Contacts of the helix formed by residues 43 - 51 (chain B) in PDB entry 1OH7
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 ASP 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B TYR* 3.7 3.1 + - - +
21B LYS* 3.4 31.8 + - - +
25B PRO 5.0 4.3 - - - +
27B ILE 3.8 3.8 - - - +
28B LEU* 3.6 27.2 + - + +
29B LEU* 3.0 20.6 + - - +
39B LEU* 3.6 24.5 - - + +
40B PHE 3.1 6.0 + - - +
41B TYR 3.0 5.5 + - - -
42B ASP* 1.3 79.0 - - - +
44B ALA* 1.3 60.5 + - - +
45B LYS 3.3 0.2 - - - -
46B ARG* 3.5 5.0 - - - +
47B ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 44 (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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39B LEU* 3.4 20.8 - - - +
40B PHE 2.9 10.2 + - - +
42B ASP 4.7 0.9 - - - +
43B ASP* 1.3 77.6 - - - +
45B LYS* 1.3 58.5 + - - +
47B ALA* 4.0 1.9 - - - +
48B SER* 2.6 34.7 + - - -
55B LEU* 4.8 2.3 - - + +
67B PRO* 3.0 30.3 - - + +
68B MET 3.5 13.8 - - - +
69B ALA* 3.9 6.2 - - + +
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Residues in contact with LYS 45 (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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42B ASP* 3.7 35.1 - - - +
43B ASP 3.3 0.4 - - - -
44B ALA* 1.3 80.5 - - + +
46B ARG* 1.3 63.8 + - - +
47B ALA 3.1 0.3 + - - -
48B SER* 3.3 12.9 + - - -
49B GLN* 3.4 14.4 + - - +
55B LEU* 4.8 24.3 - - + +
67B PRO* 4.7 21.1 - - + -
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Residues in contact with ARG 46 (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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28B LEU* 4.3 13.5 - - + -
42B ASP* 4.2 13.5 - - - +
43B ASP 3.5 9.2 - - - +
45B LYS* 1.3 80.3 - - + +
47B ALA* 1.3 56.2 + - - +
49B GLN* 3.4 34.4 - - - +
50B LEU* 3.1 52.1 + - + +
88B GLU* 3.9 30.3 + - - -
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Residues in contact with ALA 47 (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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28B LEU* 5.2 4.5 - - + -
39B LEU* 4.1 25.8 - - + -
43B ASP 2.9 21.7 + - - +
44B ALA* 4.0 7.2 - - - +
45B LYS 3.1 0.8 + - - -
46B ARG* 1.3 72.4 - - - +
48B SER* 1.3 60.8 + - - +
50B LEU* 3.6 3.8 + - - -
51B LEU* 3.2 45.9 + - + +
53B ILE* 4.2 5.2 - - + +
69B ALA* 4.8 5.4 - - + -
83B LEU* 5.1 2.5 - - + -
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Residues in contact with SER 48 (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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44B ALA 2.6 24.3 + - - -
45B LYS 3.4 5.2 + - - -
47B ALA* 1.3 74.6 - - - +
49B GLN* 1.3 58.4 + - - +
52B ASP* 3.4 17.4 + - - -
53B ILE* 2.8 38.9 - - - +
54B SER 4.1 13.5 - - - -
55B LEU* 3.6 22.5 - - - +
69B ALA* 4.9 1.5 - - - +
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Residues in contact with GLN 49 (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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45B LYS 3.4 9.2 + - - +
46B ARG* 3.4 49.2 - - - +
47B ALA 3.2 0.2 - - - -
48B SER* 1.3 79.6 - - - +
50B LEU* 1.3 73.2 + - + +
51B LEU 3.4 1.0 + - - -
52B ASP* 4.4 4.2 + - - +
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Residues in contact with LEU 50 (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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28B LEU* 5.0 2.2 - - + -
46B ARG* 3.1 44.9 + - + +
47B ALA 4.3 0.9 - - - +
49B GLN* 1.3 86.6 - - + +
51B LEU* 1.3 62.6 + - - +
82B LYS* 5.5 0.2 - - - +
83B LEU* 4.1 19.7 - - + -
86B GLN* 3.0 49.3 + - + +
88B GLU* 4.0 33.4 - - + +
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Residues in contact with LEU 51 (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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30B PHE* 5.5 2.2 - - + -
39B LEU* 6.3 0.4 - - + -
47B ALA* 3.2 25.3 + - + +
50B LEU* 1.3 84.6 - - - +
52B ASP* 1.3 65.6 + - - +
53B ILE* 3.1 31.6 + - + +
71B ILE* 5.3 1.8 - - + -
79B TYR* 4.1 27.3 - - + +
82B LYS* 3.6 41.8 - - + +
83B LEU* 3.6 38.4 - - + -
86B GLN* 4.8 0.2 - - - +
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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