Contacts of the helix formed by residues 193 - 210 (chain B) in PDB entry 2VN9
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 LYS 193 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B HIS* 3.2 78.7 + - + +
131B GLY* 4.8 1.4 - - - -
133B VAL* 3.6 15.8 - - + +
164B VAL* 4.0 13.4 - - + +
166B GLY* 3.1 29.5 + - - +
167B ASP* 3.2 21.8 + - - +
169B GLN* 4.6 1.8 + - - +
192B GLY* 1.3 70.8 - - - -
194B PRO* 1.3 71.0 - - + +
195B VAL 3.0 1.6 + - - -
196B ASP* 3.1 11.1 + - - +
197B MET* 3.9 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLN* 4.2 15.7 - - - +
184B GLU* 4.4 0.9 - - - +
192B GLY 3.4 4.5 - - - +
193B LYS* 1.3 95.7 - - + +
195B VAL* 1.3 63.0 + - + +
197B MET* 2.9 23.2 + - + +
198B TRP 3.1 4.9 + - - -
257B PRO* 3.7 33.7 - - + +
260B ARG* 3.0 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 3.5 18.8 - - + -
135B ARG* 4.4 14.6 - - + -
180B TYR 5.0 1.6 - - - +
182B SER* 3.4 16.7 - - - +
184B GLU* 3.1 22.9 - - - +
185B VAL* 3.9 6.5 - - + -
191B TYR* 3.5 31.4 - - + -
192B GLY 3.2 18.2 - - - +
193B LYS 3.0 1.6 + - - -
194B PRO* 1.3 77.3 - - - +
196B ASP* 1.3 65.5 + - - +
198B TRP* 3.6 4.2 + - - +
199B ALA* 3.3 23.9 + - - +
260B ARG* 4.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B VAL* 4.2 3.9 - - + +
127B CYS* 5.7 0.7 - - - +
128B HIS* 2.9 34.8 + - + +
133B VAL* 3.2 11.1 - - - +
134B HIS* 3.0 22.9 + - - +
135B ARG* 2.9 28.2 + - - -
137B LEU* 3.5 27.4 - - + +
193B LYS 3.1 1.1 + - - +
194B PRO 3.1 0.6 - - - -
195B VAL* 1.3 81.1 - - - +
197B MET* 1.3 58.1 + - - +
199B ALA* 3.5 3.5 + - - +
200B CYS* 3.0 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 3.6 25.6 - - + -
124B VAL* 4.1 13.9 - - - -
128B HIS* 4.6 4.9 - - + +
193B LYS 4.4 8.3 - - - +
194B PRO* 2.9 14.1 + - + +
196B ASP* 1.3 75.4 - - - +
198B TRP* 1.3 62.8 + - - +
199B ALA 3.3 0.2 - - - -
200B CYS* 3.4 5.5 + - + +
201B GLY 3.1 16.8 + - - -
252B MET* 3.4 31.6 - - + +
260B ARG* 4.0 10.3 - - + -
261B ILE* 3.3 31.0 - - + +
262B THR* 3.9 6.5 - - - +
263B ALA* 3.5 33.4 - - - +
266B ALA* 4.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TYR 3.5 20.4 + - - -
181B LEU 3.2 16.4 + - - -
182B SER* 3.7 14.4 - - - -
183B PRO* 3.6 35.4 - - + -
194B PRO 3.1 5.9 + - - -
195B VAL 3.6 9.2 - - - +
197B MET* 1.3 75.0 - - - +
199B ALA* 1.3 62.0 + - - +
201B GLY 3.1 2.3 + - - -
202B VAL* 3.0 33.0 + - + +
214B PHE* 3.4 35.5 - + - -
226B ILE* 4.0 13.0 - - + +
229B GLY* 4.5 7.6 - - - -
252B MET 3.7 22.2 - - - -
253B LEU* 3.4 36.0 - - + +
254B THR 3.7 11.2 - - - -
255B ILE* 3.9 1.8 - - + -
260B ARG* 3.7 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ARG 6.3 1.1 - - - -
137B LEU* 3.8 31.4 - - + +
180B TYR* 4.1 20.1 - - + +
195B VAL 3.3 11.8 + - - +
196B ASP* 3.6 11.9 - - - +
198B TRP* 1.3 80.1 - - - +
200B CYS* 1.3 55.7 + - - +
202B VAL* 3.2 7.8 + - - +
203B ILE* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 4.3 7.8 - - + +
120B ILE* 4.3 20.4 - - - -
121B LEU* 4.3 14.6 - - + -
124B VAL* 4.3 8.3 - - - -
137B LEU* 4.2 13.5 - - - -
196B ASP 3.0 27.9 + - - -
197B MET* 3.7 13.0 - - + +
198B TRP 3.3 0.2 - - - -
199B ALA* 1.3 73.5 - - - +
201B GLY* 1.3 58.9 + - - +
203B ILE* 3.8 10.0 - - - +
204B LEU* 2.9 30.5 + - - +
252B MET* 3.8 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B MET 3.1 11.3 + - - -
198B TRP 3.1 4.9 + - - -
200B CYS* 1.3 71.3 - - - +
202B VAL* 1.3 59.4 + - - +
204B LEU* 3.4 4.0 + - - +
205B TYR* 2.9 30.7 + - - +
249B ILE* 4.5 5.1 - - - +
252B MET* 3.5 27.3 - - - -
