Contacts of the helix formed by residues 9 - 22 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6T GLY 2.7 14.1 + - - -
8T ALA* 1.3 80.2 - - - +
10T PHE* 1.3 58.3 + - - -
11T ILE 3.7 0.9 - - - -
13T SER* 2.7 34.4 + - - -
31T ASP* 3.2 3.4 + - - -
41T ASN* 4.2 0.4 - - - -
177T HIS* 3.8 8.7 - - - -
400T NAP 3.3 25.1 - - - -
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Residues in contact with PHE 10 (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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9T GLY* 1.3 69.5 - - - -
11T ILE* 1.3 68.8 + - + +
13T SER* 3.0 9.0 + - - -
14T ASN* 2.8 28.1 + - - -
170T VAL* 3.6 31.4 - - + -
171T TYR 3.6 5.2 - - - -
172T GLY 3.2 33.4 - - - -
173T PRO 3.1 21.3 - - - -
174T ARG 3.1 25.4 - - - +
175T GLU* 3.6 16.8 - - + -
177T HIS* 3.5 2.2 - - + -
178T LYS* 4.0 10.1 - - + -
214T VAL* 3.6 12.3 - - + -
400T NAP 2.9 43.0 + - - +
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Residues in contact with ILE 11 (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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10T PHE* 1.3 87.5 - - + +
12T GLY* 1.3 61.6 + - - +
14T ASN* 3.1 9.7 + - - +
15T ILE* 3.0 28.2 + - + +
75T GLU* 3.5 21.8 - - - +
167T TYR* 3.5 39.0 - - + +
170T VAL* 4.1 22.9 - - + -
214T VAL* 4.6 4.9 - - + -
217T VAL* 4.1 13.9 - - + -
218T ALA* 6.3 0.2 - - - -
400T NAP 2.7 44.2 + - + +
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Residues in contact with GLY 12 (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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4T VAL* 3.7 15.1 - - - +
6T GLY 3.5 19.9 + - - -
7T GLY* 3.8 6.7 - - - -
9T GLY 4.3 0.4 - - - -
10T PHE 3.3 0.8 - - - -
11T ILE* 1.3 78.4 - - - +
13T SER* 1.3 62.6 + - - +
15T ILE* 3.0 6.1 + - - +
16T VAL* 2.9 24.3 + - - +
75T GLU* 4.0 14.8 - - - +
400T NAP 4.3 0.8 + - - -
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Residues in contact with SER 13 (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 GLY 3.3 17.2 + - - -
9T GLY 2.7 24.5 + - - -
10T PHE 3.0 8.3 + - - -
12T GLY* 1.3 75.6 - - - +
14T ASN* 1.3 56.8 + - - +
16T VAL* 3.2 7.7 + - - +
17T LYS* 2.9 24.4 + - - +
41T ASN* 3.6 30.1 - - - +
42T LEU* 4.8 0.2 - - - -
45T LEU* 3.4 7.6 - - - +
174T ARG* 3.3 21.4 - - - +
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Residues in contact with ASN 14 (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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10T PHE* 2.8 22.4 + - - -
11T ILE 3.1 9.2 + - - +
13T SER* 1.3 80.6 + - - +
15T ILE* 1.3 60.7 + - + +
17T LYS* 3.4 11.8 + - - +
18T ALA* 3.0 27.7 + - - +
173T PRO* 2.9 31.2 + - - +
174T ARG* 3.8 14.2 + - - +
214T VAL* 3.5 35.2 - - + +
215T GLY* 5.6 1.4 - - - -
218T ALA* 3.9 12.3 - - + +
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Residues in contact with ILE 15 (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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4T VAL* 4.4 5.6 - - + -
11T ILE* 3.0 20.1 + - + +
12T GLY* 3.0 7.6 + - - +
14T ASN* 1.3 74.9 - - - +
16T VAL* 1.3 65.5 + - - +
18T ALA* 3.2 6.5 + - - +
19T LEU* 2.9 37.3 + - + +
73T PHE* 4.0 28.0 - - + -
75T GLU* 3.6 32.1 - - + +
218T ALA* 4.7 9.4 - - + +
