Contacts of the helix formed by residues 190 - 212 (chain B) in PDB entry 2RCY
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 190 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B VAL* 4.2 0.7 - - - -
188B GLY 3.9 0.8 + - - -
189B LEU* 1.3 74.0 - - - +
191B ARG* 1.3 59.4 + - - +
192B GLU* 3.8 8.0 + - - +
193B LEU* 3.1 30.7 + - - +
194B SER* 2.8 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ILE* 3.8 19.7 - - + +
182B ASP* 3.2 24.2 + - - +
185B VAL* 3.7 39.5 - - + +
190B SER* 1.3 73.1 - - - +
192B GLU* 1.3 56.7 + - - +
194B SER* 3.9 1.8 - - - -
195B LYS* 3.0 31.5 + - + +
217C GLN* 5.6 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B SER* 3.2 6.6 - - - +
191B ARG* 1.3 76.5 - - - +
193B LEU* 1.3 60.3 + - - +
195B LYS* 3.4 13.5 + - - +
196B ASN* 3.1 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 3.7 27.1 - - + -
190B SER* 3.1 22.7 + - - +
192B GLU* 1.3 74.0 - - - +
194B SER* 1.3 60.7 + - - +
196B ASN* 3.4 6.9 + - + +
197B LEU* 3.0 54.1 + - + +
152C HIS* 4.2 20.4 - - + +
154C ILE* 3.7 33.0 - - + -
158C ASP* 5.5 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU 4.9 0.7 - - - -
181B ILE* 3.7 27.8 - - - -
184B GLY* 3.6 16.7 - - - -
185B VAL 3.7 0.9 + - - -
189B LEU* 3.3 23.8 - - - +
190B SER 2.8 20.9 + - - -
191B ARG* 3.9 4.5 - - - -
193B LEU* 1.3 77.1 - - - +
195B LYS* 1.3 57.1 + - - +
197B LEU* 3.4 4.4 + - - +
198B VAL* 2.9 37.2 + - - +
165C ILE* 5.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ILE* 3.8 26.4 - - + +
191B ARG* 3.0 21.9 + - + +
192B GLU* 3.6 12.0 - - - +
194B SER* 1.3 75.6 - - - +
196B ASN* 1.3 66.3 + - - +
198B VAL* 3.3 0.7 + - - +
199B LEU* 2.9 54.1 + - + +
209C VAL* 4.1 26.2 + - + -
210C LYS* 6.3 0.2 - - - +
216C VAL* 5.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B GLU* 3.1 36.1 + - - +
193B LEU* 3.8 8.5 - - - +
195B LYS* 1.3 85.4 - - - +
197B LEU* 1.3 64.0 + - + +
199B LEU* 4.3 5.8 - - - +
200B GLN* 3.3 25.8 + - - +
152C HIS* 4.3 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 4.3 12.3 - - + -
193B LEU* 3.0 36.8 + - + +
194B SER* 3.8 3.6 - - - +
196B ASN* 1.3 74.6 - - - +
198B VAL* 1.3 62.2 + - - +
201B THR* 2.6 34.6 + - - -
124C SER* 4.0 12.8 + - - +
125C PHE 4.9 0.2 - - - +
126C ILE* 3.9 26.2 - - + -
152C HIS* 3.7 30.1 - - + +
162C ALA* 4.1 18.8 - - + +
165C ILE* 4.4 12.1 - - + -
166C SER* 4.0 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ILE* 3.9 22.9 - - + -
180B LEU* 3.5 47.8 - - + +
181B ILE* 4.0 5.8 - - + +
194B SER* 2.9 26.0 + - - +
195B LYS* 3.8 2.9 - - - +
197B LEU* 1.3 72.8 - - - +
199B LEU* 1.3 60.3 + - - +
201B THR* 3.3 3.9 + - - -
202B ILE* 3.0 53.4 + - + +
165C ILE* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ILE* 4.0 26.0 - - + -
195B LYS* 2.9 33.8 + - + +
196B ASN* 4.3 5.2 - - - +
198B VAL* 1.3 76.8 - - - +
200B GLN* 1.3 52.5 + - - +
202B ILE* 3.4 4.1 + - + +
203B LYS* 2.8 35.7 + - - +
206C VAL* 3.8 26.4 - - + +
209C VAL* 3.8 35.9 - - + -
210C LYS* 4.0 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ASN 3.3 18.1 + - - +
197B LEU 4.2 2.2 - - - +
199B LEU* 1.3 75.8 - - - +
201B THR* 1.3 59.0 + - - +
203B LYS* 3.7 17.4 - - - +
204B GLY* 2.9 27.2 + - - -
115C ASN* 5.3 0.2 + - - -
122C GLU* 3.1 47.8 + - - +
123C GLY 3.3 20.7 + - - +
124C SER* 3.8 15.4 - - - +
149C GLY* 4.6 1.0 - - - -
150C ILE* 3.4 37.0 - - + +
210C LYS* 4.3 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU 2.6 24.1 + - - -
198B VAL* 3.6 6.5 - - - -
200B GLN* 1.3 77.8 - - - +
202B ILE* 1.3 52.6 + - + +
204B GLY* 3.7 1.1 + - - -
205B SER* 2.6 37.3 + - - -
115C ASN* 4.1 8.5 - - - +
117C PRO* 4.6 1.7 - - - +
124C SER* 3.9 5.4 - - - -
165C ILE* 3.7 4.9 + - - +
166C SER* 3.5 21.6 + - - +
