Contacts of the helix formed by residues 9 - 22 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E GLY 2.7 14.6 + - - -
8E ALA* 1.3 81.1 - - - +
10E PHE* 1.3 56.9 + - - -
11E ILE 3.7 0.7 - - - -
13E SER* 2.7 34.8 + - - -
31E ASP* 3.2 3.4 + - - -
38E LYS* 4.9 0.2 - - - -
41E ASN* 4.2 0.4 - - - -
177E HIS* 3.8 9.9 - - - -
400E NAP 3.7 24.5 - - - -
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Residues in contact with PHE 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E GLY* 1.3 69.6 - - - -
11E ILE* 1.3 68.1 + - + +
13E SER* 3.0 8.8 + - - -
14E ASN* 2.8 28.8 + - - -
170E VAL* 3.6 31.9 - - + -
171E TYR* 3.5 4.7 - - - -
172E GLY 3.2 34.5 - - - -
173E PRO 3.1 22.0 - - - -
174E ARG 3.1 25.4 - - - +
175E GLU* 3.5 15.9 - - + -
177E HIS* 3.5 2.4 - - + -
178E LYS* 4.0 8.5 - - + -
214E VAL* 3.6 12.1 - - + -
400E NAP 3.0 43.3 + - - +
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Residues in contact with ILE 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E PHE* 1.3 86.6 - - + +
12E GLY* 1.3 64.3 + - - +
14E ASN* 3.1 10.3 + - + +
15E ILE* 2.9 27.2 + - + +
75E GLU* 3.5 21.3 - - - +
167E TYR* 3.5 38.1 - - + +
170E VAL* 4.1 23.6 - - + -
214E VAL* 4.5 4.3 - - + -
217E VAL* 4.0 14.6 - - + -
400E NAP 2.9 44.6 + - + +
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Residues in contact with GLY 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 3.7 15.6 - - - +
6E GLY 3.5 18.3 + - - -
7E GLY* 3.8 6.5 - - - -
9E GLY 4.3 0.2 - - - -
10E PHE 3.3 0.6 - - - -
11E ILE* 1.3 79.5 - - - +
13E SER* 1.3 61.8 + - - +
15E ILE* 3.0 6.8 + - - +
16E VAL* 2.9 23.9 + - - +
75E GLU* 4.0 15.7 - - - +
400E NAP 4.6 0.8 + - - -
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Residues in contact with SER 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E GLY 3.3 17.5 + - - -
9E GLY 2.7 24.6 + - - -
10E PHE 3.0 8.0 + - - -
12E GLY* 1.3 75.4 - - - +
14E ASN* 1.3 57.1 + - - +
16E VAL* 3.2 7.7 + - - +
17E LYS* 2.9 24.4 + - - +
41E ASN* 3.6 29.6 - - - +
42E LEU* 4.8 0.2 - - - -
45E LEU* 3.4 7.8 - - - +
174E ARG* 3.3 21.9 - - - +
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Residues in contact with ASN 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E PHE* 2.8 22.4 + - - -
11E ILE* 3.1 9.2 + - + +
13E SER* 1.3 80.3 + - - +
15E ILE* 1.3 60.2 + - - +
17E LYS* 3.4 12.3 + - - +
18E ALA* 3.0 27.7 + - - +
173E PRO* 2.9 30.1 + - - +
174E ARG* 3.8 14.0 + - - +
214E VAL* 3.5 37.8 - - + +
215E GLY* 5.3 1.2 + - - -
218E ALA* 3.9 13.4 - - + +
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Residues in contact with ILE 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 4.4 6.1 - - + -
11E ILE* 2.9 19.9 + - + +
12E GLY* 3.0 8.0 + - - +
14E ASN* 1.3 74.3 - - - +
16E VAL* 1.3 65.5 + - - +
18E ALA* 3.2 6.9 + - - +
19E LEU* 2.9 37.2 + - + +
73E PHE* 4.0 28.0 - - + -
75E GLU* 3.6 31.6 - - + +
218E ALA* 4.7 8.7 - - + -
221E ASN* 3.5 39.5 - - + +
222E LEU* 4.5 5.8 - - + -
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Residues in contact with VAL 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 4.2 16.4 - - + -
7E GLY 4.1 8.5 - - - +
12E GLY 2.9 18.3 + - - +
13E SER 3.2 7.6 + - - +
15E ILE* 1.3 75.6 - - - +
17E LYS* 1.3 57.7 + - - +
19E LEU* 3.1 12.1 + - - +
20E ASN* 2.8 29.9 + - - +
27E ILE* 4.0 10.8 - - + -
29E VAL* 4.1 22.2 - - + -
42E LEU* 4.7 1.6 - - + -
45E LEU* 3.7 21.8 - - + -
47E ILE* 3.8 25.6 - - + -
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Residues in contact with LYS 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E SER 2.9 13.3 + - - +
14E ASN* 3.7 15.9 - - - +
16E VAL* 1.3 76.2 - - - +
18E ALA* 1.3 58.1 + - - +
20E ASN* 3.1 7.5 + - + +
21E ASP* 2.8 61.2 + - - +
45E LEU* 3.9 28.4 - - + +
174E ARG* 4.1 20.4 - - - +
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Residues in contact with ALA 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ASN 3.0 16.8 + - - +
15E ILE* 3.5 6.3 - - - +
16E VAL 3.2 0.2 - - - -
17E LYS* 1.3 77.9 - - - +
19E LEU* 1.3 61.7 + - - +
21E ASP* 3.2 12.9 + - - +
22E LYS* 3.1 18.4 + - - +
218E ALA* 4.0 20.0 - - + +
219E ASP* 5.3 4.9 - - - +
222E LEU* 3.8 26.8 - - + +
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Residues in contact with LEU 19 (chain E).
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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2E ILE* 3.8 46.4 - - + -
4E VAL* 4.2 7.0 - - + -
15E ILE* 2.9 33.5 + - + +
16E VAL* 3.4 6.1 - - - +
18E ALA* 1.3 72.7 - - - +
20E ASN* 1.3 67.2 + - - +
22E LYS* 3.0 11.3 + - + +
23E GLY 3.3 0.2 + - - -
24E ILE* 2.9 40.7 + - + +
27E ILE* 3.9 22.0 - - + -
73E PHE* 4.4 3.8 - - + -
222E LEU* 3.9 25.8 - - + -
225E LEU* 5.0 3.8 - - + -
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Residues in contact with ASN 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E VAL* 2.8 18.1 + - - +
17E LYS* 3.3 11.4 - - + +
19E LEU* 1.3 75.8 - - - +
21E ASP* 1.3 57.6 + - - +
23E GLY* 2.7 26.3 + - - -
24E ILE 2.9 19.6 + - - -
25E THR* 3.8 8.7 - - + +
27E ILE* 3.8 4.0 - - - +
45E LEU* 3.6 15.3 - - + +
46E ASN* 2.8 53.9 + - - +
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Residues in contact with ASP 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LYS* 2.8 50.9 + - - +
18E ALA* 3.2 12.3 + - - +
20E ASN* 1.3 79.1 - - - +
22E LYS* 1.3 61.7 + - + +
23E GLY 3.2 1.1 + - - -
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Residues in contact with LYS 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ALA 3.1 10.8 + - - +
19E LEU* 3.0 11.3 + - + +
21E ASP* 1.3 79.1 - - + +
23E GLY* 1.3 60.1 + - - +
24E ILE* 3.3 16.5 + - + +
222E LEU* 3.8 22.9 - - + -
226E GLU* 3.1 30.8 + - - +
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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