221T ASN* 3.5 38.6 - - + +
222T LEU* 4.5 6.5 - - + -
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Residues in contact with VAL 16 (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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4T VAL* 4.2 16.8 - - + -
7T GLY 4.1 14.4 - - - +
12T GLY 2.9 18.1 + - - +
13T SER 3.3 7.6 - - - +
15T ILE* 1.3 76.2 - - - +
17T LYS* 1.3 56.6 + - - +
19T LEU* 3.1 11.2 + - - +
20T ASN* 2.8 30.6 + - - +
27T ILE* 4.0 11.4 - - + -
29T VAL* 4.2 17.0 - - + -
42T LEU* 4.7 1.8 - - + -
45T LEU* 3.7 21.8 - - + -
47T ILE* 3.8 25.1 - - + -
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Residues in contact with LYS 17 (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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13T SER 2.9 13.9 + - - +
14T ASN* 3.7 15.7 - - - +
15T ILE 3.3 0.2 - - - -
16T VAL* 1.3 75.3 - - - +
18T ALA* 1.3 57.5 + - - +
20T ASN* 3.1 7.6 + - + +
21T ASP* 2.9 60.5 + - - +
45T LEU* 3.9 26.9 - - + -
174T ARG* 4.1 19.7 - - - +
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Residues in contact with ALA 18 (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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14T ASN 3.0 17.4 + - - +
15T ILE* 3.5 5.6 - - - +
17T LYS* 1.3 77.9 - - - +
19T LEU* 1.3 61.2 + - - +
21T ASP* 3.2 13.0 + - - +
22T LYS* 3.1 17.8 + - - +
218T ALA* 4.0 19.5 - - + +
219T ASP* 5.4 4.5 - - - +
222T LEU* 3.8 28.2 - - + +
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Residues in contact with LEU 19 (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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2T ILE* 3.8 46.7 - - + -
4T VAL* 4.1 7.2 - - + -
15T ILE* 2.9 32.8 + - + +
16T VAL 3.4 5.8 - - - +
18T ALA* 1.3 72.5 - - - +
20T ASN* 1.3 67.0 + - - +
22T LYS* 3.0 10.8 + - + +
23T GLY 3.3 0.2 + - - -
24T ILE* 2.9 40.2 + - + +
27T ILE* 3.9 21.8 - - + -
73T PHE* 4.4 3.6 - - + -
222T LEU* 3.9 26.5 - - + -
225T LEU* 5.0 3.8 - - + -
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Residues in contact with ASN 20 (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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16T VAL* 2.8 16.5 + - - +
17T LYS* 3.1 11.6 + - + +
19T LEU* 1.3 76.0 - - - +
21T ASP* 1.3 57.0 + - - +
23T GLY* 2.7 26.7 + - - -
24T ILE 2.9 19.0 + - - -
25T THR* 3.8 8.2 - - + +
27T ILE* 3.8 4.2 - - - +
45T LEU* 3.6 16.0 - - + +
46T ASN* 2.8 54.8 + - - +
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Residues in contact with ASP 21 (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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17T LYS* 2.9 51.2 + - - +
18T ALA* 3.2 12.7 + - - +
20T ASN* 1.3 78.6 - - - +
22T LYS* 1.3 61.4 + - + +
23T GLY 3.2 1.4 + - - -
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Residues in contact with LYS 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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18T ALA 3.1 10.4 + - - +
19T LEU* 3.0 11.7 + - - +
21T ASP* 1.3 78.5 - - + +
23T GLY* 1.3 59.0 - - - +
24T ILE* 3.3 17.1 + - + +
222T LEU* 3.8 24.0 - - + -
226T GLU* 3.1 31.5 + - - +
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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