Contacts of the helix formed by residues 56 - 72 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL* 4.0 26.4 - - + +
19D ASP* 6.0 0.7 - - - +
35D TYR* 5.2 2.2 - - + -
52D SER* 2.7 24.5 + - - -
53D TYR* 2.4 41.5 + - + +
54D PRO 4.4 3.1 - - - +
55D GLY* 1.3 81.0 - - - +
57D PHE* 1.3 65.2 + - - +
58D ASP 3.4 2.5 - - - -
59D GLU* 3.4 10.6 + - - +
60D LEU* 3.3 18.5 + - - +
91D VAL* 3.7 0.8 - - - +
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Residues in contact with PHE 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D GLY 3.5 3.0 - - - -
56D THR* 1.3 78.2 - - - +
58D ASP* 1.3 68.2 + - - +
60D LEU* 3.3 3.3 + - + +
61D MET* 2.9 75.0 + - + +
91D VAL* 3.6 24.6 - - + +
94D GLU* 3.3 75.8 - - + +
95D LEU* 4.1 7.2 - - + -
98D ARG* 4.1 18.8 - - + -
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Residues in contact with ASP 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 4.0 18.1 - - + +
55D GLY 5.1 2.9 + - - +
56D THR 3.4 1.2 - - - -
57D PHE* 1.3 85.8 - - - +
59D GLU* 1.3 56.9 + - - +
61D MET* 3.9 4.9 - - - +
62D ALA* 3.1 29.5 + - - +
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A HIS* 5.3 8.5 - - - +
279A GLU* 4.4 2.2 - - - +
1D MET* 3.7 31.8 - - + +
3D ALA* 4.2 0.8 - - + +
16D GLY 4.3 0.2 - - - +
17D VAL* 3.5 22.9 - - + +
18D LEU* 3.2 25.6 + - - +
56D THR* 3.4 11.9 + - - +
57D PHE 3.3 0.8 - - - -
58D ASP* 1.3 75.8 - - - +
60D LEU* 1.3 64.9 + - - +
62D ALA* 3.4 4.5 + - - +
63D ARG* 2.8 57.7 + - - +
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Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D THR 3.5 23.1 - - - +
16D GLY* 4.6 5.2 - - - -
17D VAL* 4.6 4.7 - - + +
37D ALA* 3.9 10.3 - - + -
48D LEU* 4.3 3.8 - - + -
50D ASP 4.7 0.7 - - - +
51D ASN* 3.7 33.4 - - + -
52D SER* 3.9 14.8 - - - +
56D THR 3.3 8.9 + - - +
57D PHE* 3.3 12.4 + - + +
59D GLU* 1.3 76.0 - - - +
61D MET* 1.3 77.5 + - + +
63D ARG* 3.1 4.9 + - - +
64D VAL* 2.8 47.8 + - + +
91D VAL* 4.6 1.3 - - + -
95D LEU* 4.1 16.6 - - + -
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Residues in contact with MET 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D PHE* 2.9 53.3 + - + +
58D ASP* 3.9 4.5 - - - +
60D LEU* 1.3 82.0 - - + +
62D ALA* 1.3 57.3 + - - +
64D VAL* 3.3 24.6 + - + -
65D GLU* 2.8 42.0 + - - +
95D LEU* 3.5 22.4 - - + -
98D ARG* 3.6 39.9 - - - +
99D PHE* 3.9 16.8 - - + -
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.6 33.0 - - + +
3D ALA* 3.2 24.1 - - + +
58D ASP 3.1 19.4 + - - +
59D GLU* 3.6 6.3 - - - +
61D MET* 1.3 75.6 - - - +
63D ARG* 1.3 58.1 + - - +
65D GLU* 3.6 11.6 + - - +
66D ASP* 3.1 22.7 + - - +
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Residues in contact with ARG 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLU* 2.9 37.8 + - - -
282A MET* 5.5 4.4 - - - +
3D ALA* 3.7 17.9 - - + +
4D ALA 3.0 26.7 + - - +
5D ALA* 3.4 12.3 - - - +
14D TRP* 3.3 33.9 - - - -
15D THR* 3.7 16.6 - - + +
16D GLY 2.7 28.4 + - - +
18D LEU* 4.1 5.3 - - - +
59D GLU* 2.8 38.2 + - - +
60D LEU 3.1 9.4 + - - +
62D ALA* 1.3 73.1 - - - +
64D VAL* 1.3 63.8 + - - +
66D ASP* 3.3 1.6 + - - +
67D ALA* 3.0 19.6 + - - +