253B LEU* 3.8 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B GLY 3.8 18.4 - - - +
180B TYR* 3.6 28.5 - - + -
198B TRP* 3.0 37.0 + - + +
199B ALA 3.2 7.4 + - - +
201B GLY* 1.3 76.1 - - - +
203B ILE* 1.3 61.5 + - - +
205B TYR* 3.3 3.6 + - - +
206B ILE* 3.1 29.1 + - + +
212B PRO* 5.2 1.8 - - + -
213B PRO* 3.8 22.7 - - + -
214B PHE* 4.2 11.9 - - + -
253B LEU* 3.7 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PHE* 4.2 12.7 - - + -
117B ILE* 4.1 15.7 - - + -
120B ILE* 4.4 7.4 - - + -
137B LEU* 3.7 37.5 - - + -
138B LYS* 3.8 7.6 - - - +
139B PRO* 4.8 3.1 - - + -
142B LEU* 4.3 21.8 - - + -
180B TYR* 4.4 16.6 - - + -
199B ALA 2.9 22.8 + - - +
200B CYS* 3.8 7.0 - - - +
201B GLY 3.3 0.2 - - - -
202B VAL* 1.3 73.5 - - - +
204B LEU* 1.3 54.8 + - - +
206B ILE* 3.2 8.8 + - - +
207B LEU* 2.7 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ALA* 5.1 0.7 - - + +
117B ILE* 3.8 21.7 - - + +
200B CYS 2.9 17.9 + - - +
201B GLY 3.6 4.7 - - - +
203B ILE* 1.3 78.2 - - - +
205B TYR* 1.3 62.3 + - - +
207B LEU* 3.2 6.9 + - + +
208B LEU* 3.0 30.5 + - + +
245B ALA 4.6 2.0 - - - +
248B LEU* 3.8 34.5 - - + -
249B ILE* 3.7 24.7 - - + -
252B MET* 4.2 11.9 - - + -
271B TRP* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLY 2.9 14.7 + - - +
202B VAL 3.4 9.6 - - - +
203B ILE 3.3 0.2 - - - -
204B LEU* 1.3 75.6 - - - +
206B ILE* 1.3 60.5 + - - +
208B LEU* 3.1 12.0 + - - +
209B VAL* 3.2 31.0 + - + +
211B TYR* 3.3 35.7 - + - -
213B PRO* 3.5 41.7 + - + +
231B TYR* 4.2 7.0 - + + -
232B ASP* 2.7 29.8 + - - -
233B PHE* 3.9 12.3 - + - -
234B PRO* 4.0 2.8 - - - +
238B TRP* 3.3 32.2 + + - -
249B ILE* 4.1 19.0 - - + +
253B LEU* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PHE* 3.6 24.7 - - + -
180B TYR* 4.1 13.0 - - + -
202B VAL* 3.1 35.5 + - + +
203B ILE* 3.7 6.1 - - + +
205B TYR* 1.3 75.7 - - - +
207B LEU* 1.3 59.1 + - - +
210B GLY* 2.7 35.1 + - - +
211B TYR 3.5 19.3 - - - +
212B PRO* 3.6 17.5 - - + -
213B PRO* 4.2 0.2 - - + -
291B LEU* 3.7 12.3 - - + +
294B PHE* 3.7 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.7 3.6 - - + -
99B PHE* 3.7 25.4 - - + -
102B ILE* 3.3 34.3 - - + -
108B TYR* 2.7 38.3 + - - +
113B ALA* 4.2 10.5 - - + +
116B CYS* 4.2 18.2 - - + -
117B ILE* 3.7 33.9 - - + -
120B ILE* 4.8 0.7 - - + -
203B ILE* 2.7 25.9 + - + +
204B LEU* 3.2 7.4 + - + +
206B ILE* 1.3 75.5 - - - +
208B LEU* 1.3 58.9 + - - +
287B THR* 3.6 2.6 - - - +
291B LEU* 4.9 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLU* 3.9 16.8 - - + -
113B ALA* 4.0 16.4 - - + -
204B LEU* 3.0 20.4 + - + +
205B TYR 3.1 6.2 + - - +
207B LEU* 1.3 77.6 - - - +
209B VAL* 1.3 56.2 + - + +
238B TRP* 4.0 10.1 - - + -
241B VAL* 3.9 15.7 - - + -
245B ALA* 3.7 27.4 - - + -
249B ILE* 3.8 23.1 - - + -
271B TRP* 3.9 23.3 - - + -
284B ARG* 3.0 20.5 + - - +
287B THR* 2.6 24.2 + - - +
----------------------------------------------------------
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 TYR* 3.2 29.6 + - + +
208B LEU* 1.3 79.5 - - + +
210B GLY* 1.3 63.9 + - - +
211B TYR* 3.4 30.0 + - + +
237B GLU* 3.9 15.9 - - + +
238B TRP* 3.3 45.8 - - + +
284B ARG* 4.3 11.0 - - - +
286B GLU 5.0 0.3 - - - -
287B THR* 3.7 12.5 - - - -
290B CYS* 3.3 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 2.7 31.6 + - - -
209B VAL* 1.3 73.5 - - - +
211B TYR* 1.3 56.7 + - - +
287B THR* 3.7 2.7 - - - +
290B CYS* 3.0 32.0 - - - +
291B LEU* 3.7 20.9 - - - -
294B PHE* 3.4 10.6 - - - +
----------------------------------------------------------
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