Contacts of the helix formed by residues 270 - 275 (chain B) in PDB entry 2OQH
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 270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B TYR* 4.3 4.5 + - - -
246B ASN* 6.3 0.2 - - + -
268B HIS 4.9 0.4 - - - +
269B GLY* 1.3 74.7 - - - +
271B VAL* 1.3 60.1 + - - +
272B TYR* 2.9 27.6 + - - +
273B LYS* 3.0 27.3 + - + +
274B TRP* 2.8 36.2 + - + +
280B THR* 4.1 6.5 + - - -
296B LEU* 4.2 2.0 - - - +
297B HIS* 3.0 42.8 + - + +
299B GLY* 4.6 0.9 + - - -
301B GLU* 4.3 5.9 - - - +
309B HIS* 3.7 9.1 + - - -
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Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 3.3 4.5 - - + +
102B VAL* 4.1 14.4 - - + -
270B ASP* 1.3 72.3 + - - +
272B TYR* 1.3 78.1 + - + +
274B TRP* 5.0 0.2 - - - -
275B GLY 2.9 24.8 + - - -
276B GLY* 3.0 34.1 + - - +
277B ILE* 4.0 13.7 - - + +
280B THR* 3.4 26.1 + - + +
308B ALA* 5.4 1.6 - - + +
309B HIS* 3.2 28.4 - - + +
312B VAL* 4.3 9.0 - - + -
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Residues in contact with TYR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 5.8 0.9 - - - -
49B GLU 3.4 20.6 - - - -
50B THR* 4.0 19.7 - - - +
51B MSE 5.4 4.7 - - + +
91B TYR* 3.8 7.8 - - + +
94B TYR 3.6 0.2 - - - -
95B ALA* 3.2 31.5 + - + +
98B ALA* 3.6 17.7 - - + -
102B VAL* 3.9 21.3 - - + +
270B ASP* 2.9 14.6 + - - +
271B VAL* 1.3 82.6 - - + +
273B LYS* 1.3 57.6 + - - +
275B GLY 4.3 0.7 - - - -
301B GLU* 3.7 35.0 - - + +
305B ALA* 2.8 34.4 + - + -
308B ALA* 3.4 15.9 - - - +
309B HIS* 3.7 17.2 + + - -
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Residues in contact with LYS 273 (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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91B TYR* 3.8 45.2 + - + -
94B TYR* 3.1 26.2 - - - +
246B ASN* 3.2 39.3 + - + +
250B VAL* 3.9 27.8 - - + +
268B HIS 5.6 0.9 - - - +
270B ASP* 3.0 28.6 + - + +
272B TYR* 1.3 78.5 - - - +
274B TRP* 1.3 68.6 + - + +
275B GLY 3.3 4.3 - - - -
297B HIS* 4.5 9.2 - - - -
87D PHE* 4.1 14.3 - - - -
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Residues in contact with TRP 274 (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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94B TYR* 4.0 13.4 - - - -
249B VAL* 3.4 32.7 + - + -
250B VAL* 3.6 14.8 + - - +
251B ARG* 3.3 42.4 - - - -
252B PHE* 3.4 40.8 - + - -
255B PHE* 5.4 1.3 - + - -
267B ILE* 4.6 2.5 - - + -
268B HIS 4.0 14.1 + - - -
269B GLY* 4.6 0.2 - - - -
270B ASP 2.8 31.5 + - - +
271B VAL 4.5 0.9 - - - +
273B LYS* 1.3 89.1 - - + +
275B GLY* 1.3 60.5 + - - +
276B GLY 3.4 1.5 + - - -
279B ALA* 3.7 21.4 - - + +
280B THR* 4.6 7.0 - - - +
283B LEU* 3.7 33.8 - - + +
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Residues in contact with GLY 275 (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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79B HIS* 3.1 26.0 - - - -
94B TYR* 3.4 31.6 + - - +
97B ILE* 3.4 11.6 - - - +
98B ALA* 3.6 8.8 - - - -
101B ASP* 3.9 0.3 - - - +
271B VAL 2.9 6.2 + - - -
273B LYS 3.3 4.0 + - - -
274B TRP* 1.3 79.1 - - - +
276B GLY* 1.3 57.0 + - - +
279B ALA* 5.1 0.9 - - - -
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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
------------------------------------------------------------
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