Contacts of the helix formed by residues 186 - 205 (chain B) in PDB entry 5GKF
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 186 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LYS* 5.6 0.2 - - - +
183B ARG* 3.8 27.9 + - - -
184B ARG* 3.6 7.4 + - - +
185B ALA* 1.3 76.9 - - - +
187B LEU* 1.3 68.3 - - - +
188B HIS* 3.3 5.4 - - + +
189B ALA* 3.1 18.6 + - - +
190B VAL* 3.7 2.9 + - - +
218B THR* 3.6 22.9 - - + -
221B ALA* 4.0 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A THR* 3.6 17.9 - - + -
162A GLY* 3.6 25.1 - - - +
186B GLU* 1.3 74.9 - - + +
188B HIS* 1.3 57.6 + - - +
190B VAL* 2.8 23.2 + - - +
191B ARG* 3.1 42.0 + - - +
218B THR* 4.2 6.4 + - - +
220B GLY* 3.4 35.4 - - - +
221B ALA* 3.8 4.3 - - - +
224B LEU* 3.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A HIS* 2.9 64.3 + + + -
191A ARG* 4.2 16.7 + - + +
192A GLN* 4.0 6.6 - - + +
186B GLU* 3.3 4.9 - - + +
187B LEU* 1.3 79.7 - - - +
189B ALA* 1.3 62.8 + - - +
191B ARG* 3.1 40.4 + - + +
192B GLN* 3.0 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B GLU* 4.2 4.2 - - + +
181B LYS* 3.9 34.8 - - + +
185B ALA* 4.1 5.4 - - + -
186B GLU* 3.1 14.3 + - - +
187B LEU 3.0 0.8 + - - -
188B HIS* 1.3 77.0 - - - +
190B VAL* 1.3 63.7 + - - +
192B GLN* 3.2 14.7 + - - +
193B LEU* 3.0 23.5 + - - +
212B LEU* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLU 3.7 0.4 + - - +
187B LEU* 2.8 10.3 + - - +
189B ALA* 1.3 78.8 - - - +
191B ARG* 1.3 50.9 + - - +
193B LEU* 3.3 5.8 + - - +
194B LYS* 2.7 35.9 + - + +
212B LEU* 3.7 24.9 - - + -
221B ALA* 3.7 32.5 - - + +
224B LEU* 3.6 34.8 - - + -
225B LEU* 4.0 19.3 - - + +
228B GLU* 5.8 0.2 - - + -
230B LEU* 4.7 8.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
161A THR* 4.7 1.2 + - - +
162A GLY* 3.9 4.0 - - - -
191A ARG* 3.8 18.7 - - + +
192A GLN* 3.8 12.9 - - - +
195A SER* 3.4 33.6 + - - +
196A TYR* 3.7 29.1 + - - -
187B LEU* 3.1 44.4 + - - +
188B HIS* 3.1 48.2 + - + +
190B VAL* 1.3 76.6 - - - +
192B GLN* 1.3 57.9 + - - +
194B LYS* 3.2 7.2 + - - +
195B SER* 2.8 31.9 + - - -
224B LEU* 4.5 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ARG* 4.0 27.8 - - - +
179B GLU* 2.5 28.8 + - + +
181B LYS* 3.7 20.8 - - - +
188B HIS* 3.0 28.3 + - + +
189B ALA* 3.3 9.2 - - - +
191B ARG* 1.3 74.6 - - - +
193B LEU* 1.3 64.9 + - - +
195B SER* 3.0 13.7 + - - -
196B TYR* 3.0 43.3 + - + +
301B MG 3.5 3.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
177B VAL* 3.9 27.8 - - + +
179B GLU* 4.0 15.2 - - + +
189B ALA 3.0 13.3 + - - +
190B VAL 3.7 2.9 - - - +
192B GLN* 1.3 81.4 - - - +
194B LYS* 1.3 63.7 + - - +
196B TYR* 3.4 8.6 + - - +
197B VAL* 3.1 27.9 + - + +
210B GLY* 3.7 22.7 - - - -
211B ILE 3.6 10.5 - - - +
212B LEU* 3.6 36.8 - - + +
225B LEU* 4.2 8.1 - - + -
230B LEU* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LYS* 3.7 7.9 - - - +
195A SER* 5.7 3.4 - - - +
198A GLU* 2.6 29.4 + - - -
190B VAL* 2.7 23.9 + - + +
191B ARG* 3.6 6.5 - - - +
193B LEU* 1.3 73.4 - - - +
195B SER* 1.3 57.1 + - - +
197B VAL* 3.2 4.1 + - - +
198B GLU* 2.6 58.4 + - + +
224B LEU* 5.0 13.2 - - + -
227B LYS* 6.0 0.2 - - - +
228B GLU* 3.3 46.7 - - + +
230B LEU* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ARG* 3.4 32.3 + - - +
194A LYS* 5.7 7.5 + - - +
224A LEU* 4.6 11.8 - - - +
