Contacts of the helix formed by residues 11 - 26 (chain A) in PDB entry 2OR0
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ARG 3.4 15.7 - - - +
8A ILE* 3.1 12.3 + - + +
10A VAL* 1.3 85.3 - - + +
12A ALA* 1.3 63.8 + - - +
13A GLU 3.2 3.1 - - - -
14A GLU* 3.0 24.0 + - - +
15A ILE* 2.9 36.7 + - + +
35A LEU* 4.1 31.2 - - + +
39A SER* 5.5 1.6 - - - -
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE 2.9 10.5 + - - +
9A GLU* 3.3 21.3 + - - +
10A VAL 3.3 1.0 - - - -
11A VAL* 1.3 76.5 - - - +
13A GLU* 1.3 59.6 + - - +
15A ILE* 3.3 3.1 + - - +
16A ARG* 3.0 52.2 + - - +
70A LEU* 3.8 21.1 - - + +
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Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLU 4.1 3.3 - - - +
10A VAL 3.1 21.4 - - - +
12A ALA* 1.3 82.1 + - - +
14A GLU* 1.3 81.4 + - - +
16A ARG* 3.6 23.3 + - - +
17A GLY* 2.9 24.4 + - - -
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL 4.0 1.6 - - - +
11A VAL* 3.0 29.6 + - + +
13A GLU* 1.3 111.8 - - + +
15A ILE* 1.3 63.1 + - - +
17A GLY* 3.2 11.4 + - - +
18A GLN* 3.2 14.2 + - - +
35A LEU* 3.7 28.1 - - + +
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Residues in contact with ILE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 4.0 22.9 - - + +
11A VAL* 2.9 32.2 + - + +
12A ALA 3.6 7.0 - - - +
14A GLU* 1.3 73.9 - - - +
16A ARG* 1.3 67.0 + - - +
18A GLN* 3.2 14.7 + - - +
19A ALA* 3.5 9.9 + - - +
32A ALA* 5.9 1.3 - - - +
35A LEU* 3.8 26.9 - - + -
36A LEU* 5.1 7.9 - - + -
67A VAL* 5.1 4.0 - - + +
70A LEU* 3.9 34.5 - - + -
71A ASP* 3.9 17.9 - - + +
74A SER* 4.4 13.0 - - - +
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Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 3.0 27.0 + - - +
13A GLU* 3.6 29.1 + - - +
15A ILE* 1.3 74.8 - - - +
17A GLY* 1.3 61.2 + - - +
19A ALA* 3.3 19.9 + - - +
20A VAL* 4.7 2.3 + - - +
70A LEU* 3.5 53.3 - - + +
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Residues in contact with GLY 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU 2.9 15.9 + - - -
14A GLU* 3.5 8.5 - - - -
15A ILE 3.1 0.8 - - - -
16A ARG* 1.3 77.2 - - - +
18A GLN* 1.3 65.4 + - - +
20A VAL* 5.1 2.1 + - - +
21A GLN* 5.5 2.3 + - - +
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Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU 3.2 11.6 + - - +
15A ILE* 3.2 9.6 + - - +
17A GLY* 1.3 81.1 - - - +
19A ALA* 1.3 64.9 + - - +
20A VAL 3.4 1.8 - - - -
21A GLN* 3.2 12.5 + - - +
22A SER* 3.0 23.3 + - - -
29A THR* 2.7 43.5 + - - +
31A ALA* 3.6 21.1 - - + +
32A ALA* 3.8 24.5 - - + +
35A LEU* 4.5 3.8 - - + -
71A ASP* 5.7 0.2 - - - -
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE 3.5 4.9 + - - +
16A ARG* 3.3 17.5 + - - +
17A GLY 3.5 0.2 - - - -
18A GLN* 1.3 77.7 - - - +
20A VAL* 1.3 63.4 + - + +
22A SER* 3.4 4.6 + - - +
23A GLU* 3.1 23.6 + - - +
70A LEU 5.1 1.3 - - - +
71A ASP* 3.3 39.9 - - + +
351A ARG* 4.1 21.9 - - - +
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ARG 4.7 2.3 + - - +
17A GLY 5.1 2.4 + - - +
18A GLN 3.4 0.4 - - - -
19A ALA* 1.3 76.3 - - + +
21A GLN* 1.3 59.7 + - - +
23A GLU* 3.3 8.8 + - - +
24A ALA* 2.9 29.7 + - + +
345A TYR 5.8 0.7 - - - +
351A ARG* 3.4 30.3 - - - +
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Residues in contact with GLN 21 (chain A).
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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17A GLY 5.5 2.0 + - - +
18A GLN* 3.2 14.8 + - - +
20A VAL* 1.3 78.5 - - - +
22A SER* 1.3 59.3 + - - +
24A ALA* 3.3 11.7 + - - +
25A ASP* 2.9 64.3 + - - +
29A THR* 3.7 18.6 - - + -
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Residues in contact with SER 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLN 3.0 16.2 + - - -
19A ALA* 3.4 6.7 + - - -
21A GLN* 1.3 75.8 - - - +
23A GLU* 1.3 57.7 + - - +
26A CYS 3.0 22.2 + - - -
27A ARG 3.1 27.2 + - - +
28A LEU* 3.5 17.8 - - - +
29A THR* 3.0 22.8 + - - +
32A ALA* 3.8 10.2 - - - +
71A ASP* 5.2 3.3 + - - -
73A ALA* 5.5 1.1 - - - -
185A GLY* 3.3 8.6 - - - -
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA 3.1 14.4 + - - +
20A VAL* 3.5 11.5 - - - +
21A GLN 3.2 0.2 - - - -
22A SER* 1.3 76.8 - - - +
24A ALA* 1.3 63.0 + - - +
26A CYS* 3.0 20.6 + - - -
184A ARG* 3.8 29.6 + - + +
185A GLY* 4.2 9.4 - - - +
345A TYR* 4.7 9.0 - - - -
350A GLN* 5.8 0.2 + - - -
351A ARG* 3.7 27.6 + - + +
354A ARG* 2.6 42.0 + - - -
355A ASP* 5.3 1.7 - - - +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 2.9 19.7 + - + +
21A GLN* 3.3 18.6 + - - +
23A GLU* 1.3 77.4 + - - +
25A ASP* 1.3 61.6 + - - +
26A CYS* 4.4 5.0 - - - -
184A ARG* 5.1 2.6 + - - +
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Residues in contact with ASP 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN* 2.9 49.4 + - - +
24A ALA* 1.3 76.6 - - - +
26A CYS* 1.3 68.6 + - - +
27A ARG* 3.8 27.1 + - + +
29A THR* 4.0 12.3 - - - +
189A LYS* 6.0 0.7 - - - -
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Residues in contact with CYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER 3.0 6.7 + - - -
23A GLU 3.0 11.2 + - - -
24A ALA 4.4 3.4 - - - -
25A ASP* 1.3 79.4 - - - +
27A ARG* 1.3 58.8 + - - +
178A TRP* 3.9 22.3 - - + +
179A ASP* 5.3 1.3 - - - -
184A ARG* 3.2 61.2 - - - +
187A GLY* 3.0 18.9 - - - -
189A LYS* 4.5 8.9 - - - -
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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