Contacts of the helix formed by residues 65 - 74 (chain C) in PDB entry 1OY1
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 ASN 65 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C ASP* 3.4 21.6 + - - +
46C LYS* 3.6 19.7 + - - +
47C GLN* 4.2 3.0 - - - +
48C GLN* 4.1 1.6 - - - -
63C THR* 4.8 1.3 - - + +
64C ARG* 1.3 72.8 - - - +
66C VAL* 1.3 67.9 + - - +
67C LEU* 2.8 33.3 + - - +
68C ILE* 2.9 33.8 + - + +
69C GLU* 2.9 26.6 + - - +
60D MSE 6.5 0.2 - - + -
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Residues in contact with VAL 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C SER* 3.5 24.5 - - - +
13C GLY* 3.9 1.7 - - - +
43C ALA* 4.1 3.4 - - + -
44C PRO* 3.4 34.3 - - + +
46C LYS* 2.9 26.2 + - + +
47C GLN 4.3 1.6 - - - +
48C GLN* 3.3 32.1 - - + +
64C ARG 3.8 1.0 + - - -
65C ASN* 1.3 69.7 - - - +
67C LEU* 1.3 57.5 + - - +
69C GLU* 3.8 1.2 - - - +
70C ALA* 2.8 29.1 + - - +
103C ASN* 3.8 23.6 - - + -
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ALA* 3.8 19.3 - - + +
44C PRO 3.4 11.2 + - - +
45C ASP* 3.8 23.3 - - + +
65C ASN* 2.8 14.1 + - - +
66C VAL* 1.3 76.0 - - - +
68C ILE* 1.3 64.5 + - + +
70C ALA* 3.3 0.9 + - - +
71C ALA* 3.1 22.3 + - - +
78C ILE* 4.0 16.2 - - + +
79C ARG* 3.7 26.9 - - - +
80C PRO* 3.6 28.7 - - + -
55D LEU* 3.8 24.2 - - + -
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Residues in contact with ILE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ASN* 2.9 39.3 + - + +
67C LEU* 1.3 76.9 - - + +
69C GLU* 1.3 76.4 + - - +
71C ALA* 3.2 17.1 - - - +
72C ARG* 4.0 7.1 - - - +
52D ILE 5.7 0.2 - - - +
53D ASN* 3.2 50.0 - - - +
54D HIS* 4.4 4.1 + - - +
55D LEU* 3.9 21.1 - - + -
56D THR* 5.4 0.4 - - - +
60D MSE 4.4 15.3 - - + -
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Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C CYS* 3.5 22.2 - - + +
48C GLN* 3.4 23.8 - - - +
64C ARG* 3.6 19.6 + - + +
65C ASN 2.9 22.4 + - - +
66C VAL 4.0 0.9 - - - +
68C ILE* 1.3 85.2 - - - +
70C ALA* 1.3 66.0 + - - +
71C ALA 3.0 2.0 - - - -
72C ARG* 2.8 41.3 + - - +
60D MSE 5.1 2.4 - - - +
64D ARG* 2.8 44.4 + - - -
72D ARG* 5.6 2.1 + - - +
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.7 25.6 - - + +
13C GLY 3.7 19.0 - - - +
14C CYS* 4.7 0.7 - - - -
43C ALA* 3.8 7.0 - - + -
66C VAL 2.8 22.2 + - - +
67C LEU 3.8 0.7 - - - +
69C GLU* 1.3 72.0 - - - +
71C ALA* 1.3 60.6 + - - +
73C ILE* 3.0 22.2 + - - +
74C THR* 3.6 5.0 + - - -
78C ILE* 3.6 22.0 - - + -
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Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C LEU 3.1 11.7 + - - +
68C ILE 3.2 16.2 - - - +
69C GLU 3.0 0.4 - - - -
70C ALA* 1.3 78.2 - - - +
72C ARG* 1.3 60.2 + - - +
74C THR* 3.3 9.7 + - - -
75C ARG* 3.0 3.6 + - - -
76C GLY* 2.8 28.0 + - - -
78C ILE* 3.6 18.8 - - + +
54D HIS* 4.0 24.6 - - - +
55D LEU* 4.0 7.0 - - + +
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Residues in contact with ARG 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C CYS* 4.0 9.9 - - - -
68C ILE* 4.0 4.1 - - - +
69C GLU* 2.8 42.2 + - - +
71C ALA* 1.3 78.3 - - - +
73C ILE* 1.3 61.7 + - - +
74C THR 3.3 0.3 + - - -
75C ARG* 3.5 9.9 + - - +
14D CYS* 2.7 30.6 + - - +
15D GLY* 4.3 2.5 - - - -
16D VAL* 4.4 9.9 - - - +
18D ASP* 2.5 47.6 + - - +
21D GLU* 5.4 0.3 - - - +
22D ILE* 3.7 25.0 - - + +
48D GLN* 5.0 2.2 + - - +
51D VAL* 4.9 1.4 - - - +
52D ILE 3.7 4.6 + - - -
54D HIS* 3.2 37.2 + - + +
60D MSE 5.7 1.0 - - - -
64D ARG* 3.1 29.0 - - - +
69D GLU* 5.6 1.9 + - - +
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Residues in contact with ILE 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 4.2 13.7 - - + -
13C GLY 3.6 22.7 - - - +
14C CYS* 3.7 23.8 - - + -
20C SER* 4.2 9.2 - - - -
22C ILE* 4.3 12.6 - - + -
25C ALA* 4.0 32.3 - - + -
26C VAL* 4.2 13.0 - - + -
29C LEU* 4.2 14.5 - - + +
70C ALA 3.0 8.9 + - - +
72C ARG* 1.3 79.1 - - - +
74C THR* 1.3 51.3 + - - +
22D ILE* 4.0 12.1 - - + -
23D HIS* 2.6 35.7 + - - -
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Residues in contact with THR 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.7 18.4 - - + -
29C LEU* 4.6 5.2 - - + -
41C CYS* 3.6 37.5 - - + -
70C ALA 4.2 0.4 - - - +
71C ALA* 3.3 11.3 + - - -
72C ARG 3.2 0.2 - - - -
73C ILE* 1.3 82.8 - - + +
75C ARG* 1.3 71.9 + - - +
77C GLU* 2.9 32.4 + - - +
78C ILE* 3.3 21.5 - - + +
23D HIS* 4.3 5.2 - - - -
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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