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Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D THR* 3.4 28.3 - - + +
39D LEU* 4.3 11.6 - - + +
48D LEU* 4.4 12.3 - - + -
60D LEU* 2.8 41.6 + - + +
61D MET* 3.7 29.4 - - + -
63D ARG* 1.3 71.3 - - - +
65D GLU* 1.3 56.0 + - - +
67D ALA* 3.5 2.6 - - - +
68D LEU* 2.8 46.2 + - + +
76D VAL* 4.6 7.0 - - + -
99D PHE* 4.5 11.2 - - + -
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D MET* 2.8 31.9 + - - +
62D ALA* 3.8 10.1 + - - +
64D VAL* 1.3 75.0 - - + +
66D ASP* 1.3 63.1 + - - +
68D LEU* 3.5 14.2 + - + +
69D GLN* 3.2 20.6 + - - +
98D ARG* 2.8 32.1 + - - +
99D PHE* 6.3 0.4 - - + -
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Residues in contact with ASP 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ALA 4.0 4.9 - - - +
4D ALA* 3.5 12.5 - - - +
5D ALA* 2.7 27.3 + - - +
62D ALA 3.1 18.7 + - - +
63D ARG 3.3 4.5 + - - +
65D GLU* 1.3 73.1 - - - +
67D ALA* 1.3 55.8 + - - +
69D GLN* 2.8 48.1 + - - +
70D GLN* 2.9 31.6 + - - +
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Residues in contact with ALA 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ALA* 3.6 16.4 - - + +
13D TYR* 4.0 17.5 - - + -
15D THR* 3.8 13.7 - - + -
39D LEU* 3.8 14.1 - - + -
63D ARG 3.0 14.8 + - - +
64D VAL 3.5 4.7 - - - +
66D ASP* 1.3 80.3 + - - +
68D LEU* 1.3 55.2 + - - +
70D GLN* 3.4 3.5 + - - +
71D VAL* 2.6 37.8 + - - +
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Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 3.7 22.0 - - + -
46D VAL* 4.4 4.7 - - + -
64D VAL* 2.8 38.6 + - + +
65D GLU* 3.7 14.1 - - + +
66D ASP 3.2 0.4 - - - -
67D ALA* 1.3 72.7 - - - +
69D GLN* 1.3 57.2 + - - +
71D VAL* 4.2 2.0 - - - -
72D GLY* 3.0 23.6 + - - -
73D MET* 3.2 35.3 + - + +
74D GLU* 4.1 5.8 - - - +
75D ARG* 3.9 44.6 - - - +
76D VAL* 4.6 2.7 - - + +
99D PHE* 4.7 8.1 - - + -
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Residues in contact with GLN 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D GLU 3.2 12.4 + - - +
66D ASP* 2.8 37.8 + - - +
68D LEU* 1.3 71.3 - - - +
70D GLN* 1.3 76.9 + - - +
72D GLY* 3.6 9.2 + - - -
73D MET 5.2 0.2 - - - -
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Residues in contact with GLN 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ALA* 4.0 10.9 - - - +
7D ARG* 4.3 18.2 + - - +
13D TYR* 3.0 37.1 + - + +
66D ASP* 2.9 32.7 + - - +
67D ALA 3.5 8.1 - - - +
69D GLN* 1.3 94.0 - - - +
71D VAL* 1.3 60.9 + - - +
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Residues in contact with VAL 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLY* 4.3 8.3 - - - +
13D TYR* 3.5 33.0 - - + +
41D CYS* 3.6 36.1 - - + +
67D ALA 2.6 28.7 + - - +
68D LEU* 4.4 2.9 - - - +
70D GLN* 1.3 74.3 - - - +
72D GLY* 1.3 59.0 - - - +
73D MET* 3.6 17.3 - - + +
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Residues in contact with GLY 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU 3.0 8.9 + - - -
69D GLN* 3.6 6.5 + - - -
70D GLN 3.4 2.8 - - - -
71D VAL* 1.3 78.8 - - - +
73D MET* 1.3 65.8 + - - +
74D GLU* 5.0 5.9 - - - +
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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