161B THR* 5.5 2.8 + - - +
191B ARG 2.8 13.5 + - - -
192B GLN 3.2 9.4 - - - -
194B LYS* 1.3 78.9 - - - +
196B TYR* 1.3 64.4 + - - +
198B GLU* 3.6 6.9 + - - +
199B ILE* 3.2 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ARG* 3.7 25.6 + - - -
159B ILE* 3.9 18.5 - - + +
161B THR 4.4 3.6 - - - -
162B GLY* 3.9 2.2 - - - -
163B ILE 3.1 38.4 + - - -
164B VAL* 3.9 25.6 - - + -
165B ALA 5.1 0.7 - - - -
177B VAL* 4.3 13.7 - - + -
178B LEU 5.7 0.2 - - - -
179B GLU* 4.1 11.9 - - + -
192B GLN* 3.0 50.5 + - + -
193B LEU* 3.6 11.4 - - + +
195B SER* 1.3 78.2 - - - +
197B VAL* 1.3 56.9 + - - +
199B ILE* 3.5 2.4 + - - +
200B LEU* 3.1 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B VAL* 4.3 11.7 - - + -
193B LEU* 3.1 24.3 + - + +
194B LYS* 3.7 6.5 - - - +
195B SER 3.2 0.4 - - - -
196B TYR* 1.3 75.4 - - - +
198B GLU* 1.3 63.2 + - + +
200B LEU* 3.3 4.7 + - - +
201B ARG* 2.8 67.7 + - + +
208B VAL* 4.4 10.2 - - + +
209B ARG 4.5 0.7 - - - -
210B GLY* 3.6 30.5 - - - +
230B LEU* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LYS* 2.3 27.8 + - - -
198A GLU* 4.1 2.4 - - - +
227A LYS* 5.5 5.4 + - - +
228A GLU* 5.5 0.5 - - - +
194B LYS* 2.6 58.7 + - + +
195B SER* 3.9 6.1 - - - +
197B VAL* 1.3 77.1 - - + +
199B ILE* 1.3 64.2 + - + +
201B ARG* 3.4 12.9 + - - +
202B GLU* 3.4 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU* 5.2 7.2 - - + -
227A LYS* 4.6 19.3 - - + +
159B ILE* 3.9 22.2 - - + -
160B GLY* 4.7 6.7 - - - +
161B THR* 3.4 45.8 - - + +
195B SER* 3.2 20.8 + - - +
196B TYR 3.6 5.2 - - - +
197B VAL 3.2 0.6 - - - -
198B GLU* 1.3 77.6 - - + +
200B LEU* 1.3 63.5 + - + +
202B GLU* 3.3 25.4 - - - +
203B GLU* 3.9 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 3.9 34.5 - - + -
164B VAL* 4.7 2.2 - - + -
167B LEU* 4.3 19.3 - - + -
175B ILE* 4.7 5.2 - - + -
177B VAL* 3.4 33.2 - - + -
196B TYR 3.1 19.8 + - - +
197B VAL 3.3 2.7 + - - +
199B ILE* 1.3 75.3 - - + +
201B ARG* 1.3 60.1 + - - +
202B GLU 3.0 2.0 - - - -
203B GLU* 3.1 5.3 + - + +
204B TYR* 2.8 55.0 + - + +
208B VAL* 4.4 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 2.8 44.1 + - - +
198B GLU* 3.7 12.1 - - - +
199B ILE 3.3 0.4 - - - -
200B LEU* 1.3 77.3 - - - +
202B GLU* 1.3 60.7 + - - +
205B GLY* 2.8 45.8 + - - +
206B ASP* 3.4 30.9 + - - +
208B VAL* 2.7 34.4 + - + +
228B GLU 4.3 9.1 + - - -
229B GLY 4.8 3.8 + - - -
230B LEU* 4.0 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LYS* 3.0 40.4 + - - -
198B GLU* 3.5 18.3 - - - +
199B ILE* 3.3 15.5 - - - +
201B ARG* 1.3 80.4 - - + +
203B GLU* 1.3 58.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ILE 3.9 3.2 + - - +
200B LEU* 3.1 6.6 + - + +
202B GLU* 1.3 81.6 - - - +
204B TYR* 1.3 93.4 + - + +
205B GLY 3.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ARG* 4.7 9.2 - - - -
175B ILE* 3.3 36.1 - - + -
200B LEU* 2.8 43.7 + - + +
203B GLU* 1.3 100.0 + - + +
205B GLY* 1.3 59.4 + - - +
207B LYS* 3.9 21.1 + - + +
208B VAL* 3.7 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ARG* 2.8 44.6 + - - +
203B GLU 3.6 1.8 + - - -
204B TYR* 1.3 73.9 - - - +
206B ASP* 1.3 63.4 + - - -
207B LYS* 3.2 9.6 + - - -
208B VAL* 3.7 4.2 - - - +
----------------------------------------------------------
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