Contacts of the helix formed by residues 56 - 71 (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 HIS 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A GLU 3.8 0.4 + - - -
55A VAL* 1.3 76.4 - - - +
57A PRO* 1.3 75.9 - - + +
58A ARG* 3.0 30.8 + - + +
59A GLU* 2.9 22.6 + - + +
60A PHE 3.3 7.4 + - - -
295A ALA 4.6 0.2 - - - -
296A ASP* 3.4 37.1 + - - -
299A TYR* 3.4 50.6 - + + +
300A ASP* 5.5 0.8 + - - -
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Residues in contact with PRO 57 (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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45A LEU* 5.1 0.2 - - + -
55A VAL 3.6 4.2 - - - +
56A HIS* 1.3 93.9 - - + +
58A ARG* 1.3 55.7 - - - +
60A PHE* 3.3 10.6 + - + +
61A ALA* 2.9 30.7 + - - +
224A LEU* 4.1 11.0 - - + -
227A MSE 3.9 22.0 - - + -
232A MSE 4.0 15.3 - - + -
235A LEU* 3.8 13.7 - - + +
295A ALA* 3.7 24.9 - - + +
299A TYR* 3.6 19.7 - - + -
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Residues in contact with ARG 58 (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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56A HIS* 3.0 19.7 + - + +
57A PRO* 1.3 76.3 - - - +
59A GLU* 1.3 58.7 + - - +
61A ALA* 3.3 3.4 + - - +
62A GLU* 2.8 70.9 + - - +
289A VAL* 5.4 2.6 + - - +
292A ILE* 3.2 39.1 - - + +
293A GLU* 4.8 1.8 - - - +
295A ALA* 5.0 1.7 - - - +
296A ASP* 2.9 37.5 + - - +
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Residues in contact with GLU 59 (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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2A GLY* 3.3 34.3 - - - +
3A ARG 4.1 1.9 + - - -
4A VAL* 4.7 4.3 + - - +
5A LEU* 5.4 1.7 + - + +
44A LEU* 4.6 6.1 - - + +
55A VAL* 3.5 31.6 - - + +
56A HIS* 2.9 17.1 + - + +
58A ARG* 1.3 79.0 - - - +
60A PHE* 1.3 62.6 + - - +
62A GLU* 4.1 8.1 - - - +
63A THR* 2.6 43.1 + - - +
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Residues in contact with PHE 60 (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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41A ALA 5.2 0.2 - - - -
44A LEU* 3.8 24.0 - - + -
45A LEU* 3.7 42.8 - - + -
55A VAL* 3.7 7.9 - - + +
56A HIS 3.3 3.2 + - - -
57A PRO* 3.3 8.9 + - + +
59A GLU* 1.3 77.4 - - - +
61A ALA* 1.3 65.7 + - - +
63A THR* 3.2 3.6 + - - -
64A VAL* 3.0 45.6 + - + +
78A THR* 4.1 8.5 - - + -
79A GLY* 4.1 6.3 - - - -
82A GLY* 4.1 10.3 - - - -
83A VAL* 3.7 26.0 - - + -
232A MSE 4.8 2.0 - - + -
235A LEU* 4.0 17.3 - - + -
236A GLY* 3.6 29.2 - - - -
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Residues in contact with ALA 61 (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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57A PRO 2.9 17.2 + - - +
58A ARG* 3.3 5.1 + - - +
60A PHE* 1.3 80.9 - - - +
62A GLU* 1.3 57.5 + - - +
64A VAL* 3.4 3.0 + - - +
65A MSE 3.0 34.5 + - + +
235A LEU* 4.1 24.2 - - + -
239A ALA* 3.7 14.2 - - + +
292A ILE* 4.1 20.0 - - + -
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Residues in contact with GLU 62 (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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5A LEU* 4.0 16.0 - - + +
58A ARG* 2.8 60.3 + - - +
59A GLU* 4.1 6.8 - - - +
61A ALA* 1.3 75.7 - - - +
63A THR* 1.3 58.1 + - - +
65A MSE 3.5 8.4 + - - +
66A GLY* 2.9 24.3 + - - -
288A ARG* 4.0 18.1 + - - +
292A ILE* 3.7 16.8 - - + +
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Residues in contact with THR 63 (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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4A VAL* 3.8 28.3 - - + -
5A LEU* 4.2 32.4 + - + +
8A ILE* 4.8 1.1 - - + -
41A ALA* 5.1 1.8 - - + -
44A LEU* 3.8 18.5 - - + +
59A GLU* 2.6 33.3 + - - +
60A PHE 3.7 2.9 - - - -
62A GLU* 1.3 75.5 - - - +
64A VAL* 1.3 60.1 + - - +
66A GLY* 3.1 1.9 + - - -
67A VAL* 2.9 43.8 + - + +
78A THR* 5.6 0.9 - - + -
