Contacts of the helix formed by residues 33 - 42 (chain A) in PDB entry 2OX6
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 SER 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLY* 4.6 0.2 - - - -
32A HIS* 1.3 75.7 - - - +
34A GLU* 1.3 64.9 + - - +
35A ALA* 3.5 10.6 + - - +
36A GLU* 2.9 48.3 + - - +
37A VAL* 3.1 15.1 + - - +
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Residues in contact with GLU 34 (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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23A ALA* 4.1 10.3 - - + +
24A ALA* 3.9 43.6 + - + +
27A GLY* 4.9 1.4 - - - -
32A HIS 4.0 0.4 + - - -
33A SER* 1.3 70.9 - - - +
35A ALA* 1.3 58.0 + - - +
37A VAL* 3.2 7.6 + - - +
38A LEU* 2.9 41.8 + - + +
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Residues in contact with ALA 35 (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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33A SER* 3.2 9.2 + - - +
34A GLU* 1.3 78.1 + - - +
36A GLU* 1.3 58.8 + - + +
38A LEU* 3.5 10.0 + - - +
39A ALA* 2.9 29.5 + - - +
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Residues in contact with GLU 36 (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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32A HIS* 3.3 9.9 - - + +
33A SER* 2.9 41.2 + - - +
35A ALA* 1.3 73.5 - - + +
37A VAL* 1.3 64.0 + - - +
39A ALA* 3.2 7.4 + - - +
40A TRP* 3.1 33.6 + - + +
45A THR* 4.4 1.0 + - - -
167A MG 2.5 29.7 - - - -
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Residues in contact with VAL 37 (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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23A ALA* 3.6 36.8 - - + +
26A VAL* 4.1 9.9 - - + -
27A GLY* 3.6 18.4 - - - +
32A HIS* 4.6 0.9 - - + -
33A SER 3.1 13.8 + - - +
34A GLU 3.2 6.3 + - - +
36A GLU* 1.3 78.1 - - - +
38A LEU* 1.3 63.2 + - - +
40A TRP* 3.3 34.7 + - + +
41A GLU* 3.0 47.4 + - - +
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Residues in contact with LEU 38 (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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16A ARG* 5.6 2.0 - - - +
23A ALA* 3.7 22.7 - - + -
34A GLU* 2.9 40.0 + - + +
35A ALA* 3.8 8.5 - - - +
37A VAL* 1.3 76.2 - - - +
39A ALA* 1.3 57.8 + - - +
41A GLU* 3.3 14.6 + - + +
42A ASN* 2.9 38.9 + - - +
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Residues in contact with ALA 39 (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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35A ALA 2.9 17.8 + - - +
36A GLU* 3.4 9.2 - - - +
37A VAL 3.2 0.2 - - - -
38A LEU* 1.3 76.4 - - - +
40A TRP* 1.3 61.4 + - - +
42A ASN 3.1 6.2 + - - -
44A GLU* 2.9 51.6 + - + +
45A THR* 3.9 17.5 - - + +
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Residues in contact with TRP 40 (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 ALA* 3.2 16.5 - - - +
12A MET* 3.4 44.6 + - + +
26A VAL* 4.0 12.3 - - + +
30A THR* 3.7 20.0 - - - -
32A HIS* 3.8 20.6 - + + -
36A GLU* 3.1 26.0 + - + -
37A VAL* 3.5 29.7 + - + +
39A ALA* 1.3 74.9 - - - +
41A GLU* 1.3 76.7 + - + +
43A ALA* 3.2 11.1 + - - -
45A THR* 3.3 29.3 + - - +
47A ALA* 3.7 17.9 - - + +
48A PRO* 3.7 28.0 - - + -
51A ALA* 3.8 11.4 - - + -
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Residues in contact with GLU 41 (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 ALA* 3.6 21.2 - - - +
10A ILE* 5.2 0.7 - - - +
12A MET 4.0 1.6 - - - +
13A SER* 3.2 33.7 + - - +
16A ARG* 2.6 53.8 + - - +
26A VAL* 5.6 0.3 - - - +
37A VAL* 3.0 31.6 + - - +
38A LEU* 3.6 14.8 - - + +
40A TRP* 1.3 89.5 + - + +
42A ASN* 1.3 61.4 + - - +
43A ALA 3.4 0.7 - - - -
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Residues in contact with ASN 42 (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 ALA* 4.3 0.4 - - - -
38A LEU* 2.9 24.4 + - - +
39A ALA 3.1 1.7 + - - +
41A GLU* 1.3 78.3 + - - +
43A ALA* 1.3 66.3 + - - +
44A GLU* 3.1 39.3 + - - +
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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