Contacts of the helix formed by residues 21 - 31 (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 21 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25O ILE* 4.0 14.4 - - + -
29O GLU* 3.4 20.6 + - - +
35O LEU* 5.1 7.4 - - + -
38O MET* 4.6 5.4 - - + -
11T ILE* 3.9 17.4 - - + +
15T GLY 4.2 0.2 + - - -
16T VAL* 4.1 28.3 - - + -
20T LEU* 1.3 78.4 - - - +
22T GLY* 1.3 64.8 + - - +
24T ILE* 3.4 1.2 + - - +
25T ILE* 3.0 49.0 + - + +
74T VAL* 4.1 24.5 - - + -
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Residues in contact with GLY 22 (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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22O GLY* 3.3 30.6 - - - -
25O ILE* 4.1 5.1 - - - +
26O LYS* 3.9 11.0 - - - -
29O GLU* 3.0 16.0 + - - -
21T VAL* 1.3 75.7 - - - +
23T GLU* 1.3 57.4 + - - +
25T ILE* 4.7 0.7 - - - -
26T LYS* 2.9 32.6 + - - +
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Residues in contact with GLU 23 (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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26O LYS* 3.0 42.6 + - - +
29O GLU* 4.8 0.6 + - - -
19T GLY 5.7 0.7 - - - +
20T LEU* 3.5 18.9 + - + +
21T VAL 3.3 0.6 - - - -
22T GLY* 1.3 76.7 - - - +
24T ILE* 1.3 63.3 + - + +
26T LYS* 3.4 17.9 - - - +
27T ARG* 3.1 54.5 + - - +
108T PHE* 4.0 28.6 - - + -
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Residues in contact with ILE 24 (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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11T ILE* 3.9 39.3 - - + -
20T LEU* 3.0 32.8 + - + +
21T VAL 3.8 2.5 - - - +
23T GLU* 1.3 76.0 - - + +
25T ILE* 1.3 64.6 + - - +
27T ARG* 3.3 10.1 + - - +
28T PHE* 3.2 28.5 + - + -
76T MET* 4.8 4.7 - - + -
104T ILE* 3.9 32.5 - - + -
108T PHE* 5.4 2.7 - - + -
116T ILE* 4.7 8.3 - - + +
117T ILE* 3.6 32.1 - - + -
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Residues in contact with ILE 25 (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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21O VAL* 4.0 18.6 - - + -
22O GLY* 4.1 2.9 - - - +
25O ILE* 3.5 30.5 - - + -
11T ILE* 4.7 1.1 - - + -
21T VAL* 3.0 29.7 + - + +
22T GLY 4.0 2.5 - - - +
24T ILE* 1.3 74.1 - - - +
26T LYS* 1.3 66.2 + - - +
28T PHE* 2.9 16.3 + - - +
29T GLU* 3.0 24.1 + - - +
35T LEU* 5.3 3.4 - - + -
38T MET* 3.9 20.0 - - - -
74T VAL* 5.2 0.4 - - + -
76T MET* 4.0 21.3 - - + -
78T TRP* 4.0 20.6 - - + -
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Residues in contact with LYS 26 (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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22O GLY* 3.9 4.7 - - - -
23O GLU* 3.0 48.0 + - + +
26O LYS* 5.0 4.7 - - + +
22T GLY 2.9 19.8 + - - +
23T GLU* 3.4 24.7 - - - +
25T ILE* 1.3 75.7 - - - +
27T ARG* 1.3 58.1 + - + +
29T GLU* 3.0 16.8 + - + +
30T GLN* 2.8 50.0 + - + +
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Residues in contact with ARG 27 (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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107R ASP 4.5 0.5 - - - +
23T GLU* 3.1 28.9 + - - +
24T ILE* 3.5 9.0 - - - +
25T ILE 3.1 0.4 + - - -
26T LYS* 1.3 80.0 - - + +
28T PHE* 1.3 62.4 + - + +
30T GLN* 3.2 33.8 - - - +
31T LYS* 3.3 12.1 + - - +
90T MET* 3.7 15.5 + - + +
102T GLY 3.1 18.2 + - - -
104T ILE* 3.5 34.0 - - + +
107T ASP* 2.7 30.7 + - - +
108T PHE* 3.3 28.0 - - - -
30U GLN* 5.6 0.8 + - - -
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Residues in contact with PHE 28 (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* 5.5 1.6 - - + -
9T ILE* 3.9 28.9 - - + -
24T ILE* 3.2 29.4 - - + -
25T ILE* 2.9 7.6 + - - +
27T ARG* 1.3 77.6 - - - +
29T GLU* 1.3 61.6 + - - +
31T LYS* 3.4 7.7 + - - +
33T PHE* 3.3 41.4 + + - +
76T MET* 6.0 0.4 - - + -
78T TRP* 3.7 44.4 - + + -
83T VAL* 5.5 0.9 - - + -
87T GLY* 4.2 11.2 - - - -
90T MET* 4.0 23.3 - - + -
91T LEU* 3.6 24.7 - - + -
104T ILE* 3.8 24.0 - - + -
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Residues in contact with GLU 29 (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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16O VAL* 4.2 3.1 - - - +
19O GLY* 3.3 37.0 - - - +
20O LEU* 4.4 0.2 - - - -
21O VAL* 3.4 29.7 + - - +
22O GLY* 3.0 26.4 + - - -
23O GLU 4.9 0.2 + - - -
18R ARG* 4.8 1.4 + - - -
25T ILE* 3.0 16.5 + - + +
26T LYS* 3.0 11.6 + - - +
28T PHE* 1.3 76.1 - - - +
30T GLN* 1.3 62.8 + - - +
31T LYS 3.1 0.2 - - - -
32T GLY* 3.1 16.1 + - - -
33T PHE 4.3 8.0 + - - +
35T LEU* 6.1 0.3 - - - +
78T TRP* 3.9 16.4 - - + -
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Residues in contact with GLN 30 (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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18R ARG* 3.3 10.5 + - - +
20R LEU* 5.2 3.2 - - + +
23R GLU* 6.2 0.2 - - - +
27R ARG* 5.5 0.5 + - - -
107R ASP* 3.6 16.1 - - - +
108R PHE* 3.3 48.9 - - + -
26T LYS* 2.8 32.8 + - + +
27T ARG* 3.2 34.5 - - - +
29T GLU* 1.3 75.7 - - - +
31T LYS* 1.3 59.4 + - - +
32T GLY 3.3 0.2 - - - -
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Residues in contact with LYS 31 (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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18R ARG* 3.7 1.7 + - - -
96R PRO 4.3 10.9 + - - -
99R SER 5.3 1.4 + - - -
105R ARG 3.6 4.2 + - - -
106R GLY* 3.0 30.9 + - - +
107R ASP* 3.3 11.4 + - - +
108R PHE 3.3 13.0 - - - +
109R CYS* 2.6 28.2 + - - +
110R ILE* 3.3 21.2 - - + +
27T ARG 3.3 12.8 + - - +
28T PHE 3.5 11.0 - - - +
29T GLU 3.1 0.8 - - - -
30T GLN* 1.3 77.7 - - - +
32T GLY* 1.3 58.1 + - - +
33T PHE* 3.3 36.1 - - + -
86T THR* 4.9 11.6 - - - +
90T MET* 4.1 14.8 - - + -
150T VAL* 4.7 0.2 - - - +
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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