Contacts of the helix formed by residues 182 - 198 (chain S) in PDB entry 3MQT
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 SER 182 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181S VAL* 1.3 76.6 - - - +
183S ASP* 1.3 59.4 + - - +
184S LYS* 3.2 11.9 + - - +
185S GLU* 2.7 40.3 + - - +
186S ILE* 3.0 25.8 + - - +
210S ARG* 3.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 183 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182S SER* 1.3 73.0 - - - +
184S LYS* 1.3 56.8 + - - +
186S ILE* 3.1 8.0 + - - +
187S VAL* 2.9 31.5 + - - +
210S ARG* 2.7 34.4 + - - +
211S TRP* 2.8 25.9 + - - -
216S LYS* 3.2 34.2 - - - +
219S TRP* 4.1 13.4 - - + -
220S THR* 3.5 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 184 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182S SER* 3.2 9.9 + - - +
183S ASP* 1.3 76.5 - - - +
185S GLU* 1.3 63.3 + - + +
187S VAL* 3.4 23.1 + - + +
188S ALA* 3.3 19.6 + - + +
191S ARG* 4.6 6.7 - - - +
219S TRP* 3.4 36.1 - - + -
223S GLN* 4.5 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 185 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149S LEU* 3.9 19.0 - - + +
180S LYS 4.7 1.2 - - - +
181S VAL* 3.5 14.6 - - + +
182S SER* 2.7 48.7 + - - +
184S LYS* 1.3 76.6 - - + +
186S ILE* 1.3 56.2 + - - +
188S ALA* 3.1 8.8 + - - +
189S TYR* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149S LEU* 4.2 13.5 - - + -
175S ILE* 3.7 43.1 - - + -
178S ASN* 6.3 0.2 - - + -
181S VAL* 3.8 18.2 - - + -
182S SER 3.0 15.6 + - - +
183S ASP* 3.3 11.0 - - - +
185S GLU* 1.3 75.7 - - - +
187S VAL* 1.3 64.2 + - - +
189S TYR* 3.3 13.6 + - + +
190S LEU* 2.9 33.2 + - + +
210S ARG* 3.7 24.5 - - - +
211S TRP* 4.3 3.8 - - + -
220S THR* 4.3 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183S ASP 2.9 20.0 + - - +
184S LYS* 3.6 22.2 - - + +
185S GLU 3.3 0.2 - - - -
186S ILE* 1.3 72.3 - - - +
188S ALA* 1.3 62.6 + - - +
190S LEU 3.2 2.1 + - - -
191S ARG* 3.0 53.4 + - - +
219S TRP* 4.2 9.6 - - + -
220S THR* 3.7 33.9 - - + +
223S GLN* 3.8 9.9 - - + -
224S LEU* 3.7 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184S LYS* 3.3 10.9 + - + +
185S GLU* 3.1 11.7 + - - +
187S VAL* 1.3 80.5 - - - +
189S TYR* 1.3 58.0 + - - +
191S ARG* 3.4 8.7 + - - +
192S GLU* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 189 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149S LEU* 3.9 37.5 - - + -
152S ILE* 3.5 20.9 - - + +
153S VAL* 3.7 28.2 - - + +
156S TYR* 3.4 18.9 - + - -
174S CYS 2.8 27.9 + - - -
175S ILE* 4.4 11.4 - - + -
176S ILE 5.0 1.1 + - - -
185S GLU 2.9 12.9 + - - +
186S ILE* 3.3 19.7 - - + +
188S ALA* 1.3 75.8 - - - +
190S LEU* 1.3 81.3 + - + +
192S GLU* 3.3 8.6 + - - +
193S LEU* 3.0 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173S VAL* 4.2 14.1 - - + -
174S CYS 5.5 0.2 - - - +
175S ILE* 4.3 7.0 - - + -
186S ILE* 2.9 32.4 + - + +
187S VAL 3.2 2.2 + - - +
189S TYR* 1.3 93.4 - - + +
191S ARG* 1.3 64.5 + - - +
193S LEU* 3.3 5.0 + - + +
194S ARG 3.0 18.2 + - - -
203S MET* 3.6 6.2 - - + +
205S VAL* 4.0 41.3 - - + -
221S PHE* 4.4 5.6 - - + -
224S LEU* 3.6 24.9 - - + -
227S ILE* 3.6 23.6 - - + +
