Contacts of the strand formed by residues 7 - 11 (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 THR 7 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6T ARG* 1.3 77.7 - - - +
8T PHE* 1.3 64.5 + - - +
9T ILE* 3.8 27.6 - - + -
28T PHE* 5.5 1.3 - - + -
77T VAL* 3.1 8.1 - - - +
78T TRP* 2.8 34.1 + - + +
83T VAL* 3.9 25.8 - - + +
84T VAL* 3.5 22.7 - - - +
87T GLY* 5.5 0.2 - - - -
120T SER* 3.4 23.9 + - - -
126T ALA* 4.1 5.8 - - - -
130T ILE* 4.4 5.4 - - - -
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Residues in contact with PHE 8 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7T THR* 1.3 76.4 + - - +
9T ILE* 1.3 61.0 + - - +
10T ALA* 3.5 29.8 - - + -
51T HIS* 4.3 2.7 - - - -
75T ALA* 3.7 9.4 - - + -
76T MET 3.4 14.1 - - - -
77T VAL* 4.7 0.9 - - + -
118T HIS* 3.6 11.8 - + - +
119T GLY* 3.5 4.0 - - - -
120T SER* 3.2 34.9 + - - +
126T ALA* 4.5 0.2 - - - +
129T GLU* 3.2 33.4 - - + +
130T ILE* 4.1 12.5 - - + +
133T TRP* 3.5 47.1 - + + -
134T PHE* 3.4 31.0 - + - -
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Residues in contact with ILE 9 (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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7T THR* 3.8 20.4 - - + -
8T PHE* 1.3 79.7 - - - +
10T ALA* 1.3 62.6 + - - +
28T PHE* 3.9 27.6 - - + -
75T ALA 3.7 0.2 - - - -
76T MET* 2.8 56.8 + - + +
78T TRP* 3.7 27.6 - - + -
87T GLY* 5.1 5.2 - - - -
91T LEU* 4.3 7.2 - - + -
117T ILE* 3.7 25.1 - - + -
118T HIS 3.3 2.5 - - - +
119T GLY* 3.7 17.5 - - - -
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Residues in contact with ALA 10 (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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8T PHE* 3.5 29.5 - - + -
9T ILE* 1.3 74.3 - - - +
11T ILE* 1.3 64.8 + - - +
12T LYS* 3.5 1.4 + - - +
68T MET* 5.7 7.6 - - + -
73T VAL* 5.4 5.6 - - + -
74T VAL 3.2 7.4 - - - +
75T ALA* 4.6 2.5 - - + -
117T ILE* 3.3 4.4 - - - +
118T HIS* 2.8 50.2 + - + +
133T TRP* 5.4 5.8 - - + -
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Residues in contact with ILE 11 (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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10T ALA* 1.3 72.0 - - - +
12T LYS* 1.3 60.2 + - - +
15T GLY 3.9 22.7 - - - +
16T VAL* 3.9 8.1 - - + +
21T VAL* 3.9 29.4 - - + +
24T ILE* 3.9 42.6 - - + -
25T ILE* 4.7 1.8 - - + -
73T VAL* 3.1 12.2 - - - +
74T VAL* 2.7 40.6 + - + +
76T MET* 3.8 26.9 - - + -
116T ILE 3.8 11.4 - - - +
117T ILE* 4.4 2.9 - - + -
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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