Contacts of the helix formed by residues 83 - 91 (chain T) in PDB entry 1NSK
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 83 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5T GLU* 3.5 1.9 + - + -
6T ARG 3.2 25.4 - - - +
7T THR* 3.9 16.6 - - + +
28T PHE* 5.5 2.2 - - + -
33T PHE* 3.7 29.4 - - + -
78T TRP* 3.3 30.7 - - + +
80T GLY 2.8 32.5 + - - +
81T LEU 3.4 1.6 - - - -
82T ASN* 1.3 71.9 - - - +
84T VAL* 1.3 54.6 + - - +
86T THR* 3.9 5.6 - - - -
87T GLY* 2.7 33.6 + - - -
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Residues in contact with VAL 84 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T GLU* 2.9 32.2 + - - +
6T ARG 3.4 19.1 - - - +
7T THR* 3.5 16.6 + - - +
83T VAL* 1.3 74.1 - - - +
85T LYS* 1.3 61.5 + - - +
87T GLY* 4.0 0.2 - - - -
88T ARG* 3.0 30.1 + - - +
120T SER 3.4 20.9 - - - +
121T ASP 3.9 3.8 - - - +
122T SER* 3.6 25.6 - - - +
123T VAL* 3.9 14.8 - - + +
126T ALA* 4.0 9.6 - - + -
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Residues in contact with LYS 85 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82T ASN* 3.0 34.0 + - - +
84T VAL* 1.3 82.6 - - - +
86T THR* 1.3 67.0 + - + +
88T ARG* 3.5 6.4 + - - +
89T VAL* 3.2 28.7 + - + +
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Residues in contact with THR 86 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96R PRO 5.8 0.9 - - - +
97R ALA* 5.0 19.7 - - + +
110R ILE* 5.8 3.8 - - + -
31T LYS* 4.9 12.6 - - - +
33T PHE* 2.9 33.8 - - + -
81T LEU 4.8 2.2 - - - +
82T ASN* 3.1 26.2 + - + +
85T LYS* 1.3 77.3 - - + +
87T GLY* 1.3 67.6 + - - +
89T VAL* 2.9 12.7 + - + +
90T MET* 2.9 28.5 + - - +
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Residues in contact with GLY 87 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9T ILE* 5.1 5.2 - - - -
28T PHE* 4.2 13.9 - - - -
33T PHE* 5.0 1.1 - - - -
83T VAL 2.7 26.1 + - - -
84T VAL 4.0 0.2 - - - -
86T THR* 1.3 74.1 + - - +
88T ARG* 1.3 55.2 + - - +
90T MET* 3.1 15.9 + - - +
91T LEU* 2.9 36.7 + - - +
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Residues in contact with ARG 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84T VAL* 3.0 19.1 + - - +
85T LYS* 3.9 5.4 - - - +
87T GLY* 1.3 74.9 - - - +
89T VAL* 1.3 58.5 + - + +
91T LEU* 3.0 11.4 + - + +
92T GLY* 2.8 34.1 + - - +
94T THR* 3.8 20.9 + - - +
105T ARG* 5.8 3.8 - - - +
118T HIS* 5.7 0.8 + - - -
119T GLY* 3.4 23.3 + - - +
120T SER 2.9 25.1 + - - +
121T ASP* 3.6 31.9 + - - +
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Residues in contact with VAL 89 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99R SER 5.3 3.1 - - - +
100R LYS* 5.4 6.3 - - + -
101R PRO* 3.5 27.4 - - + +
85T LYS* 3.2 23.3 + - + +
86T THR* 2.9 15.1 + - + +
88T ARG* 1.3 77.9 - - + +
90T MET* 1.3 62.0 + - + +
92T GLY* 3.4 5.1 + - - +
103T THR* 3.4 19.2 - - - +
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Residues in contact with MET 90 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101R PRO* 4.1 15.7 - - + -
106R GLY 5.2 3.8 - - - +
107R ASP 6.0 0.2 - - - +
27T ARG* 3.7 36.7 + - + +
28T PHE* 4.0 26.7 - - + +
31T LYS* 4.1 19.7 - - + +
33T PHE* 3.5 30.1 - - - -
86T THR* 2.9 17.6 + - - +
87T GLY* 3.1 7.2 + - - +
89T VAL* 1.3 77.0 - - + +
91T LEU* 1.3 62.5 + - + +
103T THR* 3.3 5.9 - - - -
104T ILE* 3.0 30.8 + - + +
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Residues in contact with LEU 91 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9T ILE* 4.3 2.7 - - + -
28T PHE* 3.6 26.7 - - + -
87T GLY 2.9 22.9 + - - +
88T ARG* 3.0 14.8 + - + +
90T MET* 1.3 77.6 - - - +
92T GLY* 1.3 58.1 + - - +
103T THR* 4.1 0.4 - - - -
104T ILE* 4.0 9.6 - - + -
105T ARG* 3.0 52.0 + - - +
117T ILE* 3.8 30.1 - - + -
118T HIS* 3.7 7.4 - - - +
119T GLY* 3.3 38.8 - - - +
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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