LYS 3.9 12.3 - - - +
79E ALA* 4.6 4.7 - - + -
100E PHE* 4.1 11.0 - - + -
103E SER 4.8 1.4 - - - +
105E PRO* 3.4 37.3 - - + +
125E ALA* 4.3 15.9 - - + -
126E ILE 3.5 11.9 - - - +
127E ALA* 4.1 2.7 - - + -
6F ARG* 4.0 10.4 + - - -
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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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75E ASN 3.5 9.8 + - - +
76E VAL* 1.3 77.5 - - - +
78E LYS* 1.3 60.4 + - - +
105E PRO* 3.5 7.9 - - - +
106E ALA* 2.8 21.8 + - - +
126E ILE* 2.9 26.6 + - + +
128E VAL* 4.1 22.2 - - + -
132E LEU* 5.3 1.8 - - + -
6F ARG* 4.6 11.2 - - - +
25F VAL* 3.6 32.2 - - + +
27F VAL* 4.2 9.6 - - + -
32F TYR* 4.0 29.1 - - + +
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Residues in contact with LYS 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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76E VAL* 3.9 2.3 - - - +
77E VAL* 1.3 83.0 - - + +
79E ALA* 1.3 71.7 + - - +
80E THR* 3.7 20.0 + - - +
105E PRO* 3.7 1.8 - - - +
106E ALA* 3.3 23.8 - - + +
107E ARG 4.4 1.6 - - - +
108E ALA* 4.4 9.0 - - - +
125E ALA* 3.3 3.6 - - - +
126E ILE* 2.9 51.1 + - + +
32F TYR* 4.1 26.8 - - + +
33F ILE 5.0 9.6 + - - +
124F GLU* 3.0 29.3 + - - +
126F ILE* 5.7 6.9 - - - +
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Residues in contact with ALA 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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76E VAL* 4.6 10.5 - - + -
78E LYS* 1.3 77.4 - - - +
80E THR* 1.3 63.4 + - - +
81E VAL* 4.1 0.7 - - + -
96E TYR* 3.3 35.2 - - + +
100E PHE* 5.6 1.3 - - + -
105E PRO* 4.9 0.2 - - + -
106E ALA 3.0 8.3 + - - +
107E ARG* 3.3 8.6 - - + +
108E ALA 3.2 21.5 + - - -
123E ILE* 4.7 7.0 - - + -
124E GLU 3.4 9.2 - - - +
125E ALA* 4.7 4.0 - - + -
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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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78E LYS* 3.7 19.1 + - - +
79E ALA* 1.3 74.7 - - - +
81E VAL* 1.3 63.6 + - - +
82E LEU* 3.8 16.6 + - + +
108E ALA* 3.4 13.1 - - + +
110E TYR* 3.8 27.8 - - + +
122E GLU 3.7 1.4 - - - +
123E ILE* 3.4 6.1 - - - +
124E GLU* 2.9 53.9 + - - +
124F GLU* 4.7 3.0 + - - +
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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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79E ALA 5.1 0.4 - - - -
80E THR* 1.3 76.9 - - - +
82E LEU* 1.3 62.3 + - - +
83E LEU* 3.8 27.8 + - + +
89E PHE* 5.6 3.6 - - + -
92E VAL* 4.2 16.8 - - + -
96E TYR* 4.2 28.0 - - + -
107E ARG* 4.3 17.9 - - + +
108E ALA 2.8 9.9 + - - +
109E ALA* 3.3 13.3 - - + +
110E TYR 3.2 25.8 + - - +
121E VAL* 4.4 7.9 - - + -
122E GLU 3.9 2.0 - - - -
123E ILE* 4.5 11.0 - - + -
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Residues in contact with LEU 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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110D TYR* 3.5 37.9 - - + +
80E THR* 4.0 13.5 - - + +
81E VAL* 1.3 71.7 - - - +
83E LEU* 1.3 61.1 + - - +
110E TYR* 3.5 42.4 - - + +
112E VAL* 4.0 11.2 - - + -
115E LEU* 3.8 16.6 - - + +
121E VAL* 3.2 8.5 - - - +
122E GLU* 2.8 62.0 + - + +
124E GLU* 4.1 12.3 - - + +
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Residues in contact with LEU 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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51E VAL* 4.8 0.2 - - + -
81E VAL* 4.1 13.2 - - + +
82E LEU* 1.3 75.4 - - - +
84E ALA* 1.3 60.3 + - - +
85E ASP 3.2 16.2 - - - +
86E ILE* 4.4 11.4 - - + -
88E ASP* 4.5 8.1 - - + -
89E PHE* 3.9 41.7 - - + +
92E VAL* 3.7 30.1 - - + -
110E TYR 3.1 17.7 + - - +
111E GLN* 3.2 5.9 - - - -
112E VAL* 2.9 31.0 + - - +
115E LEU* 4.6 1.1 - - - -
120E ARG 3.8 7.2 - - - +
121E VAL* 4.1 15.9 - - + -
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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