Contacts of the strand formed by residues 73 - 79 (chain O) 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 73 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10O ALA* 5.4 4.0 - - + -
11O ILE 3.2 16.4 - - - +
12O LYS* 4.1 2.2 - - - -
13O PRO* 3.7 26.2 - - + -
16O VAL* 4.2 0.4 - - - -
39O LYS 4.0 0.3 - - - +
40O PHE* 3.3 7.2 - - - -
41O LEU* 2.7 44.9 + - + +
43O ALA 4.6 5.4 - - - +
68O MET* 4.2 21.1 - - + +
71O GLY 4.1 3.4 - - - +
72O PRO* 1.3 77.5 - - - +
74O VAL* 1.3 68.1 + - - +
75O ALA* 4.7 0.7 - - + +
133O TRP* 3.8 32.1 - - + -
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Residues in contact with VAL 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O ILE 3.8 1.2 - - - +
10O ALA* 3.2 3.9 - - - -
11O ILE* 2.8 48.9 + - + +
16O VAL* 3.9 13.9 - - + -
21O VAL* 4.1 17.9 - - + -
38O MET* 4.0 17.9 - - + -
39O LYS 3.5 4.0 - - - +
40O PHE* 3.5 26.5 - - + -
73O VAL* 1.3 71.4 - - - +
75O ALA* 1.3 60.9 + - - +
76O MET* 4.0 12.6 - - + +
35T LEU* 5.0 0.4 - - + -
38T MET* 3.6 26.9 - - + -
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Residues in contact with ALA 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O PHE* 3.7 17.5 - - + -
9O ILE 3.8 2.9 - - - -
10O ALA* 4.4 2.9 - - + +
38O MET* 3.2 2.1 - - - -
39O LYS* 2.9 43.5 + - + -
41O LEU* 4.2 3.3 - - + +
73O VAL* 3.9 1.6 - - + -
74O VAL* 1.3 73.2 - - - +
76O MET* 1.3 62.0 + - - +
133O TRP* 3.7 23.6 - - + -
134O PHE* 3.2 19.1 - - + -
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Residues in contact with MET 76 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8O PHE* 3.4 11.7 - - - -
9O ILE* 2.8 62.8 + - + +
11O ILE* 3.8 28.7 - - + -
24O ILE* 4.8 4.3 - - + -
25O ILE* 4.0 23.8 - - + -
28O PHE* 6.0 0.7 - - + -
35O LEU* 4.3 2.2 - - + -
37O ALA 3.0 10.1 - - - +
38O MET* 3.6 24.7 - - + +
74O VAL* 4.0 7.4 - - + +
75O ALA* 1.3 80.1 - - - +
77O VAL* 1.3 64.7 + - - +
78O TRP* 3.6 26.9 - - - +
134O PHE* 3.5 2.2 - - - -
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Residues in contact with VAL 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O ARG* 3.5 30.5 - - + -
7O THR 3.1 8.7 - - - +
8O PHE* 4.7 0.7 - - + -
35O LEU* 3.7 4.9 - - - +
36O VAL* 2.7 50.3 + - + -
37O ALA* 2.8 12.7 + - + +
76O MET* 1.3 78.7 - - - +
78O TRP* 1.3 59.5 + - - +
130O ILE* 3.9 24.9 - - + -
134O PHE* 3.5 28.9 - - + -
139O LEU* 4.1 10.3 - - + -
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Residues in contact with TRP 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O ARG* 3.2 2.7 - - - -
7O THR* 2.8 40.9 + - + -
9O ILE* 3.7 28.0 - - + +
25O ILE* 4.0 17.9 - - + -
28O PHE* 3.7 37.9 - + + -
29O GLU* 3.8 22.9 - - + -
33O PHE* 3.4 28.0 - - + -
34O ARG 3.2 22.4 - - - -
35O LEU* 3.3 40.6 - - + -
36O VAL* 4.4 1.3 - - - -
76O MET* 3.6 27.6 - - + +
77O VAL* 1.3 75.7 - - - +
79O GLU* 1.3 59.3 + - - +
83O VAL* 3.4 20.2 - - + +
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Residues in contact with GLU 79 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4O LEU* 4.3 18.2 - - + +
5O GLU 3.6 17.8 - - - +
6O ARG* 4.2 11.0 - - + +
32O GLY 4.9 0.2 - - - +
33O PHE* 3.5 7.8 - - - -
34O ARG* 2.8 66.8 + - + +
36O VAL* 3.5 20.5 - - + +
78O TRP* 1.3 73.9 - - - +
80O GLY* 1.3 63.9 + - - +
83O VAL* 3.7 2.5 - - - -
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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