Contacts of the helix formed by residues 123 - 133 (chain R) 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 123 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5R GLU* 3.5 42.2 - - + +
6R ARG 5.2 1.8 - - - +
84R VAL* 4.0 6.5 - - + +
122R SER* 1.3 75.2 - - - +
124R LYS* 1.3 63.5 + - + +
126R ALA* 3.2 7.9 - - - +
127R GLU* 3.0 35.7 + - + +
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Residues in contact with LYS 124 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122R SER* 3.2 8.4 + - - +
123R VAL* 1.3 87.3 - - + +
125R SER* 1.3 61.6 + - - +
127R GLU* 3.7 4.6 + - - +
128R LYS* 3.3 44.2 + - - +
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Residues in contact with SER 125 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121R ASP* 3.0 33.3 + - - -
122R SER* 2.8 25.5 + - - -
124R LYS* 1.3 75.2 - - - +
126R ALA* 1.3 60.8 + - - +
128R LYS* 3.2 12.1 + - - +
129R GLU* 2.8 43.8 + - - +
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Residues in contact with ALA 126 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6R ARG 3.8 22.2 - - - +
7R THR* 4.2 4.5 - - - -
84R VAL* 4.1 2.9 - - + -
120R SER* 3.4 24.4 - - - +
122R SER 2.7 17.9 + - - +
123R VAL* 3.2 11.2 - - - +
125R SER* 1.3 77.0 - - - +
127R GLU* 1.3 53.7 + - + +
129R GLU* 3.1 1.7 + - - +
130R ILE* 2.8 42.8 + - + +
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Residues in contact with GLU 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6R ARG* 2.8 49.6 + - - +
123R VAL* 3.0 18.5 + - + +
124R LYS* 4.1 4.7 - - - +
126R ALA* 1.3 77.8 - - - +
128R LYS* 1.3 61.8 + - - +
130R ILE* 3.7 10.6 - - - +
131R SER* 2.9 30.5 + - - -
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Residues in contact with LYS 128 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124R LYS* 3.3 32.8 + - - +
125R SER* 3.2 14.7 + - - +
127R GLU* 1.3 77.9 - - - +
129R GLU* 1.3 60.1 + - + +
131R SER* 3.1 8.4 + - - -
132R LEU* 2.9 28.9 + - - +
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Residues in contact with GLU 129 (chain R).
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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8R PHE* 3.1 17.3 - - + -
51R HIS* 3.5 23.7 + - + +
118R HIS* 2.9 36.6 + - - -
120R SER* 2.6 31.6 + - - -
121R ASP* 4.6 3.3 - - - +
125R SER* 2.8 26.3 + - - +
126R ALA 3.6 2.9 - - - +
128R LYS* 1.3 72.2 - - + +
130R ILE* 1.3 59.8 + - - +
132R LEU* 4.3 6.7 - - - -
133R TRP* 2.8 39.1 + - + +
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Residues in contact with ILE 130 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6R ARG* 3.5 37.9 - - + +
7R THR 4.6 3.1 - - - -
8R PHE* 4.2 15.5 - - + +
77R VAL* 4.0 18.6 - - + -
126R ALA* 2.8 39.8 + - + +
127R GLU* 3.7 19.7 - - - +
129R GLU* 1.3 71.5 - - - +
131R SER* 1.3 54.3 + - - +
134R PHE* 2.7 40.5 + - + +
139R LEU* 3.8 30.1 - - + -
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Residues in contact with SER 131 (chain R).
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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127R GLU* 2.9 16.4 + - - +
128R LYS* 3.4 9.1 - - - -
130R ILE* 1.3 77.8 - - - +
132R LEU* 1.3 59.8 + - - +
134R PHE 3.0 19.2 - - - +
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Residues in contact with LEU 132 (chain R).
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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47R HIS* 2.7 60.9 + - + +
50R GLN* 4.0 31.9 - - + +
51R HIS* 3.9 24.5 - - + +
128R LYS 2.9 15.8 + - - +
129R GLU* 3.7 6.5 - - - +
131R SER* 1.3 78.4 - - - +
133R TRP* 1.3 77.6 + - + +
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Residues in contact with TRP 133 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8R PHE* 3.5 35.3 - + + -
39R LYS* 3.2 27.3 + - + +
41R LEU* 4.1 15.3 - - + +
43R ALA* 3.4 30.5 - - + -
47R HIS* 3.2 26.3 - + - -
48R LEU* 4.1 15.0 - - + -
51R HIS* 3.0 36.4 - + + -
68R MET* 5.3 7.6 - - + -
73R VAL* 3.9 23.1 - - + -
75R ALA* 3.9 16.2 - - + -
129R GLU 2.8 31.7 + - - +
132R LEU* 1.3 88.2 - - + +
134R PHE* 1.3 61.6 + - + +
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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