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Residues in contact with VAL 64 (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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60A PHE* 3.0 47.2 + - + +
61A ALA 3.6 6.5 - - - +
63A THR* 1.3 76.5 - - - +
65A MSE 1.3 52.4 + - - +
67A VAL* 3.1 8.3 + - - +
68A ALA* 2.7 36.2 + - - +
75A GLY* 3.6 18.1 - - - +
78A THR* 4.1 9.2 - - + -
79A GLY* 3.9 11.4 - - - +
236A GLY* 3.5 11.4 - - - +
239A ALA* 3.9 4.0 - - + -
240A ALA* 3.5 28.3 - - - +
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Residues in contact with MSE 65 (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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61A ALA* 3.0 18.9 + - + +
62A GLU* 3.7 6.5 - - - +
64A VAL* 1.3 74.9 - - - +
66A GLY* 1.3 60.8 + - - +
68A ALA* 4.3 0.2 - - - -
69A ALA* 3.1 22.9 + - - +
239A ALA* 3.3 25.6 - - + +
242A ILE* 4.2 8.7 - - + -
243A GLY* 3.5 22.8 - - - +
246A GLU* 4.6 0.7 - - - +
288A ARG* 3.5 62.6 - - - +
291A LEU* 3.9 23.6 - - + -
292A ILE* 3.8 29.2 - - + -
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Residues in contact with GLY 66 (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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5A LEU* 4.2 16.6 - - - -
8A ILE* 4.9 2.0 - - - +
62A GLU 2.9 15.8 + - - -
63A THR 3.1 4.2 + - - -
65A MSE 1.3 77.7 - - - +
67A VAL* 1.3 60.7 + - - +
69A ALA* 3.5 10.8 + - - +
70A LEU* 3.6 17.5 + - - +
288A ARG* 5.1 2.2 - - - +
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Residues in contact with VAL 67 (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 36.3 - - + +
15A ILE* 5.3 6.3 - - + -
36A LEU* 3.8 13.5 - - + -
41A ALA* 5.2 1.6 - - + -
63A THR* 2.9 25.6 + - + +
64A VAL* 3.7 6.3 - - - +
66A GLY* 1.3 74.6 - - - +
68A ALA* 1.3 59.0 + - - +
70A LEU* 2.9 22.6 + - - +
71A ASP* 3.1 11.4 + - - +
74A SER* 3.7 17.5 - - - +
75A GLY* 3.6 22.9 - - - +
78A THR* 4.0 12.1 - - + +
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Residues in contact with ALA 68 (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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64A VAL 2.7 20.4 + - - +
65A MSE 3.8 3.4 - - - +
67A VAL* 1.3 73.1 - - - +
69A ALA* 1.3 60.5 + - - +
70A LEU 3.4 0.3 + - - -
71A ASP 3.8 2.5 - - - -
72A GLY* 3.5 11.9 + - - -
75A GLY* 3.5 19.0 - - - -
240A ALA* 3.4 31.9 - - - +
243A GLY* 3.8 4.0 - - - -
244A ILE* 3.7 13.2 - - + +
352A PHE* 3.4 16.1 - - - -
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Residues in contact with ALA 69 (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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65A MSE 3.1 15.2 + - - +
66A GLY* 3.9 7.4 - - - +
67A VAL 3.2 0.2 - - - -
68A ALA* 1.3 76.7 - - - +
70A LEU* 1.3 63.5 + - + +
243A GLY 3.3 17.7 + - - +
246A GLU* 4.5 7.4 - - + +
247A GLY* 3.7 18.4 - - - +
250A ALA* 6.4 0.4 - - + -
352A PHE* 3.4 15.1 - - - -
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Residues in contact with LEU 70 (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* 3.7 30.5 - - + -
9A GLU* 5.6 0.7 - - - -
12A ALA* 3.8 27.1 - - + +
15A ILE* 3.9 20.4 - - + -
16A ARG* 3.5 54.7 - - + +
19A ALA* 5.1 1.9 - - - +
66A GLY 3.6 10.8 - - - +
67A VAL* 2.9 9.1 + - - +
69A ALA* 1.3 81.9 - - + +
71A ASP* 1.3 60.6 + - - +
352A PHE* 3.6 11.2 - - - -
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Residues in contact with ASP 71 (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* 3.9 16.1 - - + +
19A ALA* 3.3 36.7 - - + +
22A SER* 5.2 2.6 + - - -
28A LEU* 4.2 4.3 - - - +
32A ALA* 5.5 1.6 - - - +
67A VAL 3.1 8.4 + - - +
68A ALA 3.5 2.2 + - - +
70A LEU* 1.3 79.6 - - - +
72A GLY* 1.3 67.9 + - - +
73A ALA* 3.8 12.7 + - - +
74A SER* 2.6 35.1 + - - +
75A GLY 3.0 18.0 + - - -
351A ARG* 4.7 8.3 - - - -
352A PHE* 4.3 4.0 - - - -
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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