Contacts of the helix formed by residues 226 - 240 (chain B) in PDB entry 1GQC
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 226 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG* 3.2 28.9 - - - +
16B LEU* 4.0 5.7 - - - +
225B ASP* 1.3 91.2 + - + +
227B PRO* 1.3 62.5 - - - +
228B ALA* 3.8 9.1 + - - +
229B CYS* 2.9 31.6 + - - +
230B LEU* 2.7 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG* 3.6 30.7 - - - +
16B LEU* 4.0 23.9 - - + -
226B THR* 1.3 87.8 - - - +
228B ALA* 1.3 62.0 + - - +
230B LEU* 3.2 12.6 + - + +
231B GLU* 3.1 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 3.0 9.4 - - - +
227B PRO* 1.3 80.7 - - + +
229B CYS* 1.3 63.0 + - - +
231B GLU* 3.3 9.8 + - - +
232B LYS* 3.3 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PRO* 5.0 6.2 - - - +
223B GLY 3.4 22.7 - - - +
225B ASP* 4.3 7.6 - - - +
226B THR* 2.9 29.3 + - - +
228B ALA* 1.3 75.8 - - - +
230B LEU* 1.3 56.6 + - - +
232B LYS* 2.9 49.3 - - - +
233B VAL* 3.0 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.8 5.6 - - + -
22B LEU* 4.0 26.5 - - + -
24B ILE* 4.2 21.8 - - + -
224B VAL* 4.2 23.9 - - + +
226B THR 2.7 15.9 + - - +
227B PRO* 3.4 14.8 - - + +
228B ALA 3.2 0.4 - - - -
229B CYS* 1.3 73.1 - - - +
231B GLU* 1.3 64.5 + - - +
233B VAL* 3.3 7.0 + - - +
234B ARG* 3.1 66.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B PRO* 3.1 19.2 + - - +
228B ALA* 3.3 8.9 + - - +
230B LEU* 1.3 78.7 - - - +
232B LYS* 1.3 56.0 + - - +
234B ARG* 3.0 39.7 + - - +
235B ALA* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PRO* 4.8 11.9 - - + -
228B ALA* 3.3 10.5 + - - +
229B CYS* 2.9 49.6 - - - +
231B GLU* 1.3 79.2 - - - +
233B VAL* 1.3 56.2 + - + +
235B ALA* 3.5 4.2 + - - +
236B LEU* 2.9 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 4.1 9.9 - - + -
100B PRO* 3.8 17.9 - - + -
101B MET* 4.0 7.9 - - + -
222B PRO* 4.3 15.7 - - + +
223B GLY 4.1 8.7 - - - +
224B VAL* 3.4 24.9 - - + -
229B CYS 3.0 15.4 + - - +
230B LEU 3.3 6.0 + - - +
232B LYS* 1.3 72.8 - - - +
234B ARG* 1.3 57.0 + - - +
236B LEU* 4.2 7.4 - - - -
237B MET* 2.7 66.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.8 3.6 - - - +
23B ASP* 2.7 37.8 + - - +
24B ILE* 4.3 23.3 - - + +
25B VAL* 3.9 9.9 - - + +
230B LEU* 3.1 43.4 + - + +
231B GLU* 3.0 44.7 + - - +
233B VAL* 1.3 73.9 - - - +
235B ALA* 1.3 67.0 + - - +
236B LEU 3.1 0.2 + - - -
237B MET 3.8 0.2 - - - -
238B ALA* 2.8 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLU 2.9 17.2 + - - +
232B LYS* 3.9 5.2 - - - +
234B ARG* 1.3 75.5 - - - +
236B LEU* 1.3 63.1 + - + +
238B ALA* 3.8 4.6 - - - +
239B GLN* 3.2 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B MET* 3.6 21.9 - - + +
222B PRO* 3.5 39.7 - - + -
232B LYS* 2.9 31.0 + - + +
233B VAL 3.6 2.2 - - - +
235B ALA* 1.3 76.2 - - + +
237B MET* 1.3 64.9 + - - +
239B GLN* 3.1 36.6 + - - +
240B GLU* 3.1 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.9 21.3 - - + -
25B VAL* 4.5 8.0 - - + +
32B HIS* 3.9 22.7 - - + +
36B ARG* 3.0 33.0 - - - +
100B PRO* 3.6 22.0 - - - +
101B MET* 3.7 21.8 - - + -
233B VAL* 2.7 42.6 + - + +
234B ARG 4.1 1.3 - - - +
236B LEU* 1.3 70.9 - - - +
238B ALA* 1.3 65.6 + - - +
240B GLU* 3.3 20.0 - - - +
241B LEU* 3.3 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 3.7 19.2 - - + +
234B ARG 2.8 20.3 + - - +
235B ALA* 3.8 5.2 - - - +
237B MET* 1.3 74.6 - - - +
239B GLN* 1.3 57.5 + - - +
241B LEU* 2.7 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ALA 3.2 13.0 + - - +
236B LEU* 3.1 35.7 + - - +
238B ALA* 1.3 73.4 - - - +
240B GLU* 1.3 60.1 + - - +
241B LEU 2.8 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 3.6 26.5 + - - -
101B MET* 5.1 9.7 - - + +
236B LEU 3.1 15.2 + - - +
237B MET* 3.3 21.7 - - - +
239B GLN* 1.3 80.5 - - - +
241B LEU* 1.3 65.9 + - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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