Contacts of the helix formed by residues 197 - 215 (chain B) in PDB entry 1I6O
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 ASN 197 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B TRP* 3.4 25.4 - - + +
196B THR* 1.3 96.5 + - - +
198B ARG* 1.3 63.5 + - - +
199B GLU* 2.7 30.1 + - - +
200B THR* 2.6 41.0 + - - +
201B LEU* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLN* 3.5 43.9 + - - +
168B TRP* 3.5 26.4 + - + -
169B LYS* 3.0 49.8 - - - +
197B ASN* 1.3 75.0 - - - +
199B GLU* 1.3 75.9 + - - +
201B LEU* 4.1 5.9 - - - +
202B GLU* 3.9 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ASN* 2.7 39.6 + - - +
198B ARG* 1.3 93.6 + - - +
200B THR* 1.3 69.0 + - + +
201B LEU 2.9 2.5 + - - -
202B GLU* 3.0 14.5 + - - +
203B GLN* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B THR 4.6 1.3 - - - -
195B ALA* 4.6 2.5 - - - -
196B THR* 3.1 33.7 + - + +
197B ASN* 2.6 32.6 + - - +
199B GLU* 1.3 74.9 - - + +
201B LEU* 1.3 55.2 + - - +
203B GLN* 4.1 13.9 + - - +
204B ARG* 2.9 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 4.2 10.1 - - + +
156B TYR* 4.4 15.5 - - + +
159B GLY* 3.6 42.4 - - - +
160B HIS* 4.1 22.0 - - + +
165B GLN* 4.4 3.8 - - - +
168B TRP* 3.9 6.5 - - + -
176B ILE* 4.0 7.4 - - + -
193B VAL 5.4 1.8 - - - +
195B ALA* 3.6 24.9 - - + -
197B ASN 3.1 20.1 + - - +
198B ARG 4.1 7.2 - - - +
199B GLU 2.9 0.4 + - - -
200B THR* 1.3 78.5 + - - +
202B GLU* 1.3 63.2 + - - +
204B ARG* 4.1 1.1 - - - +
205B TYR* 3.2 25.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
156B TYR* 2.4 31.9 + - - -
160B HIS* 3.3 21.4 + - - -
198B ARG 3.9 8.7 + - - +
199B GLU* 3.0 8.5 + - - +
201B LEU* 1.3 80.5 - - - +
203B GLN* 1.3 63.6 + - + +
205B TYR* 3.4 5.2 + - - +
206B ARG* 3.1 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLU* 3.3 20.7 + - - +
200B THR* 4.1 13.1 + - - +
202B GLU* 1.3 74.2 - - + +
204B ARG* 1.3 62.5 + - + +
205B TYR 3.0 1.7 + - - -
206B ARG* 3.1 6.6 + - - +
207B HIS* 2.8 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ASP* 2.8 47.8 + - - +
193B VAL* 4.1 14.3 - - - +
194B THR* 3.2 29.2 - - - +
200B THR* 2.9 31.5 + - + +
201B LEU 4.3 1.6 - - - +
203B GLN* 1.3 75.5 - - + +
205B TYR* 1.3 53.0 + - - +
207B HIS* 3.2 34.1 + - - +
208B GLY* 2.7 31.0 + - - -
211B ASN* 5.0 3.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
129B LYS* 2.9 19.5 + - - -
130B HIS* 4.4 0.7 + - - -
152B MSE 4.2 15.4 - - + +
153B GLU* 2.6 35.0 + - - -
156B TYR* 3.5 59.2 - + + -
193B VAL* 4.7 8.9 + - + +
201B LEU* 3.2 21.1 + - + +
202B GLU* 3.5 5.6 - - - +
203B GLN 3.0 0.2 - - - -
204B ARG* 1.3 74.5 - - - +
206B ARG* 1.3 72.3 + - + +
208B GLY* 3.0 11.1 + - - -
209B ILE* 3.0 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLU* 3.1 14.1 + - + +
203B GLN* 3.7 5.2 - - - +
205B TYR* 1.3 87.3 - - + +
207B HIS* 1.3 61.5 + - + +
209B ILE* 3.6 5.3 + - - +
210B SER* 3.1 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLN* 2.8 34.5 + - + +
204B ARG* 3.2 26.1 + - - +
206B ARG* 1.3 80.3 - - + +
208B GLY* 1.3 62.7 + - - +
210B SER* 2.6 25.2 + - - -
211B ASN* 2.7 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B MSE 3.1 25.6 - - - +
191B LEU 4.9 0.6 - - - +
192B ASP* 4.3 16.8 - - - -
204B ARG* 2.7 22.9 + - - +
205B TYR 3.0 0.6 + - - -
207B HIS* 1.3 76.1 - - - +
209B ILE* 1.3 61.2 + - - +
211B ASN* 3.6 15.9 - - - +
212B LEU* 3.8 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B HIS* 3.8 34.5 - - + +
133B LEU* 4.5 7.7 - - + +
149B LEU* 4.0 14.8 - - + -
152B MSE 3.3 20.8 - - + +
153B GLU* 4.3 2.7 - - - +
205B TYR* 3.0 44.2 + - + +
206B ARG* 3.9 5.6 - - - +
208B GLY* 1.3 73.7 - - - +
210B SER* 1.3 67.2 + - - +
212B LEU* 3.2 9.7 + - - +
213B LYS* 3.1 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ARG* 3.1 13.1 + - - -
207B HIS* 2.6 32.7 + - - -
209B ILE* 1.3 77.4 - - - +
211B ASN* 1.3 62.3 + - - +
213B LYS* 2.7 34.1 + - - +
214B LEU* 2.8 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ASP* 5.0 14.5 + - - +
204B ARG* 5.0 2.7 + - - +
207B HIS* 2.7 28.7 + - - +
208B GLY* 3.6 11.7 - - - +
210B SER* 1.3 84.1 + - - +
212B LEU* 1.3 56.7 + - + +
214B LEU* 3.2 3.1 + - - -
215B LYS* 2.6 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.4 22.6 - - + +
137B MSE 5.8 3.3 - - - +
145B THR* 4.8 8.3 - - + -
148B GLU* 4.1 27.8 - - + +
149B LEU* 3.8 29.6 - - + -
152B MSE 4.0 19.1 - - - -
208B GLY 3.8 11.9 - - - +
209B ILE* 3.2 6.8 + - - +
211B ASN* 1.3 82.9 - - + +
213B LYS* 1.3 62.0 + - - +
214B LEU 3.4 0.5 + - - -
215B LYS* 3.6 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B SER* 6.2 4.7 - - - -
133B LEU* 3.5 26.5 - - + +
136B GLU* 5.5 4.6 - - - +
209B ILE* 3.1 18.2 + - + +
210B SER* 2.7 23.1 + - - +
212B LEU* 1.3 73.1 - - - +
214B LEU* 1.3 63.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B SER* 2.8 25.2 + - - +
211B ASN* 4.0 3.1 - - - +
213B LYS* 1.3 85.4 - - + +
215B LYS* 1.3 78.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B MSE 6.0 3.8 - - - +
211B ASN* 2.6 32.1 + - + +
212B LEU* 3.6 16.6 + - - -
214B LEU* 1.3 91.4 + - + +
----------------------------------------------------------
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