Contacts of the helix formed by residues 218 - 227 (chain B) in PDB entry 3C6Q
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 218 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B HIS* 6.0 5.8 - - + -
191B ALA* 4.4 23.1 + - + +
195B PRO* 4.8 0.7 - - - +
216B ASP* 3.8 5.7 - - + -
217B THR* 1.3 76.7 - - - +
219B PRO* 1.3 77.0 - - + +
220B ASP* 3.9 11.7 + - - +
221B ILE* 3.0 32.0 + - + +
222B LEU* 2.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B THR 4.5 1.6 - - - +
218B THR* 1.3 88.7 - - + +
220B ASP* 1.3 60.2 + - - +
222B LEU* 3.9 7.0 - - + +
223B GLN* 2.9 29.6 + - - +
303B ILE* 4.8 9.2 - - + -
304B LYS* 4.0 16.6 - - + +
305B PHE* 3.5 39.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B PRO* 4.4 18.5 - - + +
218B THR* 3.2 11.0 + - - +
219B PRO* 1.3 81.2 - - - +
221B ILE* 1.3 57.4 + - - +
223B GLN* 3.3 9.0 - - - +
224B TYR* 3.0 36.7 + - + -
305B PHE 5.4 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ALA 3.8 13.9 - - - +
194B GLY* 5.5 0.2 - - - -
195B PRO* 3.6 22.9 - - + -
214B CYS* 4.7 3.4 - - - -
215B PHE 3.1 27.1 - - - +
216B ASP* 3.5 25.6 - - + +
217B THR* 4.5 1.8 - - - -
218B THR* 3.0 28.4 + - + +
220B ASP* 1.3 74.9 - - - +
222B LEU* 1.3 60.6 + - - +
224B TYR* 3.1 8.1 + - - +
225B VAL* 2.8 33.3 + - + +
230B ILE* 4.4 10.1 - - + -
233B THR* 3.7 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B THR* 2.9 47.8 - - + +
218B THR 2.9 24.4 + - - +
219B PRO* 3.9 6.7 - - + +
221B ILE* 1.3 72.7 - - + +
223B GLN* 1.3 61.4 + - - +
225B VAL* 3.2 9.5 + - + +
226B LYS* 2.8 26.7 + - - +
284B VAL* 5.8 0.9 - - + -
289B LEU* 3.9 16.7 - - + +
292B TYR* 4.6 11.0 - - + -
293B LEU* 3.5 32.1 - - + -
303B ILE* 4.1 16.6 - - + -
304B LYS 5.5 0.4 - - - +
305B PHE* 3.5 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B PRO 2.9 19.1 + - - +
220B ASP* 3.3 10.1 - - - +
222B LEU* 1.3 76.3 - - - +
224B TYR* 1.3 66.0 + - + +
226B LYS* 3.1 18.4 + - - +
227B GLU* 3.0 64.2 + - - +
305B PHE* 3.3 35.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B PRO* 3.5 34.1 - - + -
198B ALA* 3.5 30.7 - - + -
199B LEU* 3.5 26.8 - - - +
202B LYS* 4.4 14.9 + - + +
220B ASP* 3.0 26.2 + - + -
221B ILE 3.1 7.6 + - - +
223B GLN* 1.3 76.4 - - + +
225B VAL* 1.3 59.2 + - - +
227B GLU* 3.4 21.0 + - - -
228B GLY 3.2 3.5 + - - -
229B VAL* 2.9 40.1 + - + +
230B ILE* 3.6 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE 2.8 24.5 + - - +
222B LEU* 3.2 10.7 + - + +
224B TYR* 1.3 74.5 - - - +
226B LYS* 1.3 66.3 + - - +
228B GLY* 2.9 15.2 + - - -
230B ILE* 3.5 25.6 - - + +
233B THR* 4.2 17.9 - - + -
284B VAL* 4.8 4.7 - - + +
285B THR* 3.5 13.2 - - - +
286B PRO* 3.4 42.0 - - + +
289B LEU* 4.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU 2.8 16.1 + - - +
223B GLN* 3.4 19.5 + - - +
225B VAL* 1.3 75.0 - - - +
227B GLU* 1.3 59.5 + - + +
228B GLY* 3.1 5.0 + - - -
286B PRO* 5.6 1.5 - - - +
289B LEU* 3.7 17.2 - - + +
305B PHE* 3.7 31.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LYS* 3.0 37.4 + - - +
207B VAL* 5.0 2.3 - - - +
223B GLN* 3.0 49.9 + - - +
224B TYR* 3.8 18.1 - - - +
225B VAL 3.2 0.2 - - - -
226B LYS* 1.3 75.3 - - + +
228B GLY* 1.3 62.0 + - - +
229B VAL* 3.5 12.1 + - + +
----------------------------------------------------------
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