Contacts of the helix formed by residues 45 - 54 (chain B) in PDB entry 1OJ7
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 GLY 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B VAL 3.6 4.7 + - - -
42B LYS* 3.7 6.6 + - - -
43B LYS 3.5 2.8 - - - -
44B THR* 1.3 78.3 - - - +
46B VAL* 1.3 62.5 + - - +
47B LEU 3.3 2.2 - - - -
48B ASP* 3.3 17.8 + - - +
49B GLN* 3.2 29.1 + - - +
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Residues in contact with VAL 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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41B VAL* 3.4 7.8 + - + +
44B THR* 3.3 23.3 - - - +
45B GLY* 1.3 76.1 - - - +
47B LEU* 1.3 65.0 + - - +
49B GLN* 3.1 21.4 + - - +
50B VAL* 3.2 11.9 + - + +
92B VAL* 4.1 21.8 - - + -
136B VAL* 4.6 3.6 - - + -
138B THR* 4.5 11.2 - - + -
179B TYR* 3.7 55.9 - - + +
1388B NZQ 6.3 0.7 - - - +
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Residues in contact with LEU 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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34B ILE* 3.7 28.7 - - + -
36B TYR* 4.3 9.9 - - + -
41B VAL* 3.1 33.8 + - + +
42B LYS* 3.6 42.6 - - + +
46B VAL* 1.3 77.9 - - - +
48B ASP* 1.3 59.1 + - - +
50B VAL* 3.2 14.1 + - + +
51B LEU* 3.0 42.4 + - + +
61B GLU* 4.3 9.9 - - - +
92B VAL* 4.7 9.9 - - + -
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Residues in contact with ASP 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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41B VAL 4.9 0.2 + - - -
42B LYS* 5.3 7.0 - - - +
45B GLY* 3.3 18.2 + - - +
46B VAL 3.2 0.6 - - - -
47B LEU* 1.3 75.6 - - - +
49B GLN* 1.3 61.4 + - + +
51B LEU* 3.8 17.0 - - - +
52B ASP* 2.9 43.3 + - - +
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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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19B ILE* 3.8 22.7 - - + +
44B THR 5.4 2.2 + - - -
45B GLY 3.2 19.5 + - - +
46B VAL* 3.1 10.8 + - - +
48B ASP* 1.3 77.4 - - - +
50B VAL* 1.3 56.8 + - - +
52B ASP* 3.8 7.5 - - - +
53B ALA* 3.1 27.2 + - - +
179B TYR* 2.8 38.2 + - - +
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Residues in contact with VAL 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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19B ILE* 3.6 20.2 - - + -
22B LEU* 4.2 3.8 - - + -
34B ILE* 4.0 17.9 - - + -
46B VAL* 3.2 13.1 + - + +
47B LEU* 3.2 12.6 + - + +
49B GLN* 1.3 78.1 - - - +
51B LEU* 1.3 57.1 + - - +
53B ALA* 3.2 4.7 + - - +
54B LEU* 3.1 29.1 + - + +
90B LEU* 3.7 28.7 - - + -
92B VAL* 4.1 27.1 - - + -
136B VAL* 4.2 13.2 - - + -
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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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34B ILE* 3.6 28.3 - - + -
42B LYS* 5.8 1.1 - - - +
47B LEU* 3.0 33.8 + - + +
48B ASP* 3.4 19.7 + - - +
50B VAL* 1.3 73.0 - - - +
52B ASP* 1.3 62.8 + - - +
54B LEU* 3.4 5.7 + - - +
55B LYS* 3.0 27.7 + - - +
59B VAL* 4.0 15.7 - - + -
61B GLU* 3.9 24.9 - - - +
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Residues in contact with ASP 52 (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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23B ARG* 5.0 0.2 + - - -
48B ASP* 2.9 31.3 + - - +
49B GLN* 3.8 7.4 - - - +
51B LEU* 1.3 76.9 - - - +
53B ALA* 1.3 65.8 + - - +
55B LYS* 3.3 33.1 + - + +
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Residues in contact with ALA 53 (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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19B ILE* 4.4 17.5 - - + +
22B LEU* 4.1 22.2 - - + -
23B ARG* 2.9 34.2 + - + +
49B GLN 3.1 15.1 + - - +
50B VAL* 3.2 8.7 + - - +
52B ASP* 1.3 76.1 - - - +
54B LEU* 1.3 59.8 + - + +
55B LYS 3.4 0.2 - - - -
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Residues in contact with LEU 54 (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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22B LEU* 4.2 8.7 - - + -
23B ARG* 3.4 25.8 - - - +
26B ILE* 4.1 18.8 - - + -
32B VAL* 4.4 11.2 - - + -
34B ILE* 4.2 16.6 - - + -
50B VAL 3.1 16.8 + - - +
51B LEU* 3.4 7.4 + - - +
52B ASP 3.2 0.2 - - - -
53B ALA* 1.3 80.0 - - - +
55B LYS* 1.3 63.7 + - - +
56B GLY 3.3 0.3 + - - -
57B MET* 3.0 39.1 + - - +
59B VAL* 4.1 17.6 - - + +
90B LEU* 3.8 27.4 - - + -
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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