Contacts of the helix formed by residues 192 - 208 (chain A) in PDB entry 5I0H
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 192 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLU 4.9 0.2 + - - -
189A LYS 4.5 6.8 + - - -
190A THR* 3.3 16.3 - - - -
191A SER* 1.4 77.8 + - - +
193A VAL* 1.4 59.2 + - - +
194A GLU* 3.3 7.7 + - - +
195A ARG* 3.3 49.7 + - + +
196A ALA 3.0 23.6 + - - -
420A ARG* 3.4 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLU* 4.7 0.7 - - - +
191A SER* 3.0 25.2 + - - +
192A CYS* 1.4 78.4 - - - +
194A GLU* 1.4 64.8 + - - +
196A ALA* 3.2 4.6 + - - +
197A ILE* 2.9 33.6 + - + +
235A ILE* 3.5 34.8 - - + +
236A GLN 4.3 8.7 - - - +
237A GLY* 3.9 20.6 - - - -
420A ARG* 4.5 6.7 - - - +
421A ILE* 3.9 25.6 - - + +
422A LYS 5.3 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A SER* 3.9 28.2 + - - +
178A SER* 2.6 29.1 + - - +
179A GLN* 3.0 29.2 - - + +
188A GLU 4.7 4.9 - - - +
191A SER* 4.6 3.1 + - - -
192A CYS* 4.5 3.5 - - - -
193A VAL* 1.4 90.1 + - - +
195A ARG* 1.3 62.2 + - - +
197A ILE* 3.2 9.0 + - - +
198A LEU* 3.0 30.2 + - + +
234A ASN* 3.2 12.0 + - - -
235A ILE* 4.0 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A CYS* 3.3 44.4 + - + +
194A GLU* 1.3 77.6 - - - +
196A ALA* 1.4 55.6 + - - +
198A LEU* 3.3 8.3 + - - +
199A GLU* 2.9 42.5 + - + +
315A VAL* 4.0 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A CYS 3.0 12.9 + - - +
193A VAL 3.2 8.3 + - - +
195A ARG* 1.4 73.0 - - - +
197A ILE* 1.3 66.0 + - - +
199A GLU 3.1 1.4 + - - -
200A SER* 3.0 19.9 + - - -
315A VAL* 3.8 14.5 - - + +
316A MET* 3.2 10.9 - - - +
420A ARG* 3.7 40.6 - - + +
421A ILE* 3.8 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 4.4 21.1 - - + +
175A SER* 4.9 8.3 - - - +
193A VAL* 2.9 31.0 + - + +
194A GLU* 3.2 7.8 + - - +
196A ALA* 1.3 73.9 - - - +
198A LEU* 1.3 62.3 + - + +
200A SER* 2.7 28.4 + - - +
201A SER* 4.3 1.6 + - - -
225A VAL* 5.0 5.2 - - + -
227A LEU* 3.9 27.6 - - + -
235A ILE* 3.7 31.9 - - + -
237A GLY 4.3 8.5 - - - -
238A GLY 4.5 0.2 - - - +
240A ILE* 6.0 1.1 - - + -
421A ILE* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LYS* 5.0 1.8 - - - +
171A LEU* 3.7 33.0 - - + -
172A LYS* 3.7 20.6 - - + +
175A SER* 3.6 31.6 - - - +
176A VAL* 6.2 1.1 - - + -
194A GLU 3.0 20.5 + - - +
195A ARG* 3.8 6.3 - - - +
197A ILE* 1.3 75.4 - - + +
199A GLU* 1.3 63.6 + - + +
200A SER 3.2 1.4 + - - -
201A SER* 3.4 17.3 + - - -
202A PRO* 3.6 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ARG* 2.9 27.3 + - + +
196A ALA 3.1 4.4 + - - +
198A LEU* 1.3 74.8 - - + +
200A SER* 1.3 64.3 + - - +
201A SER 3.3 0.4 - - - -
202A PRO* 3.3 21.4 - - - +
203A ILE* 3.7 5.0 - - - +
308A GLU* 4.6 3.8 - - - +
311A THR* 4.7 9.4 - - - +
312A ALA* 3.4 42.6 + - + +
315A VAL* 3.9 26.4 - - + +
316A MET* 3.6 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 5.8 1.9 - - - +
196A ALA 3.0 9.4 + - - -
197A ILE* 2.7 22.3 + - - +
199A GLU* 1.3 78.8 - - - +
201A SER* 1.4 58.9 + - - +
203A ILE* 3.3 4.5 + - - +
