Contacts of the helix formed by residues 182 - 198 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180I LYS 4.4 0.2 + - - -
181I VAL* 1.3 71.3 - - - +
183I ASP* 1.3 59.1 + - - +
184I LYS* 3.5 8.8 + - - +
185I GLU* 2.8 42.7 + - - +
186I ILE* 2.9 28.1 + - - +
210I ARG* 3.4 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 183 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182I SER* 1.3 70.5 - - - +
184I LYS* 1.3 59.8 + - - +
186I ILE* 3.0 7.6 + - - +
187I VAL* 2.8 32.4 + - - +
210I ARG* 2.8 33.2 + - - +
211I TRP* 2.8 27.6 + - - -
216I LYS* 3.4 29.2 + - - +
219I TRP* 3.9 14.3 - - + -
220I THR* 3.4 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 184 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182I SER* 3.3 8.6 + - - +
183I ASP* 1.3 76.6 - - - +
185I GLU* 1.3 63.5 + - + +
187I VAL* 3.1 33.8 + - - +
188I ALA* 3.2 14.3 + - + +
191I ARG* 4.5 6.7 - - - +
219I TRP* 3.3 38.5 - - + -
223I GLN* 4.5 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 185 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149I LEU* 3.7 18.0 - - + +
180I LYS 4.4 2.4 - - - +
181I VAL* 3.3 16.1 - - - +
182I SER* 2.8 51.9 + - - +
184I LYS* 1.3 75.0 - - + +
186I ILE* 1.3 61.8 + - - +
188I ALA* 3.5 6.5 + - - +
189I TYR* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149I LEU* 4.5 14.1 - - + -
175I ILE* 3.8 45.5 - - + -
178I ASN* 6.1 0.4 - - + -
181I VAL* 3.6 22.7 - - + -
182I SER 2.9 16.4 + - - +
183I ASP* 3.0 10.1 + - - +
185I GLU* 1.3 73.5 - - - +
187I VAL* 1.3 66.4 + - - +
189I TYR* 3.3 7.3 - - + +
190I LEU* 3.0 32.7 + - + +
210I ARG* 3.6 25.1 - - - +
211I TRP* 4.4 12.1 - - + -
220I THR* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I ASP 2.8 17.8 + - - +
184I LYS* 3.1 19.7 + - - +
186I ILE* 1.3 78.6 - - - +
188I ALA* 1.3 62.8 + - - +
190I LEU 3.4 0.2 + - - -
191I ARG* 3.0 60.5 + - - +
219I TRP* 4.0 13.5 - - + -
220I THR* 3.9 30.3 - - + +
223I GLN* 3.9 14.6 - - + -
224I LEU* 3.7 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I LYS* 3.2 11.9 + - + +
185I GLU* 3.9 8.7 - - - +
186I ILE 3.4 0.2 - - - -
187I VAL* 1.3 78.1 - - - +
189I TYR* 1.3 57.6 + - - +
191I ARG* 3.4 10.8 + - - +
192I GLU* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 189 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149I LEU* 3.8 35.7 - - + -
152I ILE* 3.5 20.4 - - + +
153I VAL* 3.7 25.1 - - + -
156I TYR* 3.5 17.3 - - - -
174I CYS 2.6 29.5 + - - -
175I ILE* 4.1 15.8 - - + -
176I ILE 5.0 1.5 + - - -
185I GLU 3.1 14.9 + - - +
186I ILE* 3.3 16.6 - - + +
188I ALA* 1.3 74.7 - - - +
190I LEU* 1.3 77.9 + - + +
192I GLU* 3.2 9.5 + - - +
193I LEU* 3.0 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173I VAL* 4.4 4.5 - - + -
174I CYS 5.4 0.2 - - - +
175I ILE* 4.4 4.3 - - + -
186I ILE* 3.0 27.1 + - + +
187I VAL 4.0 2.7 - - - +
189I TYR* 1.3 99.7 - - + +
191I ARG* 1.3 66.1 + - - +
193I LEU* 3.2 11.9 + - + -
194I ARG 3.0 18.4 + - - -
203I MET* 3.5 11.0 - - + +
205I VAL* 4.1 42.8 - - + -
221I PHE* 4.3 8.1 - - + -
224I LEU* 3.4 26.2 - - + -
