Contacts of the helix formed by residues 9 - 22 (chain N) in PDB entry 2X86
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 GLY 9 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6N GLY 2.8 13.9 + - - -
8N ALA* 1.3 80.8 - - - +
10N PHE* 1.3 57.2 + - - -
11N ILE 3.7 0.9 - - - -
13N SER* 2.7 34.7 + - - -
31N ASP* 3.2 3.2 + - - -
38N LYS* 4.9 0.2 - - - -
41N ASN* 4.2 0.7 - - - -
177N HIS* 3.8 9.4 - - - -
400N NAP 3.4 24.9 - - - -
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Residues in contact with PHE 10 (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 GLY* 1.3 69.6 - - - -
11N ILE* 1.3 64.7 + - + +
13N SER* 3.0 9.5 + - - -
14N ASN* 2.8 28.1 + - - -
170N VAL* 3.6 28.5 - - + -
171N TYR 3.5 4.9 - - - -
172N GLY 3.2 34.5 - - - -
173N PRO 3.1 22.0 - - - -
174N ARG 3.1 24.9 - - - +
175N GLU* 3.5 16.8 - - + -
177N HIS* 3.5 1.8 - - + -
178N LYS* 4.0 9.4 - - + -
214N VAL* 3.6 12.6 - - + -
400N NAP 3.0 48.5 + - - +
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Residues in contact with ILE 11 (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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10N PHE* 1.3 88.9 - - + +
12N GLY* 1.3 62.2 + - - +
14N ASN* 3.1 5.4 + - - +
15N ILE* 2.9 25.1 + - + +
75N GLU* 3.5 23.3 - - - +
167N TYR* 3.5 37.5 - - + +
170N VAL* 4.1 19.1 - - + -
214N VAL* 4.5 8.3 - - + -
217N VAL* 4.0 14.6 - - + -
400N NAP 2.8 48.4 + - + +
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Residues in contact with GLY 12 (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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4N VAL* 3.7 15.3 - - - +
6N GLY 3.5 19.0 + - - -
7N GLY* 3.8 7.0 - - - -
10N PHE 3.3 0.6 - - - -
11N ILE* 1.3 78.8 - - - +
13N SER* 1.3 62.3 + - - +
15N ILE* 3.0 6.3 + - - +
16N VAL* 2.9 24.4 + - - +
75N GLU* 4.0 15.0 - - - +
400N NAP 4.3 1.0 + - - -
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Residues in contact with SER 13 (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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7N GLY 3.3 18.3 + - - -
9N GLY 2.7 25.0 + - - -
10N PHE 3.0 8.5 + - - -
12N GLY* 1.3 74.8 - - - +
14N ASN* 1.3 57.3 + - - +
16N VAL* 3.2 7.9 + - - +
17N LYS* 2.9 24.8 + - - +
41N ASN* 3.6 29.2 - - - +
42N LEU* 4.8 0.2 - - - -
45N LEU* 3.4 7.7 - - - +
174N ARG* 3.3 21.2 - - - +
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Residues in contact with ASN 14 (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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10N PHE* 2.8 22.6 + - - -
11N ILE 3.1 9.2 + - - +
13N SER* 1.3 80.5 + - - +
15N ILE* 1.3 60.4 + - - +
17N LYS* 3.4 12.3 + - - +
18N ALA* 3.0 27.7 + - - +
173N PRO* 2.9 29.2 + - - +
174N ARG* 3.8 14.8 + - - +
214N VAL* 3.5 37.4 - - + +
215N GLY* 5.3 1.4 + - - -
218N ALA* 3.9 12.4 - - + +
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Residues in contact with ILE 15 (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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4N VAL* 4.3 6.5 - - + -
11N ILE* 2.9 20.3 + - + +
12N GLY* 3.0 7.2 + - - +
14N ASN* 1.3 74.9 - - - +
16N VAL* 1.3 64.9 + - - +
18N ALA* 3.2 6.7 + - - +
19N LEU* 2.9 38.1 + - + +
73N PHE* 4.0 25.8 - - + -
75N GLU* 3.6 34.1 - - + +
