Contacts of the helix formed by residues 227 - 239 (chain D) 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 VAL 227 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B HIS* 5.8 7.6 - - - +
253B GLU* 3.8 29.8 - - + +
200D ALA* 3.6 28.2 + - + +
202D TRP 4.6 0.6 + - - +
204D VAL* 5.4 0.9 - - - +
226D CYS* 1.3 76.0 - - - +
228D GLY* 1.3 71.8 + - - +
231D GLY* 3.7 15.9 + - - -
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Residues in contact with GLY 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B GLU* 4.9 15.3 - - - -
226D CYS 4.0 1.0 + - - -
227D VAL* 1.3 89.3 - - - +
229D ILE* 1.3 66.2 + - - -
230D GLU* 3.3 2.9 - - - -
231D GLY 4.7 0.2 - - - -
232D MSE 3.0 21.8 + - - +
248D CYS* 3.7 18.0 - - - +
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Residues in contact with ILE 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ILE* 6.3 1.1 - - + -
253B GLU 5.1 2.0 + - - +
257B PRO* 4.0 16.8 - - + +
228D GLY* 1.3 72.5 - - - +
230D GLU* 1.3 63.4 + - - +
232D MSE 3.5 0.2 + - - -
233D ALA* 3.0 23.4 + - - +
248D CYS* 3.6 33.6 - - + +
254D ASP* 3.9 26.9 - - + +
257D PRO* 4.3 9.6 - - + -
258D ALA* 4.0 14.4 - - + +
261D LEU* 3.6 31.0 - - + -
263D ALA* 3.6 21.3 - - + +
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B GLU 5.6 0.2 + - - -
256B ALA* 3.6 33.8 - - + +
257B PRO* 4.3 7.6 - - + +
260B ARG* 2.5 41.7 + - - -
228D GLY 3.3 0.8 - - - -
229D ILE* 1.3 81.5 - - - +
231D GLY* 1.3 65.4 + - - +
233D ALA* 3.4 5.8 + - - +
234D GLN* 3.0 54.0 + - + +
261D LEU* 5.5 2.9 - - - +
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Residues in contact with GLY 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D VAL* 3.7 22.0 - - - +
226D CYS* 3.5 7.0 - - - -
227D VAL 3.7 15.9 + - - -
228D GLY 3.4 3.2 + - - -
229D ILE 3.4 0.2 - - - -
230D GLU* 1.3 80.3 - - - +
232D MSE 1.3 63.2 + - - +
234D GLN* 3.0 16.7 + - - +
235D VAL* 3.1 15.6 + - - +
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Residues in contact with MSE 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D ASP* 3.6 17.9 - - - +
225D PRO* 3.4 25.4 - - - -
226D CYS* 3.5 28.5 - - - +
228D GLY 3.0 18.6 + - - +
229D ILE 3.9 3.1 - - - +
231D GLY* 1.3 74.6 - - - +
233D ALA* 1.3 57.4 + - - +
235D VAL* 3.1 1.3 + - - -
236D LYS* 2.9 26.3 + - - +
243D LEU* 3.2 31.0 - - + +
244D CYS 3.3 26.7 - - - +
245D THR* 3.8 10.5 - - - -
248D CYS* 4.0 11.4 - - + -
263D ALA* 3.6 16.2 - - + +
264D VAL* 4.4 3.6 - - + -
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Residues in contact with ALA 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D ILE 3.0 19.0 + - - +
230D GLU* 3.7 7.6 - - - +
231D GLY 3.2 0.2 - - - -
232D MSE 1.3 76.2 - - - +
234D GLN* 1.3 66.7 + - + +
236D LYS* 3.4 2.8 + - - +
237D ALA* 3.0 23.2 + - - +
261D LEU* 3.3 30.3 - - + +
262D ASN 3.8 13.2 - - - +
263D ALA* 3.8 5.3 - - + +
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Residues in contact with GLN 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B ARG* 3.7 14.8 - - - +
204D VAL* 3.9 19.3 - - + -
208D VAL* 4.7 3.0 - - + +
230D GLU* 3.0 36.2 + - + +
231D GLY* 3.0 9.7 + - - +
233D ALA* 1.3 80.9 - - - +
235D VAL* 1.3 62.2 + - - +
237D ALA* 3.3 17.9 + - - +
238D LYS* 3.5 14.7 + - - +
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Residues in contact with VAL 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D VAL* 4.3 10.5 - - + +
207D SER* 3.6 28.7 - - - -
208D VAL* 4.5 7.9 - - + -
222D LEU* 4.4 10.3 - - + -
225D PRO* 4.4 2.7 - - + -
226D CYS* 3.8 14.1 - - - -
231D GLY 3.1 13.3 + - - +
232D MSE 3.1 7.4 + - - +
234D GLN* 1.3 77.4 - - - +
236D LYS* 1.3 58.1 + - - +
238D LYS* 3.1 2.4 + - - -
239D VAL* 2.8 49.0 + - + +
243D LEU* 4.2 23.3 - - + -
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Residues in contact with LYS 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D MSE 2.9 15.7 + - - +
233D ALA 3.7 5.2 - - - +
235D VAL* 1.3 77.8 - - - +
237D ALA* 1.3 62.0 + - - +
238D LYS 3.4 0.5 + - - -
239D VAL* 3.7 15.3 - - - +
241D ILE 5.9 0.9 - - - -
243D LEU* 4.1 11.9 - - + +
262D ASN* 3.3 38.4 - - - +
263D ALA 3.9 12.3 - - - +
264D VAL 3.9 10.3 - - - +
265D ASP* 2.6 40.1 + - - +
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Residues in contact with ALA 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ALA 3.0 17.3 + - - +
234D GLN* 3.6 12.6 - - - +
235D VAL 3.2 0.4 - - - -
236D LYS* 1.3 77.8 - - - +
238D LYS* 1.3 65.5 + - + +
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Residues in contact with LYS 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D VAL* 4.0 31.3 - - + +
212D ILE* 5.0 11.0 - - + +
215D GLU* 4.1 4.0 - - - +
234D GLN 3.5 9.1 + - - +
235D VAL 3.1 4.9 + - - +
237D ALA* 1.3 85.2 - - + +
239D VAL* 1.3 61.4 + - - +
240D ARG* 3.8 8.9 + - - +
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Residues in contact with VAL 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D VAL* 4.0 23.1 - - + +
211D GLY* 3.8 29.6 - - - +
212D ILE* 4.2 1.8 - - + +
215D GLU* 3.7 3.6 - - - +
222D LEU* 4.6 7.2 - - + -
235D VAL* 2.8 37.5 + - + +
236D LYS* 3.7 15.6 - - - +
238D LYS* 1.3 74.5 - - + +
240D ARG* 1.3 62.2 + - - +
241D ILE* 3.1 45.9 + - + +
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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
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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