Contacts of the strand formed by residues 76 - 83 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ILE* 5.4 1.8 - - + -
66A LEU* 3.9 31.6 - - + -
73A PHE* 3.3 27.4 + - + +
74A THR 4.4 1.4 - - - +
75A ASN* 1.3 77.4 - - - +
77A VAL* 1.3 62.9 + - - +
78A LYS 3.8 13.0 - - - +
79A ALA* 4.6 4.3 - - + -
100A PHE* 4.1 5.6 - - + -
103A SER 4.8 3.1 - - - +
105A PRO* 3.5 36.2 - - + +
125A ALA* 4.3 15.3 - - + -
126A ILE 3.6 12.3 - - - +
127A ALA* 4.1 2.5 - - + +
6B ARG* 4.1 8.3 + - - -
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ASN 3.8 9.4 - - - +
76A VAL* 1.3 78.2 - - - +
78A LYS* 1.3 64.1 + - + +
105A PRO* 3.6 7.7 - - - +
106A ALA* 2.9 23.4 + - - +
126A ILE* 2.9 30.5 + - + +
128A VAL* 4.1 21.3 - - + -
132A LEU* 5.2 0.7 - - + -
6B ARG* 4.1 14.6 - - - +
25B VAL* 3.8 20.1 - - + +
27B VAL* 4.2 16.4 - - + -
32B TYR* 4.0 24.6 - - + +
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 3.7 3.7 - - - +
77A VAL* 1.3 85.0 - - + +
79A ALA* 1.3 80.6 + - - +
80A THR* 3.8 14.2 + - - +
105A PRO* 3.8 0.6 - - - +
106A ALA* 3.4 22.9 - - + +
107A ARG* 4.5 1.6 - - - +
108A ALA* 4.5 8.3 - - - +
125A ALA* 3.3 4.6 - - - +
126A ILE* 2.8 49.3 + - + +
32B TYR* 4.0 30.6 - - + -
33B ILE 5.1 8.7 + - - +
124B GLU* 2.8 28.7 + - - -
126B ILE* 6.0 4.4 - - - +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 4.6 6.7 - - + -
78A LYS* 1.3 81.2 - - - +
80A THR* 1.3 64.4 + - - +
81A VAL* 4.2 0.9 - - + -
96A TYR* 3.4 34.1 - - + +
100A PHE* 6.0 0.4 - - + -
105A PRO* 4.8 0.2 - - + -
106A ALA 3.0 8.1 + - - +
107A ARG* 3.3 8.7 - - + +
108A ALA 3.3 21.5 + - - -
123A ILE* 4.7 6.3 - - + -
124A GLU 3.4 9.6 - - - +
125A ALA* 4.5 6.5 - - + -
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Residues in contact with THR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LYS* 3.8 18.4 + - - +
79A ALA* 1.3 76.1 + - - +
81A VAL* 1.3 63.4 + - - +
82A LEU* 3.7 26.3 - - + +
108A ALA* 3.4 11.6 - - + +
110A TYR* 4.0 15.9 - - + +
122A GLU 3.6 1.7 - - - +
123A ILE* 3.3 8.7 - - - +
124A GLU* 2.9 52.9 + - - +
124B GLU* 4.8 3.4 + - - +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ALA 5.3 0.2 - - - -
80A THR* 1.3 75.5 - - - +
82A LEU* 1.3 63.4 + - - +
83A LEU* 3.7 27.8 + - + +
89A PHE* 5.2 4.7 - - + -
92A VAL* 4.1 17.5 - - + -
96A TYR* 4.4 19.1 - - + -
107A ARG* 4.3 23.6 - - + +
108A ALA 2.9 9.3 + - - -
109A ALA* 3.3 13.8 - - + -
110A TYR 3.3 24.3 + - - +
121A VAL* 4.3 7.6 - - + -
122A GLU 3.7 2.7 - - - -
123A ILE* 4.3 13.5 - - + -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A THR* 3.7 16.2 - - + +
81A VAL* 1.3 72.1 - - - +
83A LEU* 1.3 59.4 - - - +
110A TYR* 3.5 43.5 - - + +
112A VAL* 4.1 9.2 - - + -
115A LEU* 4.0 15.7 - - + +
121A VAL* 3.3 8.1 - - - +
122A GLU* 2.8 57.0 + - + +
124A GLU* 4.3 9.9 - - + +
108C ALA* 5.7 0.7 - - + -
110C TYR* 3.3 42.4 - - + +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A VAL* 3.7 26.7 - - + +
82A LEU* 1.3 77.6 - - - +
84A ALA* 1.3 62.1 + - - +
85A ASP 3.2 24.0 - - - +
86A ILE* 4.3 14.8 - - + -
88A ASP* 5.0 3.6 - - + +
89A PHE* 4.0 35.9 - - + -
92A VAL* 3.8 24.9 - - + -
109A ALA* 5.2 0.2 - - + -
110A TYR 3.1 15.8 + - - +
111A GLN* 3.2 3.1 - - - -
112A VAL* 2.9 31.3 + - - +
115A LEU* 4.7 1.1 - - - -
120A ARG 3.8 4.5 - - - +
121A VAL* 4.0 8.5 - - + -
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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