Contacts of the helix formed by residues 169 - 183 (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 GLU 169 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B HIS* 5.5 7.6 + - - -
166M LYS 4.6 2.0 - - - +
167M SER* 2.7 22.8 + - - +
168M MET* 1.3 75.0 - - - +
170M SER* 1.3 60.0 + - - +
171M ILE 3.4 0.2 - - - -
172M MET* 3.3 6.9 + - - +
173M ALA* 2.9 29.1 + - - +
196M ILE* 4.4 22.2 - - + +
197M HIS 3.7 18.0 - - - +
198M VAL* 4.3 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 170 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166M LYS* 3.6 13.9 + - - -
169M GLU* 1.3 77.1 - - - +
171M ILE* 1.3 61.7 + - - +
173M ALA* 4.1 0.6 - - - +
174M ALA* 2.9 33.3 + - - +
198M VAL* 3.5 22.1 - - - +
202M GLU* 2.8 39.5 + - - -
203M PHE* 3.7 5.7 - - - -
206M THR* 3.2 14.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 171 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154M TYR* 3.5 34.5 - - + -
157M CYS* 5.0 6.3 - - - -
158M HIS 5.9 0.2 - - - +
163M LEU* 4.1 28.9 - - + -
165M GLY 4.7 6.3 - - - +
166M LYS* 4.6 9.1 - - + +
168M MET* 3.3 49.6 - - + +
170M SER* 1.3 78.2 - - - +
172M MET* 1.3 72.3 + - + +
174M ALA* 4.3 2.2 - - - +
175M SER* 2.9 30.1 + - - -
206M THR* 4.1 19.3 - - + -
210M MET* 6.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 172 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129M ALA* 4.8 7.0 - - + +
132M LYS* 3.6 38.8 - - + -
133M ILE* 3.6 33.4 - - + +
136M LEU* 3.6 30.3 - - + -
154M TYR* 5.4 0.7 - - + -
168M MET* 3.1 32.8 - - + +
169M GLU* 3.3 8.0 + - - +
170M SER 3.2 0.4 - - - -
171M ILE* 1.3 86.0 - - + +
173M ALA* 1.3 60.8 + - - +
175M SER* 2.6 20.5 + - - -
176M ILE* 2.9 23.2 + - - +
196M ILE* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169M GLU 2.9 16.3 + - - +
170M SER 4.1 0.4 - - - +
172M MET* 1.3 75.8 - - - +
174M ALA* 1.3 58.0 + - - +
176M ILE* 3.2 6.4 + - - +
177M LEU* 2.9 27.7 + - - +
192M ILE* 3.8 15.6 - - + +
196M ILE* 3.7 23.5 - - + +
198M VAL* 3.9 13.9 - - + -
203M PHE* 3.6 20.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170M SER 2.9 19.6 + - - +
171M ILE* 4.3 3.8 - - - +
173M ALA* 1.3 76.6 - - - +
175M SER* 1.3 57.0 + - - +
177M LEU* 3.4 3.2 + - - +
178M ILE* 2.9 34.2 + - - +
203M PHE* 3.5 17.6 - - + -
206M THR* 4.7 6.1 - - + +
207M LEU* 4.2 29.3 - - + +
210M MET* 5.0 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 175 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133M ILE* 3.9 12.1 - - - +
150M ALA* 3.4 27.9 + - - +
153M ALA* 4.5 3.8 - - - +
154M TYR* 4.3 16.6 - - - -
157M CYS* 6.0 0.4 - - - -
171M ILE 2.9 19.6 + - - -
172M MET* 2.6 25.3 + - - -
174M ALA* 1.3 74.1 - - - +
176M ILE* 1.3 59.9 + - - +
178M ILE* 3.7 7.0 - - - +
179M GLY 2.9 24.1 + - - -
210M MET* 5.5 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 176 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133M ILE* 4.6 16.4 - - + -
136M LEU* 4.1 33.7 - - + -
137M CYS* 4.9 10.3 - - + +
142M LEU* 4.5 20.4 - - + -
146M VAL* 4.3 3.4 - - + +
150M ALA* 4.0 14.4 - - + -
172M MET 2.9 22.9 + - - +
