Contacts of the strand formed by residues 34 - 41 (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 ARG 34 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4O LEU* 6.3 0.2 - - - -
32O GLY 5.1 2.2 - - - +
33O PHE* 1.3 73.7 - - - +
35O LEU* 1.3 67.1 + - - +
36O VAL* 3.3 8.4 + - - +
78O TRP* 3.2 6.7 - - - -
79O GLU* 2.8 78.0 + - + +
80O GLY* 5.6 0.2 - - - -
140O VAL 3.4 11.9 + - - -
141O ASP* 3.9 3.8 + - - +
142O TYR* 2.7 90.0 + - - +
143O LYS* 5.8 0.2 - - - +
144O SER* 4.0 25.0 - - - +
147O HIS* 5.9 5.4 - - - -
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Residues in contact with LEU 35 (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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25O ILE* 5.3 1.6 - - + -
29O GLU* 6.1 0.7 - - - +
34O ARG* 1.3 70.7 - - - +
36O VAL* 1.3 61.5 + - - +
37O ALA 3.2 33.0 - - - +
38O MET* 3.8 32.5 - - + -
76O MET* 4.3 9.2 - - + -
77O VAL 3.7 4.9 - - - +
78O TRP* 3.3 33.8 - - + -
142O TYR* 2.6 37.4 + - - +
16T VAL* 5.8 2.0 - - + -
21T VAL* 5.1 11.2 - - + -
40T PHE* 3.2 26.3 - - + -
74T VAL* 5.0 3.1 - - + -
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Residues in contact with VAL 36 (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* 4.5 8.5 - - + +
34O ARG* 3.8 13.7 - - - +
35O LEU* 1.3 73.3 - - - +
37O ALA* 1.3 57.1 + - - +
77O VAL* 2.7 27.5 + - + +
79O GLU* 3.5 35.9 - - + +
139O LEU* 3.6 33.9 - - + -
140O VAL* 2.8 44.5 + - - +
141O ASP* 4.6 5.4 - - - +
40T PHE* 3.6 9.7 - - - -
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Residues in contact with ALA 37 (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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35O LEU* 3.2 7.2 - - - +
36O VAL* 1.3 82.8 - - - +
38O MET* 1.3 60.8 + - - +
76O MET* 3.0 5.2 - - - -
77O VAL* 2.8 28.9 + - + +
134O PHE* 3.7 16.2 - - + -
138O GLU* 3.4 13.2 - - + +
139O LEU* 3.4 31.2 - - + -
40T PHE* 3.9 6.1 - - - -
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Residues in contact with MET 38 (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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25O ILE* 3.9 17.5 - - + -
35O LEU* 3.8 25.6 - - + -
37O ALA* 1.3 78.1 - - - +
39O LYS* 1.3 65.7 + - - +
74O VAL* 4.0 8.3 - - + -
75O ALA 3.2 5.2 - - - +
76O MET* 3.6 23.8 - - + +
134O PHE* 3.9 2.6 - - - -
21T VAL* 4.6 7.0 - - + -
38T MET* 3.9 27.1 - - + -
39T LYS* 3.3 2.9 - - - +
40T PHE* 2.8 44.6 + - + +
74T VAL* 3.6 34.1 - - + -
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Residues in contact with LYS 39 (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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38O MET* 1.3 78.3 - - - +
40O PHE* 1.3 61.5 + - - +
41O LEU* 3.6 32.0 - - + +
73O VAL 4.0 0.2 - - - +
74O VAL* 3.5 4.7 - - - +
75O ALA* 2.9 37.3 + - + +
133O TRP* 3.2 22.8 + - + +
134O PHE* 3.8 17.5 - - + +
135O LYS* 5.0 6.1 - - - +
138O GLU* 3.0 39.8 + - - -
38T MET 3.3 8.7 - - - +
39T LYS* 5.0 4.5 - - + -
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Residues in contact with PHE 40 (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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16O VAL* 3.9 15.0 - - + -
39O LYS* 1.3 74.0 - - - +
41O LEU* 1.3 64.4 + - - +
72O PRO* 3.4 34.5 - - + -
73O VAL 3.3 13.0 - - - -
74O VAL* 3.5 22.4 - - + +
35T LEU* 3.2 42.6 - - + -
36T VAL 3.5 19.7 - - - -
37T ALA* 3.9 7.4 - - - -
38T MET* 2.8 31.7 + - + +
138T GLU* 4.4 8.3 - - - +
140T VAL* 3.9 12.0 - - + +
142T TYR* 3.6 12.8 - + - -
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Residues in contact with LEU 41 (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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39O LYS* 3.6 43.5 - - + +
40O PHE* 1.3 77.2 - - - +
42O ARG* 1.3 60.4 + - - +
43O ALA* 4.4 11.4 - - - +
47O HIS* 5.2 6.5 - - + +
72O PRO* 3.9 5.2 - - - -
73O VAL* 2.7 61.0 + - + +
75O ALA* 4.2 3.8 - - + -
133O TRP* 4.2 22.4 - - + +
140T 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