Contacts of the helix formed by residues 56 - 72 (chain E) in PDB entry 2OHI
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 THR 56 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E VAL* 3.8 25.0 - - + +
35E TYR* 4.9 2.7 - - + -
52E SER* 2.6 30.7 + - - -
53E TYR* 2.6 30.1 + - + +
54E PRO 4.1 4.5 - - - +
55E GLY* 1.3 81.3 - - - +
57E PHE* 1.3 63.3 + - - +
58E ASP 3.3 3.7 + - - -
59E GLU* 3.4 9.2 + - - +
60E LEU* 3.3 19.9 + - - +
91E VAL* 4.2 0.9 - - - -
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Residues in contact with PHE 57 (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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55E GLY 3.5 2.8 - - - -
56E THR* 1.3 77.7 - - - +
58E ASP* 1.3 65.0 + - - +
60E LEU* 4.5 5.8 - - + -
61E MET* 2.7 82.3 + - + +
91E VAL* 3.7 22.0 - - + +
94E GLU* 3.4 63.7 - - + +
95E LEU* 4.1 2.9 - - + -
98E ARG* 3.9 21.8 - - + -
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Residues in contact with ASP 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET* 3.8 27.2 - - + +
55E GLY 5.3 0.4 + - - -
56E THR 3.3 1.2 - - - -
57E PHE* 1.3 88.8 - - - +
59E GLU* 1.3 56.6 + - - +
61E MET* 3.9 2.3 - - - +
62E ALA* 2.9 30.8 + - - +
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Residues in contact with GLU 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B HIS* 5.2 7.1 - - - -
279B GLU* 3.6 7.0 - - - +
1E MET* 4.0 18.6 - - + +
3E ALA* 4.8 2.9 - - + -
16E GLY 3.9 0.2 - - - +
17E VAL* 3.4 27.5 - - + +
18E LEU* 2.9 28.6 + - - +
56E THR* 3.4 11.5 + - - +
57E PHE 3.4 0.2 - - - -
58E ASP* 1.3 74.5 - - - +
60E LEU* 1.3 65.0 + - - +
62E ALA* 3.4 2.6 + - - +
63E ARG* 2.6 66.3 + - - +
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Residues in contact with LEU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E THR* 4.0 13.9 - - - +
17E VAL* 4.2 7.6 - - + +
37E ALA* 3.9 17.9 - - + -
48E LEU* 4.4 4.7 - - + -
51E ASN* 3.6 38.4 - - + -
52E SER* 4.1 11.9 - - - +
56E THR 3.3 13.9 + - - +
57E PHE* 3.8 7.0 - - + +
59E GLU* 1.3 77.9 - - - +
61E MET* 1.3 69.1 + - + +
63E ARG* 3.2 4.5 + - - +
64E VAL* 3.0 36.1 + - + +
91E VAL* 4.3 10.5 - - + -
95E LEU* 3.9 28.9 - - + -
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Residues in contact with MET 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E PHE* 2.7 56.2 + - + +
58E ASP* 4.3 2.0 - - - +
60E LEU* 1.3 76.9 - - + +
62E ALA* 1.3 57.6 - - - +
64E VAL* 3.4 21.4 - - + +
65E GLU* 2.9 36.5 + - + +
95E LEU* 3.3 26.2 - - + -
98E ARG* 3.1 46.7 - - + +
99E PHE* 3.6 18.2 - - + -
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Residues in contact with ALA 62 (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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1E MET* 3.6 28.0 - - + +
3E ALA* 3.3 24.9 + - + +
58E ASP 2.9 21.4 + - - +
59E GLU* 3.6 6.1 - - - +
60E LEU 3.2 0.2 - - - -
61E MET* 1.3 77.9 - - - +
63E ARG* 1.3 60.5 + - - +
65E GLU* 3.4 15.2 - - - +
66E ASP* 3.3 16.1 + - - +
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Residues in contact with ARG 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B GLU* 2.5 41.7 + - - -
282B MET* 5.0 4.8 - - - +
3E ALA* 3.4 19.8 - - + +
4E ALA* 2.8 29.1 + - - +
5E ALA* 3.3 13.0 - - + +
14E TRP* 3.5 24.2 - - - -
15E THR* 3.7 20.9 - - + +
16E GLY 2.8 27.4 + - - +
18E LEU* 3.9 15.1 - - - +
59E GLU* 2.6 36.2 + - - +
60E LEU 3.2 1.8 + - - +
62E ALA* 1.3 71.8 - - - +
64E VAL* 1.3 64.8 + - - +
65E GLU 3.1 1.6 - - - -
66E ASP 3.1 2.3 + - - -
67E ALA 3.0 19.6 + - - -