218N ALA* 4.6 8.5 - - - -
221N ASN* 3.6 37.2 - - + +
222N LEU* 4.5 8.3 - - + -
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Residues in contact with VAL 16 (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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4N VAL* 4.2 17.0 - - + -
7N GLY 4.2 9.2 - - - +
12N GLY 2.9 18.3 + - - +
13N SER 3.2 8.5 + - - +
15N ILE* 1.3 75.0 - - - +
17N LYS* 1.3 57.0 + - - +
19N LEU* 3.1 11.6 + - - +
20N ASN* 2.8 30.5 + - - +
27N ILE* 4.0 11.7 - - + -
29N VAL* 4.1 22.4 - - + -
42N LEU* 4.8 1.1 - - + -
45N LEU* 3.7 21.8 - - + -
47N ILE* 3.7 25.1 - - + -
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Residues in contact with LYS 17 (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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13N SER 2.9 14.6 + - - +
14N ASN* 3.7 15.7 - - - +
15N ILE 3.3 0.2 - - - -
16N VAL* 1.3 74.9 - - - +
18N ALA* 1.3 58.2 + - - +
20N ASN* 3.1 6.9 + - + +
21N ASP* 2.8 61.0 + - - +
45N LEU* 3.9 27.6 - - + +
174N ARG* 4.1 19.5 - - - +
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Residues in contact with ALA 18 (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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14N ASN 3.0 17.8 + - - +
15N ILE* 3.5 6.1 - - - +
17N LYS* 1.3 79.0 - - - +
19N LEU* 1.3 60.9 + - - +
21N ASP* 3.2 12.3 + - - +
22N LYS* 3.1 18.5 + - - +
218N ALA* 4.0 20.0 - - + -
219N ASP* 5.3 4.9 - - - +
222N LEU* 3.8 27.7 - - + +
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Residues in contact with LEU 19 (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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2N ILE* 3.8 46.0 - - + -
4N VAL* 4.2 6.5 - - + -
15N ILE* 2.9 33.1 + - + +
16N VAL 3.4 6.3 - - - +
18N ALA* 1.3 71.9 - - - +
20N ASN* 1.3 66.4 + - - +
22N LYS* 3.0 10.3 + - + +
24N ILE* 2.9 40.8 + - + +
27N ILE* 3.9 23.1 - - + -
73N PHE* 4.5 3.6 - - + -
222N LEU* 3.9 26.9 - - + -
225N LEU* 5.1 3.1 - - + -
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Residues in contact with ASN 20 (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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16N VAL* 2.8 16.6 + - - -
17N LYS* 3.3 11.7 - - + +
19N LEU* 1.3 75.2 - - - +
21N ASP* 1.3 56.8 + - - +
23N GLY* 2.7 26.7 + - - -
24N ILE 2.9 19.8 + - - -
25N THR* 3.8 8.5 - - + +
27N ILE* 3.8 4.4 - - - +
45N LEU* 3.6 15.7 - - + +
46N ASN* 2.8 55.8 + - - +
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Residues in contact with ASP 21 (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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17N LYS* 2.8 51.6 + - - +
18N ALA* 3.5 12.6 - - - +
19N LEU 3.2 0.4 - - - -
20N ASN* 1.3 77.8 - - - +
22N LYS* 1.3 61.3 + - + +
23N GLY 3.2 0.7 + - - -
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Residues in contact with LYS 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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18N ALA 3.1 12.6 + - - +
19N LEU* 3.0 11.3 + - + +
21N ASP* 1.3 79.3 - - + +
23N GLY* 1.3 59.7 + - - +
24N ILE* 3.3 17.6 + - + +
222N LEU* 3.8 24.0 - - + -
226N GLU* 3.1 30.5 + - - +
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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