Contacts of the helix formed by residues 190 - 211 (chain K) in PDB entry 2I2X
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 CYS 190 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185K LEU* 3.4 7.4 + - - -
186K TYR* 3.0 15.5 + - + +
189K GLY* 1.3 79.7 - - - +
191K LEU* 1.3 68.3 + - - +
192K GLY 3.3 0.7 - - - -
193K SER* 3.2 2.8 + - - -
194K ILE* 3.1 28.4 + - + +
389K ILE* 4.5 7.0 - - + -
390K TYR* 4.0 26.2 - - - -
439K PHE* 4.0 22.0 - - - -
440K MET* 3.6 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167K GLY 4.6 0.2 - - - -
168K GLY* 3.9 12.1 - - - -
170K GLU* 4.1 2.0 - - - +
171K VAL* 3.8 28.7 - - + -
186K TYR* 2.8 50.1 + - + +
187K SER* 3.5 17.3 - - - +
190K CYS* 1.3 71.5 - - + +
192K GLY* 1.3 64.0 + - - +
194K ILE* 3.1 15.3 + - + +
195K ASP* 3.1 11.6 + - - +
454K PHE* 3.9 11.7 - - + -
459K TYR* 3.7 46.1 - - + -
461K PHE* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 192 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167K GLY* 3.6 21.4 + - - -
187K SER 3.0 12.9 + - - -
188K ILE* 3.4 12.1 + - - -
190K CYS 3.3 0.4 - - - -
191K LEU* 1.3 74.2 - - - +
193K SER* 1.3 56.2 + - - +
194K ILE 3.2 0.2 + - - -
195K ASP* 3.3 1.7 + - - +
196K MET* 2.9 33.8 + - - +
222K GLN* 5.0 0.2 - - - -
253K ARG* 3.9 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 193 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K ARG* 4.8 2.3 + - - -
188K ILE 3.6 3.0 + - - -
189K GLY* 2.4 28.7 + - - -
190K CYS 3.2 4.4 + - - -
192K GLY* 1.3 74.7 - - - +
194K ILE* 1.3 60.4 + - - +
196K MET* 3.9 1.8 - - - -
197K GLU* 3.3 18.7 + - - +
252K PRO* 4.2 3.5 + - - +
253K ARG* 3.7 18.1 + - - +
256K VAL* 3.7 28.7 - - - +
389K ILE* 3.8 24.2 + - - +
392K ARG* 5.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139K ARG* 3.7 13.1 + - - +
190K CYS 3.1 16.6 + - - +
191K LEU* 3.1 10.4 + - - +
193K SER* 1.3 75.1 - - - +
195K ASP* 1.3 65.5 + - - +
197K GLU* 3.1 18.7 + - - +
198K LEU* 3.3 10.9 + - - +
389K ILE* 3.8 17.7 - - + -
436K MET* 5.5 1.3 - - + -
440K MET* 4.0 15.5 - - + -
459K TYR* 3.7 28.0 - - + +
461K PHE* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 195 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130K ARG* 2.7 44.8 + - - -
138K LEU* 3.8 20.6 - - + +
139K ARG* 4.9 3.5 + - - +
165K SER* 4.4 2.3 + - - -
167K GLY* 3.6 30.1 + - - -
191K LEU 3.1 10.2 + - - +
192K GLY 4.0 0.7 - - - +
194K ILE* 1.3 78.2 - - - +
196K MET* 1.3 63.1 + - + +
198K LEU* 3.3 10.9 + - - +
199K ILE* 3.2 28.3 + - - +
458K ASN 4.8 2.4 - - - +
459K TYR* 4.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 196 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165K SER* 3.5 6.1 - - - +
192K GLY 2.9 24.2 + - - +
193K SER 3.8 1.1 - - - +
194K ILE 3.2 0.2 - - - -
195K ASP* 1.3 77.4 - - - +
197K GLU* 1.3 56.9 + - - +
199K ILE* 4.4 2.2 - - - -
200K TRP* 3.2 42.6 + - + +
217K ASP* 3.1 36.1 - - + +
253K ARG* 3.5 39.9 - - - +
254K SER* 3.9 7.2 - - - +
256K VAL* 3.7 15.7 - - + +
257K ALA* 3.4 40.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K ALA* 3.2 37.2 + - - +
5K ARG* 4.4 16.9 + - - +
193K SER 3.3 11.4 + - - +
194K ILE* 3.1 13.0 + - - +
196K MET* 1.3 76.6 - - - +
198K LEU* 1.3 63.5 + - - +
201K THR* 2.7 36.7 + - - +
256K VAL* 3.5 12.1 - - + +
260K ALA* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138K LEU 4.5 0.4 - - - +
139K ARG* 3.8 44.6 - - + +
143K TYR* 3.4 40.0 + - + +
194K ILE 3.3 7.9 + - - +
195K ASP* 3.3 15.8 + - - +
197K GLU* 1.3 83.7 - - - +
199K ILE* 1.3 65.7 + - + +
201K THR* 3.4 4.5 + - - -
202K ASP* 3.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 199 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130K ARG* 3.3 37.2 - - - +
143K TYR* 3.5 20.4 - - + +
146K PHE* 4.3 14.4 - - + -
147K LEU* 5.6 0.4 - - + -
163K VAL* 4.6 7.0 - - + -
165K SER* 3.4 36.1 - - - +
195K ASP* 3.2 20.1 + - - +
196K MET* 4.7 1.3 - - - -
198K LEU* 1.3 77.3 - - + +
200K TRP* 1.3 74.3 + - + +
202K ASP* 3.2 3.3 + - - +
203K ILE* 2.8 37.3 + - + +
