Contacts of the helix formed by residues 227 - 236 (chain B) in PDB entry 2QFZ
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198B LEU* 3.8 16.6 - - + -
201B PHE* 3.7 24.5 - - + -
202B LYS* 3.8 32.1 - - + -
205B LEU* 3.8 22.4 - - + +
223B ILE* 3.8 11.2 - - + -
224B PRO* 3.1 15.7 + - + +
226B PRO* 1.3 77.4 - - - +
228B ARG* 1.3 63.9 + - - +
229B PRO* 3.5 2.5 - - - -
230B MET* 3.4 6.2 + - - +
231B THR* 2.8 27.2 + - - +
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Residues in contact with ARG 228 (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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223B ILE* 3.1 30.2 + - + +
224B PRO 3.2 9.3 + - - +
225B LYS* 3.1 32.6 + - + +
227B VAL* 1.3 73.9 - - - +
229B PRO* 1.4 76.2 - - + +
231B THR* 3.1 0.4 + - - -
232B TRP* 2.8 48.6 + - + +
332B VAL* 3.9 14.7 - - + +
436B ILE* 3.4 32.3 - - - +
437B ARG* 4.6 10.1 - - - +
440B ASP* 2.9 36.4 + - - +
491B ASP* 5.8 1.2 + - - -
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Residues in contact with PRO 229 (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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225B LYS 3.5 13.0 - - - +
226B PRO 4.1 6.3 - - - +
227B VAL 3.7 3.1 - - - -
228B ARG* 1.4 93.3 - - + +
230B MET* 1.3 61.0 + - - +
232B TRP 3.5 0.2 + - - -
233B LYS* 3.2 30.9 + - - +
332B VAL* 3.5 33.0 - - + +
333B PHE* 3.7 18.0 - - + -
335B CYS* 6.2 0.2 - - + -
336B GLU* 3.4 40.6 - - + +
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Residues in contact with MET 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 4.2 25.4 - - + -
227B VAL* 3.4 7.4 + - - +
228B ARG 3.2 0.6 - - - -
229B PRO* 1.3 78.1 - - + +
231B THR* 1.3 67.8 + - - +
233B LYS* 3.3 10.6 + - + +
234B LEU* 3.1 32.7 + - + +
239B LEU* 3.7 32.3 - - + -
246B ARG* 4.3 19.3 - - - +
250B LEU* 6.0 2.5 - - + -
336B GLU* 5.1 4.0 + - - +
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Residues in contact with THR 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PHE* 4.0 6.0 - - + -
205B LEU* 3.7 23.1 - - - +
215B LEU* 4.1 11.9 - - + -
219B SER* 3.3 26.0 - - - +
223B ILE* 3.6 21.9 - - + +
227B VAL 2.8 23.0 + - - -
228B ARG 3.9 2.0 - - - -
230B MET* 1.3 75.6 - - - +
232B TRP* 1.3 58.3 + - - +
234B LEU* 3.1 4.5 + - - +
235B LEU* 2.9 47.5 + - + +
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Residues in contact with TRP 232 (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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223B ILE* 3.6 14.6 - - + +
228B ARG* 2.8 38.8 + - + +
229B PRO 3.8 4.0 - - - +
231B THR* 1.3 78.0 - - - +
233B LYS* 1.3 59.5 + - - +
235B LEU* 4.2 3.0 - - + +
236B SER* 3.2 27.4 + - - -
328B PRO* 3.9 23.1 - - + -
329B PHE* 3.7 36.8 - + + -
332B VAL* 3.9 20.4 - - + -
333B PHE* 4.5 7.6 - + + -
366B CYS* 4.9 2.3 - - - -
436B ILE* 3.4 26.2 - - + -
439B TRP* 3.8 30.3 - + + -
440B ASP* 2.9 21.9 + - - +
443B GLN* 3.3 24.9 + - - +
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Residues in contact with LYS 233 (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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229B PRO* 3.2 25.4 + - - +
230B MET* 3.3 14.3 + - + +
232B TRP* 1.3 76.2 - - - +
234B LEU* 1.3 56.7 - - - +
236B SER* 3.6 4.7 + - - -
238B TYR* 3.2 43.1 + - + -
239B LEU* 3.0 46.8 + - + -
250B LEU* 5.2 3.1 - - + +
333B PHE* 3.8 30.9 - - + +
336B GLU* 5.3 4.7 + - - -
362B ASP* 2.7 38.0 + - - +
366B CYS* 4.0 1.6 - - - -
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Residues in contact with LEU 234 (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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205B LEU* 3.4 31.9 - - + -
210B THR* 4.3 9.2 - - + +
212B LEU* 4.2 21.6 - - + +
215B LEU* 4.1 14.4 - - + -
230B MET* 3.1 16.6 + - - +
231B THR 3.1 8.3 + - - +
233B LYS* 1.3 75.7 - - - +
235B LEU* 1.3 65.9 + - - +
237B GLY* 3.3 12.8 + - - -
239B LEU* 3.5 21.4 - - + +
240B PRO 3.2 29.8 - - - +
241B ALA* 4.3 2.7 - - - +
246B ARG* 3.7 29.8 - - - +
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Residues in contact with LEU 235 (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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212B LEU* 4.7 4.3 - - + +
215B LEU* 4.0 18.6 - - + -
216B ARG* 3.6 49.6 + - + +
219B SER* 3.7 18.6 - - - +
223B ILE* 4.3 6.7 - - + -
231B THR* 2.9 41.1 + - + +
232B TRP* 4.2 3.1 - - - +
234B LEU* 1.3 76.4 - - - +
236B SER* 1.3 59.5 + - - +
237B GLY 3.5 0.7 + - - -
443B GLN* 3.9 35.3 - - + +
444B SER* 4.2 6.5 - - - +
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Residues in contact with SER 236 (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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232B TRP 3.2 19.8 + - - -
233B LYS 3.6 2.6 + - - -
235B LEU* 1.3 76.5 - - - +
237B GLY* 1.3 57.3 + - - +
238B TYR* 3.4 18.0 + - - +
366B CYS* 4.0 12.6 - - - -
369B LYS* 3.2 37.9 + - - +
443B GLN* 4.1 20.6 - - - +
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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