229S LEU* 5.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 191 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184S LYS* 4.6 6.7 - - - +
187S VAL* 3.0 39.5 + - - +
188S ALA* 3.7 7.5 - - - +
190S LEU* 1.3 71.9 - - - +
192S GLU* 1.3 66.9 + - - +
194S ARG* 3.2 4.2 + - - +
195S GLU* 3.0 30.8 + - - +
223S GLN* 3.2 27.1 + - - +
224S LEU* 4.2 4.8 - - + +
226S ASP* 2.7 35.4 + - - -
227S ILE* 3.9 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200J ASP* 4.8 7.3 - - - +
150S SER* 5.2 8.6 + - - -
153S VAL* 3.4 35.2 - - + +
154S GLU* 5.3 1.4 - - - +
157S LYS* 4.5 6.6 + - - -
188S ALA 2.9 18.2 + - - +
189S TYR* 3.3 7.8 + - - +
191S ARG* 1.3 76.9 - - - +
193S LEU* 1.3 62.6 + - - +
195S GLU* 3.1 22.1 + - - +
196S VAL* 3.0 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153S VAL* 4.2 21.5 - - + -
156S TYR* 4.0 32.1 - - + -
160S ILE* 4.3 11.0 - - + -
173S VAL* 3.9 27.8 - - + -
189S TYR* 3.0 49.6 + - + +
190S LEU* 3.7 9.9 - - + +
191S ARG 3.2 0.6 - - - -
192S GLU* 1.3 75.6 - - - +
194S ARG* 1.3 57.0 + - - +
196S VAL* 3.3 5.4 + - + +
197S ILE* 2.7 37.9 + - + +
203S MET* 3.8 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 194 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190S LEU 3.0 11.6 + - - +
191S ARG 3.2 7.6 + - - +
193S LEU* 1.3 75.4 - - - +
195S GLU* 1.3 55.8 + - + +
197S ILE* 4.1 3.3 - - - +
198S GLY* 2.7 55.0 + - - -
199S TRP* 3.7 42.1 + - + +
201S MET 3.1 22.0 + - - -
202S ASP* 5.0 2.0 + - - +
203S MET* 3.5 44.8 - - - +
227S ILE* 2.9 43.4 + - + -
228S ASP* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 195 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164J LYS* 5.8 0.2 + - - -
195J GLU 4.6 1.4 - - - +
198J GLY* 4.1 18.4 - - - -
199J TRP* 3.8 46.0 - - + +
191S ARG* 3.0 23.8 + - - +
192S GLU* 3.1 22.7 + - + +
194S ARG* 1.3 78.6 - - + +
196S VAL* 1.3 63.5 + - + +
198S GLY* 3.4 9.2 + - - -
199S TRP* 5.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164J LYS* 4.5 5.9 + - - +
198J GLY* 5.9 0.9 - - - -
200J ASP* 6.3 2.0 - - + -
153S VAL* 4.5 12.6 - - + +
157S LYS* 4.3 39.7 - - + +
160S ILE* 3.6 33.0 - - + +
164S LYS* 2.8 23.6 + - - -
192S GLU* 3.0 17.8 + - + +
193S LEU* 3.6 9.4 - - + +
195S GLU* 1.3 78.7 - - + +
197S ILE* 1.3 59.1 + - - +
198S GLY 3.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 197 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160S ILE* 4.0 28.0 - - + -
164S LYS* 3.0 22.1 - - - -
171S VAL* 4.1 14.1 - - + -
173S VAL* 4.0 26.2 - - + -
193S LEU* 2.7 31.8 + - + +
194S ARG* 3.8 14.4 - - - +
196S VAL* 1.3 73.1 - - - +
198S GLY* 1.3 70.4 + - - +
199S TRP 4.1 0.5 + - - -
200S ASP 5.0 0.7 + - - -
201S MET* 3.9 29.6 - - + +
203S MET* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 198 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195J GLU 4.1 15.5 - - - -
164S LYS* 4.9 2.2 - - - -
194S ARG* 2.7 44.9 + - - -
195S GLU 3.4 7.8 + - - -
196S VAL 3.2 2.8 - - - -
197S ILE* 1.3 78.1 - - - +
199S TRP* 1.3 70.1 + - - -
200S ASP 3.6 1.1 - - - -
201S MET 4.3 0.2 - - - +
----------------------------------------------------------
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