217K ASP* 4.3 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 200 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161K LEU 3.7 12.1 - - - -
162K SER* 4.2 3.8 - - - -
163K VAL* 3.9 14.6 - - + -
196K MET* 3.2 43.6 + - + +
199K ILE* 1.3 82.9 - - + +
201K THR* 1.3 65.3 + - - +
203K ILE* 3.7 28.9 - - + +
204K SER* 2.9 32.1 + - - -
214K SER* 3.2 27.4 - - - -
216K GLY* 3.3 47.1 - - - -
217K ASP* 2.8 27.9 + - + +
257K ALA* 3.7 21.8 - - + +
260K ALA* 3.8 10.8 - - + -
262K ALA* 4.0 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 201 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K ALA* 5.3 6.3 + - + +
197K GLU* 2.7 31.2 + - - +
198K LEU* 3.6 4.7 - - - -
200K TRP* 1.3 78.4 - - - +
202K ASP* 1.3 66.3 + - - +
204K SER* 3.7 2.3 + - - -
205K LYS* 3.3 31.9 + - + +
260K ALA* 3.8 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 202 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143K TYR* 2.6 35.8 + - - +
147K LEU* 3.7 24.9 - - + +
198K LEU* 3.3 12.8 + - - +
199K ILE 3.2 7.2 + - - +
201K THR* 1.3 79.4 - - - +
203K ILE* 1.3 64.4 + - - +
205K LYS* 3.3 28.3 + - - +
206K ILE* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146K PHE* 4.8 0.7 - - + -
147K LEU* 4.6 6.3 - - + -
150K PHE* 3.5 56.3 - - + -
161K LEU* 4.3 15.2 - - + +
163K VAL* 4.1 15.0 - - + -
199K ILE* 2.8 37.0 + - + +
200K TRP* 3.7 34.5 - - + -
202K ASP* 1.3 73.2 - - - +
204K SER* 1.3 58.9 + - - +
206K ILE* 3.1 9.0 + - - +
207K ALA* 2.8 26.7 + - - +
214K SER* 4.3 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 204 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200K TRP* 2.9 22.6 + - - -
201K THR 4.0 2.5 - - - -
203K ILE* 1.3 73.9 - - - +
205K LYS* 1.3 64.4 + - - +
207K ALA* 4.0 0.9 - - - +
208K LYS* 3.1 24.8 + - - +
214K SER* 2.9 27.6 + - - -
260K ALA 3.7 9.4 - - - -
261K GLY* 3.1 27.5 - - - -
262K ALA 3.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 205 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201K THR* 3.3 22.8 + - + +
202K ASP* 3.3 31.9 + - - +
204K SER* 1.3 78.9 - - - +
206K ILE* 1.3 57.9 + - + +
208K LYS* 3.4 5.8 + - - +
209K LYS* 3.1 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 206 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147K LEU* 3.7 46.9 - - + +
150K PHE* 4.2 10.3 - - + -
151K GLU* 3.4 45.3 - - + +
161K LEU* 4.3 10.1 - - + -
202K ASP 3.1 15.9 + - - +
203K ILE* 3.1 8.8 + - - +
205K LYS* 1.3 80.0 - - + +
207K ALA* 1.3 53.1 + - - +
209K LYS* 4.6 7.0 - - + -
210K THR* 2.7 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161K LEU* 4.3 5.6 - - + +
203K ILE 2.8 15.2 + - - +
204K SER 4.0 1.8 - - - +
205K LYS 3.3 0.2 - - - -
206K ILE* 1.3 75.2 - - - +
208K LYS* 1.3 64.8 + - - +
210K THR 3.4 0.3 + - - -
211K GLY* 3.1 4.5 + - - -
212K THR* 2.8 46.8 + - - +
213K ILE 3.8 3.6 - - - -
214K SER* 3.3 37.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 208 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204K SER 3.1 18.3 + - - +
205K LYS* 3.8 5.6 - - - +
207K ALA* 1.3 79.5 - - - +
209K LYS* 1.3 60.7 + - - +
211K GLY* 3.5 8.5 + - - -
212K THR 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 209 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151K GLU* 3.4 24.3 + - - +
155K GLU* 5.0 8.3 + - - -
205K LYS* 3.1 17.3 + - + +
206K ILE* 4.0 8.3 - - + +
208K LYS* 1.3 77.9 - - - +
210K THR* 1.3 63.8 + - + +
211K GLY 3.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 210 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151K GLU* 4.3 14.6 - - + +
154K ALA* 3.3 27.8 - - + +
155K GLU* 4.1 24.9 - - + +
206K ILE* 2.7 23.0 + - + +
207K ALA 3.5 0.3 + - - -
208K LYS 3.3 0.2 - - - -
209K LYS* 1.3 86.8 - - + +
211K GLY* 1.3 60.1 + - - +
212K THR* 2.7 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207K ALA 3.1 5.3 + - - -
208K LYS 3.5 6.9 + - - -
209K LYS 3.4 4.0 + - - -
210K THR* 1.3 78.2 - - - +
212K THR* 1.3 61.6 + - - +
----------------------------------------------------------
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