Contacts of the helix formed by residues 63 - 69 (chain A) in PDB entry 1OFV
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 GLN 63 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLY* 3.5 12.2 - - - -
9A THR 3.2 29.0 + - - +
10A GLN* 2.9 33.3 - - + +
54A CYS* 3.8 8.0 - - - -
55A PRO* 3.6 39.9 + - + +
57A TRP* 4.5 9.6 - - + -
62A LEU* 1.3 72.9 - - - +
64A SER* 1.3 68.3 + - - +
65A ASP* 2.9 41.4 + - - +
66A TRP* 3.1 15.4 + - - +
67A GLU* 3.0 17.5 + - - +
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Residues in contact with SER 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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10A GLN* 2.9 26.1 + - - +
62A LEU 3.6 2.7 + - - -
63A GLN* 1.3 75.3 + - - +
65A ASP* 1.3 69.3 + - - +
67A GLU* 3.2 9.1 + - - +
68A GLY* 3.0 18.9 + - - -
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Residues in contact with ASP 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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9A THR 4.4 4.5 + - - +
10A GLN* 4.8 0.3 + - - -
35A ASP* 4.6 2.4 - - - +
36A ILE* 3.6 24.1 - - + +
37A ALA* 3.7 30.7 - - - +
63A GLN* 2.9 30.8 + - - +
64A SER* 1.3 78.7 + - - +
66A TRP* 1.3 61.9 + - - +
68A GLY* 3.3 9.2 + - - -
69A ILE* 3.4 15.4 + - - +
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Residues in contact with TRP 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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6A PHE* 3.6 22.7 - - + -
7A TYR 3.7 0.4 - - - -
8A GLY* 3.4 14.1 - - - +
36A ILE* 3.6 30.5 - - + +
44A LEU* 4.8 4.0 - - + -
52A ILE* 3.8 30.1 - - + -
53A GLY 3.0 18.6 + - - -
54A CYS* 3.4 31.6 - - + +
62A LEU* 4.3 9.3 - - + +
63A GLN* 3.1 21.4 + - - +
65A ASP* 1.3 76.7 - - - +
67A GLU* 1.3 56.9 + - - +
69A ILE* 3.3 31.7 + - + +
70A TYR* 2.9 31.2 + - - +
73A LEU* 4.4 16.6 - - + -
105A LEU* 3.7 27.4 - - + -
109A ILE* 5.2 2.2 - - + -
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Residues in contact with GLU 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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61A GLU* 4.4 9.8 - - - +
62A LEU* 3.6 37.6 + - + +
63A GLN 3.0 12.3 + - - +
64A SER* 3.2 13.7 + - - +
66A TRP* 1.3 77.3 - - - +
68A GLY* 1.3 63.9 + - - +
70A TYR* 3.4 17.9 + - - +
71A ASP* 4.7 1.4 + - - -
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Residues in contact with GLY 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 SER 3.0 13.5 + - - -
65A ASP* 3.3 5.6 + - - -
66A TRP 3.1 0.6 - - - -
67A GLU* 1.3 79.5 - - - +
69A ILE* 1.3 57.1 + - - +
71A ASP* 4.9 2.9 + - - +
72A ASP* 4.6 5.4 - - - +
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Residues in contact with ILE 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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36A ILE* 3.8 26.2 - - + +
39A ALA 4.2 9.2 - - - +
40A ASP* 3.8 6.1 - - - -
41A ALA* 3.4 41.7 - - + +
65A ASP 3.4 10.9 + - - +
66A TRP* 3.4 38.8 - - + +
68A GLY* 1.3 74.4 - - - +
70A TYR* 1.3 68.8 + - - +
71A ASP 3.2 2.9 - - - -
72A ASP* 2.8 27.3 + - - +
73A LEU* 3.3 11.1 + - + +
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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