173M ALA* 3.5 7.9 - - - +
175M SER* 1.3 80.3 + - - +
177M LEU* 1.3 56.9 + - - +
179M GLY* 3.4 1.6 + - - -
180M CYS* 2.9 26.9 + - + +
192M ILE* 4.3 18.4 - - + -
195M LEU* 6.0 4.5 - - + -
196M ILE* 4.9 3.8 - - + -
268R MET* 6.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173M ALA 2.9 15.6 + - - +
174M ALA 3.8 4.3 - - - +
175M SER 3.3 0.2 - - - -
176M ILE* 1.3 77.7 - - - +
178M ILE* 1.3 59.1 + - + +
180M CYS* 3.2 8.3 + - + +
181M ARG* 2.9 66.1 + - + +
187M ARG 4.9 6.5 - - - +
189M PHE* 3.5 32.3 - - + -
192M ILE* 3.7 20.9 - - + -
203M PHE* 3.5 22.7 - - + -
207M LEU* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 178 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149M CYS 5.5 0.4 - - - +
153M ALA* 3.9 18.2 - - + -
174M ALA 2.9 22.5 + - - +
175M SER* 3.7 5.6 - - - +
176M ILE 3.3 0.2 - - - -
177M LEU* 1.3 78.5 - - + +
179M GLY* 1.3 59.8 + - - +
181M ARG* 3.0 12.2 + - + +
182M ARG* 2.9 34.0 + - + +
207M LEU* 5.1 18.2 - - + -
210M MET* 4.4 13.9 - - + -
211M LYS* 5.2 15.5 - - + +
214M LEU* 3.6 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 179 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146M VAL* 3.4 16.9 - - - +
149M CYS* 3.8 27.2 - - - +
150M ALA* 3.9 9.6 - - - +
175M SER 2.9 16.6 + - - -
176M ILE 3.8 1.3 - - - -
178M ILE* 1.3 78.1 - - - +
180M CYS* 1.3 58.7 + - - +
182M ARG* 4.0 1.6 - - - -
183M ALA* 3.5 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 180 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142M LEU* 5.2 1.8 - - + -
146M VAL* 3.8 11.4 - - + -
176M ILE* 2.9 16.1 + - + +
177M LEU* 3.4 13.2 - - - +
178M ILE 3.1 0.2 - - - -
179M GLY* 1.3 76.1 - - - +
181M ARG* 1.3 66.3 + - - +
182M ARG 3.3 0.8 + - - -
183M ALA 3.6 2.4 + - - -
185M VAL* 3.0 64.5 + - - +
187M ARG* 3.5 39.9 - - + -
192M ILE* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 181 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177M LEU* 2.9 36.6 + - + +
178M ILE* 3.0 11.8 + - + +
180M CYS* 1.3 81.4 - - - +
182M ARG* 1.3 63.4 + - - +
184M GLU* 3.8 9.0 + - - +
185M VAL 4.4 9.2 + - - -
186M ALA* 5.9 0.4 - - - +
187M ARG 5.0 4.8 + - - +
189M PHE* 3.4 35.8 - - - -
211M LYS* 5.8 4.6 - - - +
234M GLN* 4.4 21.5 + - - +
238M TYR* 4.3 18.6 + - - -
188O GLU* 4.7 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 182 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868B MET* 3.6 37.1 - - + +
149M CYS* 4.4 8.7 - - + -
178M ILE* 2.9 20.6 + - + +
179M GLY* 4.2 7.4 - - - +
181M ARG* 1.3 79.2 - - - +
183M ALA* 1.3 57.1 + - - +
184M GLU* 3.2 9.4 + - - +
214M LEU* 5.5 8.1 - - - +
215M ARG* 4.1 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868B MET* 4.7 4.5 - - - -
145M ILE* 4.0 30.2 - - + +
146M VAL* 3.8 12.1 - - + -
149M CYS* 4.7 3.6 - - - -
179M GLY 3.5 16.5 + - - +
180M CYS 3.6 0.4 + - - -
181M ARG 3.4 0.6 - - - -
182M ARG* 1.3 75.6 - - - +
184M GLU* 1.3 71.2 + - - +
185M VAL* 3.1 21.2 + - + +
----------------------------------------------------------
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