Contacts of the helix formed by residues 21 - 31 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11N ILE* 3.9 17.3 - - + -
15N GLY 4.1 0.6 + - - +
16N VAL* 4.1 28.0 - - + -
20N LEU* 1.3 78.3 - - - +
22N GLY* 1.3 65.0 + - - +
24N ILE* 3.8 1.2 - - - +
25N ILE* 2.9 48.3 + - + +
74N VAL* 4.3 23.8 - - + -
25U ILE* 4.1 15.0 - - + -
29U GLU* 3.4 21.1 + - - +
35U LEU* 5.2 7.0 - - + -
38U MET* 4.5 4.9 - - + -
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Residues in contact with GLY 22 (chain N).
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* 1.3 76.8 - - - +
23N GLU* 1.3 57.9 + - - +
25N ILE* 4.7 0.4 - - - -
26N LYS* 2.8 34.3 + - - +
22U GLY* 3.4 29.6 - - - -
25U ILE* 4.2 5.1 - - - +
26U LYS* 3.9 10.8 - - - -
29U GLU* 3.0 15.4 + - - -
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Residues in contact with GLU 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N GLY 5.6 1.3 - - - +
20N LEU* 3.5 19.1 + - + +
21N VAL 3.3 0.4 - - - -
22N GLY* 1.3 75.7 - - - +
24N ILE* 1.3 61.4 + - - +
26N LYS* 3.5 16.0 - - - +
27N ARG* 3.0 53.2 + - - +
108N PHE* 3.9 29.3 - - + -
30O GLN* 6.2 0.4 - - - +
26U LYS* 3.0 41.7 + - - +
29U GLU* 4.9 0.4 + - - -
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Residues in contact with ILE 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N ILE* 3.9 38.1 - - + -
20N LEU* 3.0 32.1 + - + +
21N VAL 3.8 2.7 - - - +
23N GLU* 1.3 74.6 - - + +
25N ILE* 1.3 66.7 + - - +
27N ARG* 3.3 11.4 + - - +
28N PHE* 3.3 25.1 + - + -
76N MET* 4.8 4.5 - - + -
104N ILE* 3.8 38.1 - - + -
108N PHE* 5.3 2.9 - - + -
116N ILE* 4.7 8.5 - - + +
117N ILE* 3.6 28.9 - - + -
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Residues in contact with ILE 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N ILE* 4.7 2.7 - - + -
21N VAL* 2.9 32.4 + - + +
22N GLY 4.0 2.0 - - - +
24N ILE* 1.3 75.2 - - - +
26N LYS* 1.3 64.2 + - - +
28N PHE* 3.0 16.2 + - - +
29N GLU* 3.0 26.6 + - - +
35N LEU* 5.4 2.5 - - + -
38N MET* 3.7 24.7 - - - -
74N VAL* 5.1 0.2 - - + -
76N MET* 4.1 16.8 - - - -
78N TRP* 4.0 20.6 - - + -
21U VAL* 4.0 14.6 - - + -
22U GLY* 4.1 3.8 - - - +
25U ILE* 3.6 30.3 - - + -
38U MET* 4.9 0.4 - - + -
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Residues in contact with LYS 26 (chain N).
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 2.8 22.9 + - - +
23N GLU* 3.5 24.2 - - - +
25N ILE* 1.3 71.1 - - - +
27N ARG* 1.3 59.4 + - + +
29N GLU* 3.1 15.5 + - - +
30N GLN* 2.8 49.1 + - + +
22U GLY* 3.9 6.4 - - - -
23U GLU* 2.9 48.1 + - + +
26U LYS* 5.0 5.4 - - + +
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Residues in contact with ARG 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107L ASP 4.5 0.7 - - - +
23N GLU* 3.0 30.7 + - - +
24N ILE* 3.5 7.4 - - - +
25N ILE 3.2 0.2 - - - -
26N LYS* 1.3 77.2 - - + +
28N PHE* 1.3 63.6 + - + +
30N GLN* 3.1 34.9 + - - +
31N LYS* 3.2 11.6 + - - +
90N MET* 3.9 15.4 - - + +
102N GLY 3.1 17.8 + - - -
103N THR* 3.5 14.1 - - - +
104N ILE* 3.5 18.4 - - + +
107N ASP* 2.8 31.3 + - - -
108N PHE* 3.2 30.9 - - - -
30O GLN* 5.5 1.0 + - - -
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Residues in contact with PHE 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N ILE* 3.9 28.9 - - + -
24N ILE* 3.3 28.5 - - + -
25N ILE* 3.0 8.1 + - - +
27N ARG* 1.3 77.1 - - - +
29N GLU* 1.3 63.8 + - - +
31N LYS* 3.2 12.0 + - - +
33N PHE* 3.3 37.3 + + - +
76N MET* 6.0 0.2 - - + -
78N TRP* 3.7 41.7 - + + -
83N VAL* 5.4 2.0 - - + -
87N GLY* 4.2 14.8 - - - -
90N MET* 4.0 21.1 - - + -
91N LEU* 3.6 24.2 - - + -
104N ILE* 3.8 23.8 - - + -
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Residues in contact with GLU 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ARG* 4.8 1.2 + - - -
25N ILE* 3.0 15.8 + - - +
26N LYS* 3.3 10.8 - - - +
28N PHE* 1.3 76.5 - - - +
30N GLN* 1.3 63.1 + - - +
31N LYS 3.0 1.7 + - - -
32N GLY* 3.0 15.2 + - - -
33N PHE 4.3 9.5 + - - +
78N TRP* 3.8 16.4 - - + -
16U VAL* 4.1 3.3 - - - +
19U GLY* 3.2 38.4 - - - +
21U VAL* 3.4 29.2 + - - +
22U GLY* 3.0 28.4 + - - -
23U GLU 4.9 0.2 + - - -
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Residues in contact with GLN 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ARG* 3.4 6.8 + - - +
20L LEU* 5.2 3.2 - - + +
23L GLU* 6.3 0.2 - - - +
27L ARG* 5.6 0.9 + - - -
107L ASP* 3.6 16.5 - - - +
108L PHE* 3.3 52.4 - - + +
26N LYS* 2.8 37.7 + - + +
27N ARG* 3.1 38.5 - - - +
29N GLU* 1.3 72.0 - - - +
31N LYS* 1.3 58.6 + - - +
32N GLY 3.3 0.2 - - - -
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Residues in contact with LYS 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ARG* 3.8 2.4 + - - -
96L PRO 4.3 10.1 + - - -
99L SER 5.2 1.0 + - - -
105L ARG 3.6 1.2 + - - -
106L GLY* 3.0 36.2 + - - +
107L ASP* 3.4 10.5 - - - +
108L PHE 3.4 12.0 - - - +
109L CYS* 2.6 27.9 + - - +
110L ILE* 3.3 22.9 - - + +
27N ARG 3.2 12.8 + - - +
28N PHE 3.3 11.7 - - - +
29N GLU 3.0 0.4 + - - -
30N GLN* 1.3 78.6 - - - +
32N GLY* 1.3 57.4 + - - +
33N PHE* 3.4 35.7 - - + -
86N THR* 4.9 11.4 - - - +
90N MET* 3.9 17.3 - - + -
150N 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