Contacts of the helix formed by residues 266 - 274 (chain A) in PDB entry 2OXD
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 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A ASP* 5.3 5.4 - - - +
239A HIS* 4.8 7.7 + - - +
264A GLU 4.9 2.6 - - - +
265A LEU* 1.3 75.4 - - - +
267A PRO* 1.3 69.2 - - + +
268A GLN* 4.2 24.3 - - + +
269A LEU* 2.9 31.0 + - + +
270A GLU* 3.0 12.0 + - - +
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Residues in contact with PRO 267 (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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265A LEU 3.7 3.8 - - - +
266A ASP* 1.3 86.2 - - + +
268A GLN* 1.3 63.5 + - + +
270A GLU* 3.9 13.3 - - + +
271A ALA* 3.1 26.3 + - - +
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Residues in contact with GLN 268 (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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239A HIS* 3.7 26.0 + - + -
266A ASP* 4.2 19.9 - - + +
267A PRO* 1.3 77.5 - - + +
269A LEU* 1.3 59.2 + - - +
271A ALA* 4.1 4.3 - - - +
272A LEU* 3.2 33.0 + - + +
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Residues in contact with LEU 269 (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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203A LEU 4.2 19.3 - - - +
204A VAL* 5.6 0.9 - - - -
205A ASP* 5.4 4.3 - - - +
238A ASN 5.9 0.4 - - - +
239A HIS* 3.2 51.6 - - + +
242A LEU* 3.8 13.0 - - + -
243A VAL* 5.0 1.6 - - + -
265A LEU* 3.8 21.8 - - + -
266A ASP* 2.9 25.5 + - + +
268A GLN* 1.3 75.9 - - - +
270A GLU* 1.3 67.4 + - - +
271A ALA 3.1 1.3 - - - -
272A LEU* 2.9 7.1 + - + +
273A VAL* 2.9 43.7 + - + +
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Residues in contact with GLU 270 (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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264A GLU* 6.0 0.3 - - - +
265A LEU* 3.7 41.9 + - + +
266A ASP 3.0 11.2 + - - +
267A PRO* 3.9 11.9 - - + +
269A LEU* 1.3 74.8 - - - +
271A ALA* 1.3 57.1 + - - +
273A VAL* 3.7 3.2 - - - +
274A GLY* 2.9 29.5 + - - +
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A PRO 3.1 16.8 + - - +
268A GLN* 4.1 5.6 - - - +
269A LEU 3.0 0.8 + - - -
270A GLU* 1.3 78.8 - - - +
272A LEU* 1.3 62.2 + - + +
274A GLY* 3.8 9.3 + - - -
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Residues in contact with LEU 272 (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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239A HIS* 4.0 29.8 - - + +
240A ASP* 5.6 0.7 - - - +
243A VAL* 3.6 28.3 - - + +
247A LYS* 5.2 1.6 + - - -
268A GLN* 3.2 20.6 + - + +
269A LEU* 2.9 7.4 + - - +
271A ALA* 1.3 76.8 - - + +
273A VAL* 1.3 65.9 + - - +
274A GLY* 4.8 0.2 - - - -
276A HIS* 5.0 1.4 + - - -
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Residues in contact with VAL 273 (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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242A LEU* 4.3 14.1 - - + -
243A VAL* 3.9 17.0 - - + +
246A ALA* 4.0 12.5 - - + +
251A THR* 3.5 26.9 - - + -
254A LEU* 4.2 10.8 - - + -
265A LEU* 4.4 6.5 - - + -
269A LEU* 2.9 41.4 + - + +
270A GLU* 3.7 6.3 - - - +
272A LEU* 1.3 78.1 - - - +
274A GLY* 1.3 58.7 + - - +
276A HIS* 2.9 32.7 + - - -
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Residues in contact with GLY 274 (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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251A THR* 3.6 13.6 - - - +
270A GLU 2.9 19.7 + - - +
271A ALA 3.8 8.3 + - - -
272A LEU 3.5 1.0 - - - -
273A VAL* 1.3 75.1 - - - +
275A ARG* 1.3 68.8 + - - +
276A HIS* 4.8 1.1 - - - -
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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