Contacts of the helix formed by residues 188 - 196 (chain M) in PDB entry 6GYK
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 188 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177M LEU* 5.6 0.2 - - - -
187M ARG* 1.3 76.8 - - - +
189M PHE* 1.3 73.6 + - + +
190M LYS* 4.1 17.0 - - + +
191M GLU* 3.0 43.1 + - - +
192M ILE* 3.5 8.5 + - - +
238M TYR* 3.5 23.8 - - + -
242M PHE* 4.2 9.2 - - - -
275M ILE* 5.0 18.6 - - + +
188O GLU* 4.3 16.6 - - - +
270R MET* 4.5 8.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 189 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177M LEU* 3.5 33.0 - - + -
181M ARG* 3.4 29.8 - - - -
187M ARG 4.7 1.6 - - - -
188M THR* 1.3 80.3 - - + +
190M LYS* 1.3 58.6 + - + +
192M ILE* 3.8 2.6 + - - +
193M GLN* 2.9 31.3 + - - +
203M PHE* 4.6 14.3 - + + -
207M LEU* 5.1 7.0 - - + -
186O GLU* 4.7 13.9 - - + -
188O GLU* 3.8 37.5 - - + -
189O LEU* 4.6 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 190 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188M THR* 3.2 9.2 - - + +
189M PHE* 1.3 78.7 - - + +
191M GLU* 1.3 57.6 + - - +
193M GLN* 3.9 8.4 - - + +
194M SER* 2.9 27.5 + - - -
275M ILE* 5.8 13.5 - - + +
303M GLN* 3.9 29.0 + - + +
270R MET* 4.0 32.1 - - + +
67T T 5.5 10.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187M ARG* 3.2 8.6 - - - -
188M THR* 3.0 36.1 + - - +
190M LYS* 1.3 74.0 - - - +
192M ILE* 1.3 61.4 + - + +
193M GLN 3.2 0.4 - - - -
194M SER* 2.3 27.5 + - - -
195M LEU* 2.9 13.3 + - - +
241M ARG* 2.8 37.3 + - - -
242M PHE* 4.7 2.9 - - - -
245M HIS* 5.5 1.4 + - - -
268R MET* 3.1 43.1 - - + +
270R MET* 3.6 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173M ALA* 3.8 31.9 - - + +
176M ILE* 4.3 15.3 - - + -
177M LEU* 3.7 50.0 - - + +
180M CYS* 5.8 0.7 - - + -
187M ARG* 4.7 15.0 - - + -
188M THR 3.5 8.6 + - - +
189M PHE 4.4 3.1 - - - +
191M GLU* 1.3 75.1 - - - +
193M GLN* 1.3 53.0 + - - +
195M LEU* 3.0 8.9 + - + +
196M ILE* 2.7 41.0 + - + +
198M VAL* 6.0 0.2 - - + -
203M PHE* 4.8 8.3 - - + -
268R MET* 4.6 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189M PHE 2.9 22.6 + - - +
190M LYS* 3.9 9.2 - - + +
192M ILE* 1.3 79.5 - - - +
194M SER* 1.3 60.0 + - - +
196M ILE 2.8 20.2 + - - +
197M HIS* 3.9 16.5 + - - +
198M VAL* 3.6 26.1 + - - +
199M LYS* 3.7 7.4 + - - -
200M THR* 3.7 34.3 + - - +
203M PHE* 5.1 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ASN* 4.4 10.6 + - - +
445B LYS* 4.7 10.1 - - - -
190M LYS 2.9 16.5 + - - -
191M GLU* 2.3 30.5 + - - -
193M GLN* 1.3 76.3 - - - +
195M LEU* 1.3 60.2 + - - +
197M HIS* 5.0 5.2 + - - -
268R MET* 4.2 8.7 - - - +
269R SER 4.6 0.2 + - - -
270R MET* 4.1 19.9 + - - -
271R ARG 4.5 6.7 - - - -
272R SER* 4.4 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ASN* 3.6 28.6 + - - +
445B LYS* 3.7 31.2 - - + -
446B LEU* 3.7 27.9 - - + +
136M LEU* 4.3 14.8 - - + +
139M ALA* 5.0 3.8 - - + -
140M ALA* 3.9 18.6 - - + -
176M ILE* 6.0 4.5 - - + -
191M GLU 2.9 11.0 + - - +
192M ILE* 3.0 10.5 + - + +
194M SER* 1.3 81.1 + - - +
196M ILE* 1.3 70.3 + - + +
197M HIS* 4.4 5.8 + - - -
268R MET* 3.8 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 196 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LEU* 6.1 1.3 - - + -
136M LEU* 3.6 33.7 - - + -
169M GLU* 4.4 24.7 - - + +
172M MET* 4.9 1.1 - - + -
173M ALA* 3.7 31.6 - - + +
176M ILE* 4.9 4.3 - - + -
192M ILE* 2.7 23.2 + - + +
193M GLN* 2.8 21.3 - - - +
195M LEU* 1.3 84.0 - - + +
197M HIS* 1.3 63.5 + - - +
198M VAL* 3.2 27.7 + - + +
----------------------------------------------------------
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