227I ILE* 3.8 16.3 - - + +
229I LEU* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 191 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I LYS* 4.5 7.9 - - - +
187I VAL* 3.0 43.2 + - - +
188I ALA* 3.6 9.6 - - - +
190I LEU* 1.3 75.9 - - - +
192I GLU* 1.3 62.7 + - - +
194I ARG* 3.3 4.2 + - - +
195I GLU* 3.1 31.5 + - - +
223I GLN* 3.0 29.7 + - - +
224I LEU* 4.0 7.9 - - + +
226I ASP* 2.5 39.8 + - - -
227I ILE* 4.0 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150I SER* 5.5 3.8 - - - -
153I VAL* 3.2 37.2 - - + +
154I GLU* 5.1 0.9 - - - +
157I LYS* 4.6 7.6 + - - -
188I ALA 2.9 17.8 + - - +
189I TYR* 3.5 7.6 - - - +
191I ARG* 1.3 75.6 - - - +
193I LEU* 1.3 65.0 + - - +
195I GLU* 3.1 22.0 + - - +
196I VAL* 3.0 28.8 + - + +
200Q ASP* 5.6 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I VAL* 4.1 24.2 - - + -
156I TYR* 4.1 27.1 - - + -
160I ILE* 4.5 9.4 - - + -
173I VAL* 3.7 28.0 - - + -
189I TYR* 3.0 51.2 + - + +
190I LEU* 3.2 11.2 + - + +
192I GLU* 1.3 77.2 - - - +
194I ARG* 1.3 55.8 + - - +
196I VAL* 3.3 5.7 + - + +
197I ILE* 2.8 39.2 + - + +
203I MET* 4.0 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 194 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I LEU 3.0 11.2 + - - +
191I ARG 3.3 7.4 + - - +
193I LEU* 1.3 75.6 - - - +
195I GLU* 1.3 59.3 + - + +
197I ILE* 4.1 4.1 - - - +
198I GLY* 2.8 50.5 + - - -
199I TRP* 3.6 45.2 + - + +
201I MET 3.2 21.6 + - - -
202I ASP* 5.0 2.0 + - - +
203I MET* 3.6 43.8 - - - +
227I ILE* 2.9 42.6 + - + -
228I ASP* 3.2 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 195 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191I ARG* 3.1 21.8 + - - +
192I GLU* 3.1 23.9 + - - +
194I ARG* 1.3 81.5 - - + +
196I VAL* 1.3 63.6 + - + +
198I GLY* 3.5 8.8 + - - -
199I TRP* 5.6 3.8 - - - +
164Q LYS* 5.7 0.5 + - - -
195Q GLU 4.7 1.6 - - - +
198Q GLY* 4.1 18.0 - - - -
199Q TRP* 3.7 45.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I VAL* 4.7 14.4 - - + +
156I TYR* 6.0 0.2 - - + -
157I LYS* 4.4 36.3 - - + +
160I ILE* 3.8 30.6 - - + +
164I LYS* 3.0 23.7 + - - -
192I GLU* 3.0 20.4 + - + +
193I LEU* 3.7 10.3 - - + +
195I GLU* 1.3 77.1 - - + +
197I ILE* 1.3 60.5 + - - +
198I GLY 3.4 0.2 + - - -
164Q LYS* 4.8 4.3 + - - +
200Q ASP* 6.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 197 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I ILE* 3.8 28.5 - - + -
164I LYS* 3.0 20.3 - - - -
171I VAL* 4.1 14.4 - - + -
173I VAL* 4.1 22.4 - - + -
193I LEU* 2.8 31.1 + - + +
194I ARG* 3.8 14.8 - - - +
196I VAL* 1.3 73.0 - - - +
198I GLY* 1.3 70.4 + - - +
200I ASP* 4.9 2.8 + - - +
201I MET* 4.0 29.2 - - + +
203I MET* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 198 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I LYS* 4.8 3.1 - - - -
194I ARG* 2.8 37.5 + - - -
195I GLU 3.5 7.4 + - - -
196I VAL 3.2 3.6 - - - -
197I ILE* 1.3 84.6 - - - +
199I TRP* 1.3 68.3 + - - -
200I ASP 3.5 1.3 - - - -
195Q GLU 4.0 16.2 - - - -
196Q VAL* 5.9 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