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Residues in contact with VAL 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E THR* 3.4 28.7 - - + +
39E LEU* 4.4 11.1 - - + +
48E LEU* 3.9 25.6 - - + -
60E LEU* 3.0 22.6 + - + +
61E MET* 3.4 40.2 - - + +
63E ARG* 1.3 75.3 - - - +
65E GLU* 1.3 60.3 + - + +
67E ALA* 3.9 2.2 - - - +
68E LEU* 3.0 41.6 + - + +
76E VAL* 5.1 2.2 - - + -
95E LEU* 5.7 0.2 - - + -
99E PHE* 4.8 7.6 - - + -
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Residues in contact with GLU 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET 5.5 0.7 - - - +
61E MET* 2.9 31.0 + - + +
62E ALA* 3.4 15.2 - - - +
63E ARG 3.1 0.4 - - - -
64E VAL* 1.3 75.4 - - + +
66E ASP* 1.3 63.1 + - - +
68E LEU* 3.5 11.1 + - + +
69E GLN* 3.2 21.5 + - - +
98E ARG* 2.9 33.1 + - - +
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Residues in contact with ASP 66 (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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3E ALA 3.9 4.9 - - - +
4E ALA* 3.4 11.9 - - - +
5E ALA 2.9 28.2 + - - +
62E ALA 3.3 9.6 + - - +
63E ARG 3.1 9.7 + - - +
65E GLU* 1.3 75.8 - - - +
67E ALA* 1.3 66.1 + - - +
69E GLN* 3.0 29.6 + - - +
70E GLN* 3.0 39.8 + - - +
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Residues in contact with ALA 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ALA* 3.8 10.4 - - + +
13E TYR* 3.7 36.8 - - + -
15E THR* 4.0 4.7 - - + -
39E LEU* 3.7 18.6 - - + -
63E ARG 3.0 13.9 + - - +
64E VAL 4.0 0.7 - - - +
66E ASP* 1.3 77.0 - - - +
68E LEU* 1.3 60.0 + - - +
70E GLN* 3.5 3.6 + - - +
71E VAL* 3.1 33.4 + - - +
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Residues in contact with LEU 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E LEU* 4.4 7.9 - - + -
46E VAL* 4.1 13.9 - - + -
64E VAL* 3.0 32.2 + - + +
65E GLU* 3.8 10.8 - - + +
66E ASP 3.2 0.2 - - - -
67E ALA* 1.3 73.8 - - - +
69E GLN* 1.3 59.7 - - - +
71E VAL* 5.1 0.9 - - - -
72E GLY* 2.9 7.3 + - - -
73E MET* 2.8 61.6 + - + +
74E GLU 4.2 12.6 - - - +
75E ARG* 3.6 31.6 - - - +
76E VAL* 4.8 2.5 - - + +
99E PHE* 4.6 14.4 - - + -
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Residues in contact with GLN 69 (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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65E GLU 3.2 11.8 + - - +
66E ASP* 3.0 32.0 + - - +
68E LEU* 1.3 75.1 - - - +
70E GLN* 1.3 70.0 + - - +
72E GLY* 3.2 13.5 + - - -
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Residues in contact with GLN 70 (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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5E ALA 3.3 22.9 - - - +
7E ARG* 4.9 5.9 - - - +
13E TYR* 3.5 35.1 + - + +
66E ASP* 3.0 31.4 + - - +
67E ALA 3.5 5.4 + - - +
69E GLN* 1.3 83.2 - - + +
71E VAL* 1.3 60.0 + - - +
10H ASP* 5.5 8.5 + - - +
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Residues in contact with VAL 71 (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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11E GLY* 5.3 4.5 - - - -
13E TYR* 3.4 36.3 - - + +
41E CYS* 4.0 18.8 - - + -
42E GLY 5.4 0.4 - - - +
67E ALA 3.1 18.2 + - - +
70E GLN* 1.3 76.6 - - - +
72E GLY* 1.3 60.5 + - - +
73E MET* 3.8 36.9 - - + +
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Residues in contact with GLY 72 (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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68E LEU 2.9 8.1 + - - -
69E GLN* 3.2 12.7 + - - -
71E VAL* 1.3 81.0 - - - +
73E MET* 1.3 64.3 + - - +
74E GLU* 5.8 0.5 - - - +
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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