169C GLY* 3.7 12.8 - - - -
170C PRO* 3.5 37.7 - - + -
173C VAL* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B VAL* 5.4 1.1 - - + -
176B PHE* 4.2 16.6 - - + -
177B ILE* 3.6 33.0 - - + -
180B LEU* 4.4 2.7 - - + -
198B VAL* 3.0 32.2 + - + +
199B LEU* 3.8 3.6 - - - +
201B THR* 1.3 75.9 - - - +
203B LYS* 1.3 65.8 + - - +
205B SER* 3.2 1.4 + - - -
206B VAL* 3.0 24.6 + - + +
263B MG 4.4 0.4 - - - -
173C VAL* 3.9 32.8 - - + -
202C ILE* 3.4 32.3 - - + -
206C VAL* 3.7 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU 2.8 21.7 + - - +
200B GLN* 3.6 18.8 - - - +
202B ILE* 1.3 74.2 - - - +
204B GLY* 1.3 59.7 + - - +
206B VAL* 3.7 2.1 + - - +
207B GLU* 3.2 30.4 + - - +
263B MG 3.5 18.6 - - - -
122C GLU* 3.0 32.3 + - + +
206C VAL* 4.7 4.2 - - + +
207C GLU* 5.6 6.3 - - - -
210C LYS* 3.5 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B GLN 2.9 12.3 + - - -
203B LYS* 1.3 75.6 - - - +
205B SER* 1.3 58.8 + - - +
207B GLU* 3.3 3.3 + - - +
208B MSE 3.0 32.6 + - - +
117C PRO* 3.5 14.3 - - - +
120C VAL* 4.3 0.3 - - - +
122C GLU* 3.5 32.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B THR 2.6 23.8 + - - -
202B ILE 3.2 4.7 + - - -
204B GLY* 1.3 73.3 - - - +
206B VAL* 1.3 64.0 + - - +
208B MSE 3.4 0.9 + - - -
209B VAL* 3.2 28.2 + - - +
117C PRO* 3.9 1.3 - - - +
170C PRO* 3.2 27.3 - - - +
173C VAL* 3.7 22.9 - - - +
174C TYR* 3.4 24.0 - - - -
177C ILE* 4.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 3.0 21.3 + - + +
203B LYS 4.1 3.4 - - - +
205B SER* 1.3 72.5 - - - +
207B GLU* 1.3 66.3 + - - +
209B VAL* 3.2 3.3 + - - +
210B LYS* 3.2 33.6 + - + +
263B MG 4.2 11.7 - - - -
173C VAL* 4.9 0.7 - - + -
177C ILE* 4.2 15.3 - - + -
199C LEU* 3.7 40.6 - - + +
202C ILE* 3.7 31.4 - - + -
203C LYS* 4.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LYS* 3.2 25.4 + - - +
204B GLY* 3.6 7.0 - - - +
206B VAL* 1.3 79.9 - - - +
208B MSE 1.3 61.5 + - - +
210B LYS* 3.6 21.6 + - - +
211B LYS* 3.2 68.7 + - - +
120C VAL* 3.9 15.5 - - + +
122C GLU* 4.7 12.5 - - + +
203C LYS* 5.0 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B GLY 3.0 18.8 + - - +
205B SER 3.4 6.3 - - - +
206B VAL 3.2 0.2 - - - -
207B GLU* 1.3 76.8 - - - +
209B VAL* 1.3 57.5 + - - +
212B SER* 2.9 40.4 + - - -
219B LEU* 3.7 27.4 - - + -
222B ASN* 6.0 0.9 - - - +
116C THR* 3.8 35.0 - - - +
117C PRO* 3.6 12.8 - - + -
119C LEU* 3.9 24.7 - - + -
120C VAL* 3.8 27.8 - - + -
174C TYR* 3.3 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B SER 3.2 15.8 + - - +
206B VAL 3.2 6.9 + - - +
208B MSE 1.3 76.5 - - - +
210B LYS* 1.3 62.1 + - - +
212B SER* 4.0 10.6 - - - +
214B GLN 5.1 3.1 - - - +
216B VAL* 3.6 34.5 - - + +
219B LEU* 3.9 8.1 - - + -
174C TYR* 3.7 20.2 - - + -
177C ILE* 4.1 11.4 - - + -
195C LYS* 4.4 20.2 + - + -
199C LEU* 3.8 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 3.2 30.2 + - + +
207B GLU* 4.0 19.2 + - - +
208B MSE 3.3 0.2 - - - -
209B VAL* 1.3 78.2 - - - +
211B LYS* 1.3 63.4 + - + +
212B SER 4.6 1.7 - - - +
195C LYS* 6.3 0.9 - - - +
199C LEU* 3.7 27.6 + - + -
200C GLN* 4.9 4.2 + - - +
203C LYS* 3.7 33.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLU* 3.2 44.5 + - - +
210B LYS* 1.3 82.7 - - + +
212B SER* 1.3 65.8 + - - +
213B ASP 3.7 0.9 + - - -
120C VAL* 3.6 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B MSE 2.9 24.1 + - - -
209B VAL 4.0 8.4 - - - +
210B LYS 4.6 1.7 - - - +
211B LYS* 1.3 80.6 - - - +
213B ASP* 1.3 62.5 + - - +
214B GLN* 3.0 38.8 + - - +
219B LEU* 3.5 19.7 - - - +
119C LEU* 6.2 2.0 - - - +
120C VAL* 5.7 0.8 - - - +
----------------------------------------------------------
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