204A MET* 2.9 47.6 + - - +
223A LYS* 5.3 0.5 + - - -
240A ILE* 3.6 10.2 - - - +
316A MET* 3.7 6.5 - - - -
417A ILE* 3.7 31.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LYS* 3.8 33.5 - - - +
171A LEU* 4.7 8.7 - - - +
197A ILE 5.0 0.7 + - - -
198A LEU* 3.4 9.7 + - - -
199A GLU 3.3 0.2 - - - -
200A SER* 1.4 77.8 + - - +
202A PRO* 1.4 64.1 - - - +
203A ILE 3.3 0.2 + - - -
204A MET* 3.3 7.4 + - - +
205A GLU* 2.8 39.5 + - - +
223A LYS* 3.9 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU 3.6 8.7 - - - +
199A GLU* 3.3 31.6 - - - +
201A SER* 1.4 92.1 - - - +
203A ILE* 1.3 59.9 + - - +
205A GLU* 4.2 6.9 - - + +
206A ALA* 3.0 24.8 + - - +
308A GLU* 3.7 43.3 - - + +
309A VAL* 3.8 6.3 - - + +
312A ALA* 4.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLU 3.7 1.6 - - - +
200A SER 3.3 5.3 + - - +
201A SER 3.2 1.0 - - - -
202A PRO* 1.3 78.5 - - - +
204A MET* 1.3 64.0 + - - +
206A ALA* 3.2 4.3 + - - +
207A PHE* 3.1 41.5 + - + -
309A VAL* 4.4 6.7 - - + +
312A ALA* 3.6 41.5 - - + +
313A MET* 3.8 23.8 - - + +
316A MET* 3.8 29.6 - - + -
318A PHE* 4.3 3.4 - - + -
413A VAL* 3.5 31.2 - - + -
417A ILE* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A SER* 2.9 42.9 + - - +
201A SER* 4.1 2.0 - - - +
203A ILE* 1.3 75.1 - - + +
205A GLU* 1.3 57.6 + - + +
207A PHE* 3.7 3.7 - - - +
208A GLY* 2.7 30.1 + - - -
221A PHE* 3.7 22.7 - - + -
223A LYS* 3.6 36.8 - - + +
240A ILE* 3.7 28.5 - - + -
410A PHE* 4.5 3.2 - - + -
413A VAL* 5.6 1.3 - - + -
414A ILE* 3.7 27.6 - - + -
417A ILE* 3.6 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A THR* 3.4 11.9 - - + +
168A LYS* 2.7 41.4 + - - +
201A SER* 2.8 27.7 + - - +
202A PRO* 4.2 5.6 - - + +
204A MET* 1.3 73.7 - - + +
206A ALA* 1.3 59.4 + - - +
209A ASN* 2.9 51.1 + - + +
217A ASN* 2.9 29.5 + - - +
221A PHE* 6.1 0.9 - - + -
261A HIS* 3.4 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PRO 3.0 19.3 + - - +
203A ILE 3.2 4.0 + - - +
205A GLU* 1.3 78.7 - - - +
207A PHE* 1.3 61.4 + - + +
209A ASN 4.2 0.2 - - - +
260A TYR* 4.0 0.3 - - - +
261A HIS* 3.5 18.7 + - + -
262A ILE* 2.9 43.7 + - + +
305A SER* 6.2 2.2 - - - -
309A VAL* 3.5 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ILE* 3.1 34.1 + - + +
204A MET* 4.3 1.1 - - - +
206A ALA* 1.3 79.3 - - + +
208A GLY* 1.3 59.1 + - - +
209A ASN 3.8 0.2 - - - -
245A LEU* 4.3 0.3 - - - +
260A TYR* 3.3 9.3 - - - -
262A ILE* 3.8 29.6 - - + -
309A VAL* 4.6 1.6 - - + -
313A MET* 3.5 26.7 - - + -
326A VAL* 3.7 31.4 - - + -
330A LEU* 4.3 11.7 - - + -
406A TYR* 2.6 45.4 + + - -
409A CYS* 4.6 7.4 - - + -
410A PHE* 3.7 27.3 - + + -
413A VAL* 4.4 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A MET 2.7 19.3 + - - -
207A PHE* 1.3 75.5 - - - +
209A ASN* 1.4 64.5 + - - +
220A ARG* 2.8 32.9 + - - +
221A PHE* 3.4 15.7 - - - -
245A LEU* 4.1 2.0 - - - -
260A TYR* 3.5 9.6 - - - -
410A PHE* 4.0 7.0 - - - -
----------------------------------------------------------
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