Contacts of the helix formed by residues 267 - 276 (chain B) in PDB entry 1OVM
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 THR 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B TYR 4.4 2.5 + - - +
260B THR 5.4 0.4 + - - -
266B SER* 1.3 78.1 - - - +
268B GLY* 1.3 65.8 + - - +
269B ALA* 3.8 7.7 + - - +
270B VAL* 3.4 27.1 + - + +
271B LYS* 2.9 21.8 + - - +
392B ASP* 5.8 3.6 - - - +
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Residues in contact with GLY 268 (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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266B SER 3.9 0.6 + - - -
267B THR* 1.3 73.6 - - - +
269B ALA* 1.3 62.1 + - - +
271B LYS* 3.8 10.6 - - - +
272B GLU* 2.9 29.5 + - - +
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Residues in contact with ALA 269 (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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258B TYR* 4.3 26.3 - - + +
267B THR* 3.2 9.1 - - - +
268B GLY* 1.3 77.4 - - - +
270B VAL* 1.3 58.0 + - - +
272B GLU* 3.5 4.6 - - - +
273B ALA* 2.8 30.0 + - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ALA* 4.9 1.3 - - + -
258B TYR* 3.2 39.5 - - + +
259B GLY* 3.6 15.5 - - - +
260B THR 3.9 4.5 - - - +
261B TYR* 3.9 41.1 - - + +
266B SER* 4.1 5.8 - - - -
267B THR* 3.2 18.4 + - + +
269B ALA* 1.3 74.3 - - - +
271B LYS* 1.3 64.8 + - - +
273B ALA* 3.1 2.5 + - - -
274B ILE* 2.9 32.6 + - + +
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Residues in contact with LYS 271 (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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261B TYR* 5.0 3.1 - - - -
263B GLY 4.0 2.7 - - - +
264B SER* 2.8 49.2 + - - +
266B SER* 3.9 16.7 + - - -
267B THR 2.9 14.6 + - - +
268B GLY* 3.8 8.0 - - - +
270B VAL* 1.3 78.1 - - - +
272B GLU* 1.3 57.6 - - - +
275B GLU* 2.9 63.3 + - + +
276B GLY 3.4 0.2 + - - -
298B GLN* 6.2 0.2 - - + -
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ARG* 2.9 16.7 + - - -
268B GLY 2.9 20.1 + - - +
269B ALA* 3.5 4.9 - - - +
271B LYS* 1.3 75.8 - - + +
273B ALA* 1.3 59.3 + - - +
276B GLY* 2.9 34.7 + - - +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ARG* 2.6 23.2 + - - +
213B ALA* 3.5 14.7 - - - +
239B ALA* 3.5 13.7 - - + +
258B TYR* 3.6 33.2 - - + -
269B ALA 2.8 17.6 + - - +
270B VAL* 3.7 4.9 - - - +
272B GLU* 1.3 75.8 - - - +
274B ILE* 1.3 65.1 + - + +
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Residues in contact with ILE 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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213B ALA* 4.1 13.1 - - + +
214B LEU 4.0 20.0 - - - +
215B LEU* 4.3 24.9 - - + -
239B ALA* 4.5 0.9 - - + -
240B HIS* 4.3 8.3 - - - +
241B ALA* 4.1 20.6 - - + +
258B TYR* 6.4 0.4 - - + -
261B TYR* 4.4 17.7 - - + -
270B VAL* 2.9 31.3 + - + +
273B ALA* 1.3 83.6 - - + +
275B GLU* 1.3 64.0 + - - +
276B GLY 3.0 4.6 + - - -
277B ALA* 3.3 18.0 + - - +
280B VAL* 4.3 21.1 - - + +
299B LEU* 4.7 5.2 - - + -
303B GLN* 4.4 0.5 + - - -
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B TYR* 2.7 38.5 + - + +
263B GLY 4.1 10.2 - - - +
264B SER* 5.1 0.3 - - - -
271B LYS* 2.9 37.1 + - + +
274B ILE* 1.3 76.4 - - - +
276B GLY* 1.3 57.0 + - - +
277B ALA 3.4 0.4 - - - +
296B THR 4.5 0.5 - - - +
297B HIS* 4.0 2.4 - - - -
298B GLN* 2.9 52.8 + - + +
299B LEU* 4.0 11.4 - - + -
303B GLN* 3.3 17.3 + - - +
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Residues in contact with GLY 276 (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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211B ARG* 3.7 12.2 + - - -
271B LYS 3.4 1.4 + - - -
272B GLU* 2.9 36.7 + - - -
275B GLU* 1.3 77.9 - - - +
277B ALA* 1.3 63.1 + - - +
278B ASP* 3.7 2.3 + - - +
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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