Contacts of the strand formed by residues 76 - 83 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ARG* 4.2 8.1 + - - -
33C ILE* 5.7 0.2 - - + -
62C ILE* 5.3 2.0 - - + -
66C LEU* 3.9 31.4 - - + -
73C PHE* 3.3 23.3 + - + +
74C THR 4.5 0.9 - - - +
75C ASN* 1.3 77.4 - - - +
77C VAL* 1.3 63.0 + - - +
78C LYS 3.7 15.0 - - - +
79C ALA* 4.6 4.5 - - + -
100C PHE* 4.0 10.8 - - + -
103C SER 5.0 1.7 - - - +
105C PRO* 3.1 34.3 - - + +
125C ALA* 4.2 15.3 - - + -
126C ILE 3.5 11.9 - - - +
127C ALA* 4.0 2.5 - - + +
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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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6A ARG* 4.0 16.8 - - + +
25A VAL* 3.7 28.8 - - + +
27A VAL* 4.5 9.6 - - + -
32A TYR* 3.9 29.1 - - + +
75C ASN 3.4 10.1 + - - +
76C VAL* 1.3 78.0 - - - +
78C LYS* 1.3 61.4 + - + +
105C PRO* 3.5 7.9 - - - +
106C ALA* 2.9 20.3 + - - +
126C ILE* 2.9 25.9 + - + +
128C VAL* 4.1 23.1 - - + -
132C LEU* 5.3 1.3 - - + -
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Residues in contact with LYS 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 4.0 27.6 - - + -
33A ILE 5.1 7.4 + - - +
124A GLU* 2.8 29.3 + - - +
126A ILE* 5.8 5.7 - - - +
76C VAL* 3.7 2.9 - - - +
77C VAL* 1.3 82.0 - - + +
79C ALA* 1.3 80.7 + - - +
80C THR* 3.7 12.1 + - - +
105C PRO* 3.6 1.4 - - - +
106C ALA* 3.4 23.6 - - + +
107C ARG 4.5 4.0 - - - +
108C ALA* 4.5 7.6 - - - -
125C ALA* 3.3 4.0 - - - +
126C ILE* 2.9 54.1 + - + +
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Residues in contact with ALA 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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76C VAL* 4.6 7.0 - - + -
78C LYS* 1.3 81.0 - - - +
80C THR* 1.3 65.5 + - - +
81C VAL* 5.4 0.4 - - + -
96C TYR* 3.4 33.0 - - + +
100C PHE* 5.6 1.6 - - + -
105C PRO* 4.9 0.7 - - + -
106C ALA 3.0 7.9 + - - +
107C ARG* 3.3 8.9 - - + +
108C ALA 3.3 20.4 + - - -
123C ILE* 4.8 6.5 - - + -
124C GLU 3.4 9.4 - - - +
125C ALA* 4.5 6.5 - - + -
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Residues in contact with THR 80 (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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124A GLU* 4.6 3.0 + - - +
78C LYS* 3.7 19.2 + - - +
79C ALA* 1.3 76.9 + - - +
81C VAL* 1.3 65.0 + - - +
82C LEU* 3.8 25.5 + - + +
108C ALA* 3.3 12.7 - - + +
110C TYR* 4.1 17.0 - - + +
122C GLU 3.7 1.0 - - - +
123C ILE* 3.3 7.0 - - - +
124C GLU* 2.9 52.5 + - - +
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Residues in contact with VAL 81 (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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80C THR* 1.3 74.9 - - - +
82C LEU* 1.3 63.4 + - - +
83C LEU* 3.8 26.4 + - + +
89C PHE* 5.9 2.7 - - + -
92C VAL* 4.1 17.7 - - + -
96C TYR* 4.2 21.1 - - + -
107C ARG* 4.2 25.8 - - + +
108C ALA 2.9 8.1 + - - +
109C ALA* 3.3 13.9 - - + +
110C TYR* 3.3 25.8 + - - +
121C VAL* 4.2 8.7 - - + -
122C GLU 3.8 2.0 - - - -
123C ILE* 4.5 11.7 - - + -
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Residues in contact with LEU 82 (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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110B TYR* 3.3 41.3 - - + +
80C THR* 3.8 17.3 - - + +
81C VAL* 1.3 72.2 - - - +
83C LEU* 1.3 61.7 + - - +
110C TYR* 3.7 38.8 - - + +
112C VAL* 4.1 9.6 - - + -
115C LEU* 3.8 15.7 - - + +
121C VAL* 3.3 9.0 - - - +
122C GLU* 2.8 60.2 + - + +
124C GLU* 4.4 9.9 - - + +
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Residues in contact with LEU 83 (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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81C VAL* 4.0 19.3 - - + +
82C LEU* 1.3 75.9 - - - +
84C ALA* 1.3 60.5 + - - +
85C ASP 3.2 19.5 - - - +
86C ILE* 4.3 13.9 - - + -
88C ASP* 4.6 5.4 - - + -
89C PHE* 3.9 40.2 - - + +
92C VAL* 3.7 30.3 - - + -
109C ALA* 5.1 0.4 - - + -
110C TYR 3.1 18.9 + - - +
111C GLN* 3.2 5.5 - - - -
112C VAL* 2.9 30.4 + - - +
115C LEU* 4.7 0.9 - - - -
120C ARG 3.9 5.4 - - - +
121C VAL* 4.2 7.2 - - + -
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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