Contacts of the helix formed by residues 65 - 74 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ASP* 3.3 22.0 + - - +
46B LYS* 3.6 17.8 + - - +
47B GLN* 4.2 3.6 - - - +
48B GLN* 4.1 1.6 - - - -
63B THR* 4.8 1.0 - - + +
64B ARG* 1.3 71.9 - - - +
66B VAL* 1.3 67.8 + - - +
67B LEU* 2.8 32.9 + - - +
68B ILE* 2.9 33.7 + - + +
69B GLU* 2.9 27.3 + - - +
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B SER* 3.5 23.8 - - - +
13B GLY* 3.9 2.3 - - - +
43B ALA* 4.1 3.4 - - + -
44B PRO* 3.4 36.6 - - + +
46B LYS* 2.9 26.3 + - + +
47B GLN 4.3 1.3 - - - +
48B GLN* 3.3 32.1 - - + +
64B ARG 3.8 0.8 + - - -
65B ASN* 1.3 69.3 - - - +
67B LEU* 1.3 56.6 + - - +
69B GLU* 3.8 1.0 - - - +
70B ALA* 2.8 32.6 + - - +
103B ASN* 3.7 23.1 - - + +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 4.0 23.3 - - + -
43B ALA* 3.8 20.0 - - + +
44B PRO 3.4 11.9 + - - +
45B ASP* 3.8 23.6 - - + +
65B ASN* 2.8 14.2 + - - +
66B VAL* 1.3 77.2 - - - +
68B ILE* 1.3 65.0 + - + +
70B ALA* 3.3 0.7 + - - +
71B ALA* 3.0 21.8 + - - +
78B ILE* 4.1 16.8 - - + +
79B ARG* 3.7 26.0 - - - +
80B PRO* 3.6 28.3 - - + -
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Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASN* 3.2 45.8 - - - +
54A HIS* 4.6 4.2 + - - +
55A LEU* 4.3 16.8 - - + -
60A MSE 4.2 19.7 - - + -
65B ASN* 2.9 38.7 + - + +
67B LEU* 1.3 76.8 - - + +
69B GLU* 1.3 76.7 + - - +
71B ALA* 3.2 19.6 - - - +
72B ARG* 4.0 7.2 - - - +
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A MSE 5.1 1.2 - - - +
64A ARG* 2.8 46.3 + - - -
72A ARG* 5.4 2.7 + - - +
14B CYS* 3.5 22.1 - - + +
48B GLN* 3.4 23.6 - - - +
64B ARG* 3.6 20.3 + - + +
65B ASN 2.9 20.9 + - - +
66B VAL 4.0 0.9 - - - +
68B ILE* 1.3 86.7 - - - +
70B ALA* 1.3 66.2 + - - +
71B ALA 3.0 2.0 - - - -
72B ARG* 2.8 40.2 + - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.7 25.7 - - + +
13B GLY 3.7 16.9 - - - +
14B CYS* 4.7 0.4 - - - -
43B ALA* 3.8 6.7 - - + -
66B VAL 2.8 22.9 + - - +
67B LEU 3.8 1.1 - - - +
69B GLU* 1.3 73.1 - - - +
71B ALA* 1.3 60.9 + - - +
73B ILE* 3.0 22.7 + - - +
74B THR* 3.6 5.0 + - - -
78B ILE* 3.6 21.8 - - + -
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A HIS* 3.8 6.1 - - - +
55A LEU* 3.9 26.9 - - + +
67B LEU 3.0 12.2 + - - +
68B ILE 3.2 16.2 - - - +
69B GLU 3.0 0.4 - - - -
70B ALA* 1.3 77.1 - - - +
72B ARG* 1.3 59.6 + - - +
73B ILE 3.3 0.2 - - - -
74B THR* 3.3 10.4 + - - -
75B ARG* 3.1 3.3 + - - -
76B GLY* 2.8 27.1 + - - -
78B ILE* 3.6 18.3 - - + +
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A CYS* 2.7 36.0 + - - +
15A GLY* 4.4 2.5 - - - -
16A VAL* 4.5 9.9 - - - +
18A ASP* 2.5 47.5 + - - +
21A GLU* 5.6 0.5 - - - +
22A ILE* 3.8 17.9 - - + +
48A GLN* 4.9 2.6 + - - +
51A VAL* 4.8 1.4 - - - +
52A ILE 3.9 4.8 + - - -
54A HIS* 3.4 32.8 + - + -
60A MSE 5.7 1.2 - - - -
64A ARG* 2.9 31.9 - - - +
69A GLU* 5.5 2.1 + - - +
14B CYS* 4.1 9.0 - - - -
68B ILE* 4.0 3.9 - - - +
69B GLU* 2.8 41.8 + - - +
71B ALA* 1.3 78.1 - - - +
73B ILE* 1.3 63.2 + - - +
74B THR 3.3 0.5 + - - -
75B ARG* 3.4 9.9 + - - +
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Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 4.0 12.3 - - + -
23A HIS* 2.8 29.6 + - - -
11B LEU* 4.2 12.6 - - + -
13B GLY 3.6 22.7 - - - +
14B CYS* 3.7 23.6 - - + -
20B SER* 4.1 9.9 - - - -
22B ILE* 4.3 12.3 - - + -
25B ALA* 4.1 32.1 - - + -
26B VAL* 4.3 12.8 - - + -
29B LEU* 4.3 15.2 - - + +
70B ALA 3.0 10.2 + - - +
72B ARG* 1.3 76.7 - - - +
74B THR* 1.3 57.3 + - - +
75B ARG* 3.8 0.7 + - - +
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Residues in contact with THR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A HIS* 4.6 3.8 - - - -
11B LEU* 3.8 17.9 - - + -
29B LEU* 4.6 5.8 - - + -
41B CYS* 3.6 37.0 - - + -
70B ALA 4.3 0.2 - - - +
71B ALA* 3.3 11.8 + - - -
72B ARG 3.2 0.2 - - - -
73B ILE* 1.3 82.8 - - + +
75B ARG* 1.3 71.9 + - - +
77B GLU* 2.9 31.0 + - - +
78B ILE* 3.3 21.4 - - + +
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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