Contacts of the helix formed by residues 46 - 58 (chain B) in PDB entry 3OX4
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 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B MET 3.5 0.4 + - - -
43B ASN 3.2 11.0 + - - -
44B LYS 2.9 7.7 - - - -
45B SER* 1.3 79.5 - - - +
47B VAL* 1.3 64.6 + - - +
48B VAL 3.3 1.8 - - - -
49B LYS* 3.4 13.3 + - - +
50B GLN* 3.1 21.9 + - - +
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Residues in contact with VAL 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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41B PHE* 5.2 1.3 - - + -
42B MET* 2.9 28.1 + - + +
45B SER* 3.5 20.0 - - - +
46B GLY* 1.3 75.0 - - - +
48B VAL* 1.3 65.5 + - - +
50B GLN* 3.1 18.0 + - + +
51B VAL* 3.0 23.5 + - + +
95B LEU* 3.7 29.4 - - + -
138B THR* 5.2 0.4 - - + -
179B LEU* 4.4 23.1 - - + +
346C LYS* 5.9 1.1 - - - +
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 4.3 8.7 - - + +
38B SER* 3.7 26.9 - - - +
42B MET 3.1 4.8 + - - +
43B ASN* 3.5 45.3 - - + +
47B VAL* 1.3 76.8 - - - +
49B LYS* 1.3 51.9 + - - +
51B VAL* 3.3 3.1 + - - +
52B ALA* 2.7 33.8 + - + +
64B VAL* 3.6 35.7 - - + -
95B LEU* 3.8 12.8 - - + -
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Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASN 5.3 1.3 + - - +
46B GLY* 3.4 17.0 + - - +
47B VAL 3.2 0.4 - - - -
48B VAL* 1.3 76.7 - - - +
50B GLN* 1.3 58.2 + - - +
52B ALA* 3.1 7.4 + - + +
53B ASP* 2.7 83.5 + - - +
56B LYS* 5.8 1.2 - - - +
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Residues in contact with GLN 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 LEU* 3.7 25.2 - - + +
20B GLU* 6.3 0.2 - - - -
46B GLY 3.1 9.9 + - - +
47B VAL* 3.1 23.4 - - - +
49B LYS* 1.3 81.9 - - - +
51B VAL* 1.3 64.8 + - + +
53B ASP* 3.1 8.1 + - - +
54B LEU* 3.0 32.8 + - + +
178B LEU* 6.1 0.2 - - - +
179B LEU* 3.9 17.0 - - - +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.4 16.8 - - + -
23B ILE* 4.6 9.2 - - + -
36B ILE* 4.1 16.6 - - + -
47B VAL* 3.0 14.9 + - + +
48B VAL 3.7 6.3 - - - +
50B GLN* 1.3 78.7 - - + +
52B ALA* 1.3 65.0 + - - +
54B LEU* 3.2 9.7 + - - +
55B LEU* 3.0 31.3 + - + +
93B ILE* 4.7 7.0 - - + -
95B LEU* 3.7 24.7 - - + -
136B ILE* 4.2 26.2 - - + -
179B LEU* 5.5 0.2 - - + -
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 4.2 8.7 - - + +
48B VAL* 2.7 24.5 + - + +
49B LYS* 3.4 10.8 - - + +
51B VAL* 1.3 72.3 - - - +
53B ASP* 1.3 61.4 + - - +
55B LEU* 3.2 7.1 + - - +
56B LYS* 3.0 34.2 + - + +
62B SER* 3.8 22.3 + - - +
64B VAL* 5.6 3.1 - - + -
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Residues in contact with ASP 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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49B LYS* 2.7 65.3 + - - +
50B GLN* 3.5 7.2 + - - +
52B ALA* 1.3 70.9 - - - +
54B LEU* 1.3 65.9 + - + +
56B LYS* 2.9 34.9 + - + +
57B ALA* 3.0 14.0 + - - +
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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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19B LEU* 3.8 35.7 - - + -
20B GLU* 4.5 24.7 - - + -
23B ILE* 3.4 30.4 - - + +
24B LYS* 5.7 4.3 - - - +
50B GLN* 3.0 25.7 + - + +
51B VAL* 3.7 7.6 - - - +
53B ASP* 1.3 76.8 - - + +
55B LEU* 1.3 63.6 + - - +
57B ALA* 3.4 17.2 + - + +
58B GLN* 3.6 9.0 + - - +
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Residues in contact with LEU 55 (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 ILE* 3.4 38.6 - - + -
26B LEU* 4.0 15.5 - - + -
34B ALA* 4.1 5.4 - - + -
36B ILE* 4.2 9.9 - - + -
51B VAL* 3.0 15.7 + - + +
52B ALA 3.2 8.5 - - - +
54B LEU* 1.3 78.2 - - - +
56B LYS* 1.3 57.4 + - - +
58B GLN* 2.9 19.5 + - - +
59B GLY 3.3 0.2 + - - -
60B ILE* 3.0 44.6 + - + +
62B SER* 4.0 23.8 - - - +
93B ILE* 3.7 23.6 - - + -
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Residues in contact with LYS 56 (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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49B LYS* 5.8 0.9 - - - +
52B ALA* 3.0 20.6 + - + +
53B ASP* 2.9 31.8 + - - +
55B LEU* 1.3 71.2 - - - +
57B ALA* 1.3 55.5 + - - +
58B GLN 2.8 4.5 - - - -
59B GLY* 2.6 26.3 + - - +
60B ILE 3.8 11.9 - - - +
61B ASN* 6.0 3.4 - - - +
62B SER* 5.7 2.0 - - - +
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ASP 3.0 11.3 + - - +
54B LEU* 3.6 17.5 - - + +
55B LEU 3.3 0.2 - - - -
56B LYS* 1.3 74.4 - - - +
58B GLN* 1.3 69.9 + - - +
59B GLY 3.4 1.2 + - - -
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Residues in contact with GLN 58 (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 ILE* 3.8 21.5 - - + +
24B LYS* 3.8 29.5 + - - +
27B ASN* 3.3 40.2 + - + +
54B LEU 3.6 14.1 - - - +
55B LEU 2.9 8.3 + - - +
56B LYS 2.8 1.0 - - - -
57B ALA* 1.3 89.3 + - - +
59B GLY* 1.3 61.3 - - - +
60B ILE* 3.3 21.1 + - + +
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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