Contacts of the helix formed by residues 21 - 31 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25N ILE* 4.0 13.9 - - + -
29N GLU* 3.4 22.2 + - - +
35N LEU* 5.2 6.7 - - + -
38N MET* 4.6 4.9 - - + -
11U ILE* 3.9 17.0 - - + -
15U GLY 4.1 0.6 + - - +
16U VAL* 4.1 27.6 - - + -
20U LEU* 1.3 78.1 - - - +
22U GLY* 1.3 65.0 + - - +
24U ILE* 3.7 1.2 - - - +
25U ILE* 2.9 48.9 + - + +
74U VAL* 4.2 24.2 - - + -
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Residues in contact with GLY 22 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N GLY* 3.4 29.9 - - - -
25N ILE* 4.1 4.7 - - - +
26N LYS* 3.9 11.2 - - - -
29N GLU* 3.0 16.2 + - - -
21U VAL* 1.3 76.9 - - - +
23U GLU* 1.3 57.0 + - - +
25U ILE* 4.7 0.9 - - - -
26U LYS* 2.8 34.4 + - - +
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Residues in contact with GLU 23 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N LYS* 2.9 42.7 + - - +
19U GLY 5.6 1.3 + - - +
20U LEU* 3.5 19.3 + - + +
21U VAL 3.3 0.4 - - - -
22U GLY* 1.3 75.8 - - - +
24U ILE* 1.3 63.3 + - - +
26U LYS* 3.5 16.4 - - - +
27U ARG* 3.1 52.7 + - - +
108U PHE* 4.0 29.5 - - + -
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Residues in contact with ILE 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11U ILE* 3.9 38.6 - - + -
20U LEU* 3.0 30.8 + - + +
21U VAL 3.7 2.7 - - - +
23U GLU* 1.3 74.8 - - + +
25U ILE* 1.3 68.3 + - - +
27U ARG* 3.2 11.2 + - - +
28U PHE* 3.3 24.9 + - + -
76U MET* 4.8 4.7 - - + -
104U ILE* 3.8 36.8 - - + -
108U PHE* 5.4 2.9 - - + -
116U ILE* 4.7 8.7 - - + +
117U ILE* 3.6 28.0 - - + -
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Residues in contact with ILE 25 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N VAL* 4.1 14.8 - - + -
22N GLY* 4.2 3.6 - - - +
25N ILE* 3.6 30.1 - - + -
11U ILE* 4.7 2.7 - - + -
21U VAL* 2.9 31.7 + - + +
22U GLY 4.0 2.7 - - - +
24U ILE* 1.3 74.6 - - - +
26U LYS* 1.3 65.7 + - - +
28U PHE* 3.0 15.4 + - - +
29U GLU* 3.0 27.0 + - - +
35U LEU* 5.4 2.7 - - + -
38U MET* 3.7 24.7 - - - -
74U VAL* 5.1 0.7 - - + -
76U MET* 4.0 16.6 - - - -
78U TRP* 4.0 20.2 - - + -
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Residues in contact with LYS 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N GLY* 3.9 5.8 - - - -
23N GLU* 3.0 47.8 + - + +
26N LYS* 5.0 5.8 - - + +
22U GLY 2.8 22.9 + - - +
23U GLU* 3.5 24.7 - - - +
25U ILE* 1.3 71.8 - - - +
27U ARG* 1.3 60.3 + - + +
29U GLU* 3.1 15.6 + - - +
30U GLN* 2.8 48.3 + - + +
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Residues in contact with ARG 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30R GLN* 5.7 0.8 + - - -
107T ASP 4.5 0.7 - - - +
23U GLU* 3.1 30.0 + - - +
24U ILE* 3.5 7.9 - - - +
25U ILE 3.2 0.2 - - - -
26U LYS* 1.3 77.2 - - + +
28U PHE* 1.3 63.8 + - + +
30U GLN* 3.1 35.1 - - - +
31U LYS* 3.2 11.6 + - - +
90U MET* 3.9 14.3 - - + +
102U GLY 3.1 18.0 + - - -
103U THR 3.5 14.1 - - - -
104U ILE* 3.5 18.4 - - + +
107U ASP* 2.9 29.7 + - - -
108U PHE* 3.2 30.3 - - - -
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Residues in contact with PHE 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U ILE* 3.9 28.3 - - + -
24U ILE* 3.3 28.3 - - + -
25U ILE* 3.0 8.5 + - - +
27U ARG* 1.3 76.2 - - - +
29U GLU* 1.3 64.6 + - - +
31U LYS* 3.2 11.1 + - - +
33U PHE* 3.3 38.2 + + - +
76U MET* 6.0 0.2 - - + -
78U TRP* 3.7 40.4 - + + -
83U VAL* 5.4 2.0 - - + -
87U GLY* 4.2 15.0 - - - -
90U MET* 4.0 19.3 - - + -
91U LEU* 3.6 24.9 - - + -
104U ILE* 3.8 24.5 - - + -
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Residues in contact with GLU 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N VAL* 4.2 3.1 - - - +
19N GLY* 3.2 39.0 - - - +
21N VAL* 3.4 29.5 + - - +
22N GLY* 3.0 27.0 + - - -
23N GLU 4.9 0.2 + - - -
18T ARG* 4.8 1.4 + - - -
25U ILE* 3.0 15.7 + - + +
26U LYS* 3.4 11.6 - - - +
28U PHE* 1.3 76.1 - - - +
30U GLN* 1.3 62.0 + - - +
31U LYS 3.0 1.6 + - - -
32U GLY* 3.0 15.1 + - - -
33U PHE 4.3 8.4 + - - +
78U TRP* 3.8 17.3 - - + -
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Residues in contact with GLN 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T ARG* 3.4 6.8 + - - +
20T LEU* 5.4 2.8 - - + +
27T ARG* 5.6 0.5 + - - -
107T ASP* 3.5 17.1 - - - +
108T PHE* 3.2 54.1 - - + +
26U LYS* 2.8 37.5 + - + +
27U ARG* 3.1 41.5 + - - +
29U GLU* 1.3 73.0 - - - +
31U LYS* 1.3 57.8 + - - +
32U GLY 3.3 0.2 - - - -
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Residues in contact with LYS 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T ARG* 4.0 1.9 + - - -
96T PRO 4.1 12.1 + - - -
99T SER 5.1 1.6 + - - -
105T ARG 3.7 2.0 + - - -
106T GLY* 3.1 34.6 + - - +
107T ASP 3.3 11.4 - - - +
108T PHE 3.5 10.8 - - - +
109T CYS* 2.7 26.8 + - - +
110T ILE* 3.2 22.6 - - + +
27U ARG 3.2 11.9 + - - +
28U PHE 3.3 12.1 - - - +
29U GLU 3.0 0.6 + - - -
30U GLN* 1.3 76.7 - - - +
32U GLY* 1.3 58.0 + - - +
33U PHE* 3.4 34.1 - - + -
86U THR* 4.9 12.1 - - - +
90U MET* 3.9 17.7 - - + +
150U VAL* 4.8 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