Contacts of the helix formed by residues 191 - 207 (chain A) in PDB entry 6C90
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 ILE 191 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER* 3.3 0.5 - - - -
190A PRO* 1.3 84.6 - - + +
192A LYS* 1.3 61.8 + - - +
193A ALA* 3.5 13.9 - - + +
194A LEU* 3.4 22.0 + - + +
195A SER* 3.1 25.3 + - - -
228A THR* 4.1 4.7 - - - -
256A TYR* 3.8 25.6 - - + +
260A SER* 3.6 17.0 - - - +
262A ARG* 3.3 28.9 - - - +
484A THR* 6.3 2.5 - - + -
1105A MLI 2.9 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 1.3 73.4 - - - +
193A ALA* 1.3 66.6 + - - +
195A SER* 3.0 4.9 + - - -
196A ASN* 3.0 30.8 + - - +
213A THR* 4.0 10.3 - - + +
214A GLY* 4.1 15.0 - - - +
215A ASP* 2.9 43.2 + - + +
228A THR* 3.7 23.0 - - + +
230A GLU* 4.8 3.6 - - - +
262A ARG* 4.5 5.1 - - - +
998A ARG* 4.3 18.8 + - - +
999A ARG* 5.1 3.0 - - - +
1002A GLU* 4.9 11.3 + - - +
1105A MLI 3.1 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 3.4 6.9 - - + -
192A LYS* 1.3 72.8 - - - +
194A LEU* 1.3 65.9 + - + +
196A ASN* 3.4 14.3 + - - +
197A GLN* 3.3 31.9 + - - +
464A LYS* 5.6 11.2 - - - +
465A GLU* 6.0 1.1 - - - +
468A GLU* 5.6 3.4 - - - +
1041A TYR* 5.3 0.7 - - - -
1105A MLI 2.8 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER* 4.2 11.2 - - - +
190A PRO* 4.4 15.3 - - + -
191A ILE* 3.4 33.0 + - + +
192A LYS 3.2 0.4 - - - -
193A ALA* 1.3 77.7 - - + +
195A SER* 1.3 61.9 + - - +
197A GLN* 3.2 24.0 + - - +
198A LYS* 2.8 32.6 + - + +
253A GLU* 5.4 7.0 - - + -
256A TYR* 5.0 2.5 - - + -
484A THR* 5.9 0.4 - - + +
487A MET* 3.4 46.2 - - + +
488A GLY* 4.1 2.7 - - - +
489A ILE* 4.8 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER* 3.5 19.7 - - - -
191A ILE 3.1 14.3 + - - -
192A LYS 3.0 9.1 + - - -
194A LEU* 1.3 76.4 - - - +
196A ASN* 1.3 56.7 + - - +
198A LYS* 4.4 0.4 - - - +
199A TYR* 2.8 31.7 + - - +
211A LEU* 3.8 7.6 - - - +
213A THR* 4.0 20.9 - - - -
226A VAL* 3.7 12.6 - - - +
227A MET 3.6 15.2 + - - -
228A THR* 3.6 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LYS* 3.0 20.2 + - - +
193A ALA* 3.5 15.5 - - - +
194A LEU 3.2 0.2 - - - -
195A SER* 1.3 76.5 - - - +
197A GLN* 1.3 61.4 + - - +
199A TYR* 3.3 8.1 + - - +
200A ARG 3.2 17.2 + - - -
211A LEU* 3.6 21.3 - - + +
213A THR* 4.3 8.3 + - - +
216A VAL* 4.6 5.5 - - - +
465A GLU* 4.4 5.1 + - - -
1039A SER* 3.7 33.5 + - - +
1041A TYR* 3.7 18.3 - - + +
1042A LEU* 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ALA* 3.3 19.1 + - - +
194A LEU* 3.2 20.1 + - - +
196A ASN* 1.3 76.8 - - - +
198A LYS* 1.3 62.1 + - - +
200A ARG* 3.3 6.1 + - - +
201A GLU* 3.0 17.8 + - - +
468A GLU* 2.9 34.0 + - - -
488A GLY* 3.9 2.7 - - - -
489A ILE* 3.2 53.4 + - + +
491A MET* 4.5 7.2 - - - +
1041A TYR* 3.7 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A THR* 3.4 24.7 + - + +
187A PHE* 3.6 36.1 - - + -
189A SER* 4.1 6.3 - - - +
194A LEU* 2.8 23.4 + - + +
195A SER 3.8 3.8 - - - +
197A GLN* 1.3 70.0 - - - +
199A TYR* 1.3 60.8 + - - +
201A GLU* 2.6 30.1 + - - +
202A MET* 2.9 39.5 + - + +
226A VAL* 4.3 8.1 - - + -
252A ASP* 3.4 22.4 - - - +
489A ILE* 3.9 29.1 - - + +
490A ASN* 5.1 2.2 + - - -
1101A ADP 5.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A SER 2.8 21.2 + - - +
196A ASN 3.6 3.4 - - - +
198A LYS* 1.3 73.1 - - - +
200A ARG* 1.3 79.8 + - - +
203A TYR* 2.7 60.9 + - + +
209A VAL* 3.8 27.9 + - + -
210A GLY* 3.7 17.0 - - - -
211A LEU* 3.7 31.0 - - + -
218A ILE* 3.8 22.9 - - + +
226A VAL* 4.1 10.7 - - + +
1041A TYR 4.3 2.5 - - - -
1042A LEU* 3.9 30.3 - - + -
681B SER* 5.4 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ASN 3.2 7.9 + - - +
197A GLN 3.3 8.3 + - - +
199A TYR* 1.3 90.9 + - - +
201A GLU* 1.3 64.8 + - - +
203A TYR* 3.6 22.8 - - - -
204A GLU* 2.9 45.9 + - + +
1041A TYR* 2.8 40.3 + - + +
1042A LEU* 3.3 24.7 + - - +
681B SER* 5.4 3.2 - - - -
685B TYR* 3.5 53.1 - - + +
686B LEU* 4.4 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A THR* 4.3 8.4 + - - +
172A GLU* 4.9 3.6 - - - +
197A GLN 3.0 13.3 + - - +
198A LYS* 2.6 46.9 + - - +
199A TYR 3.3 0.2 - - - -
200A ARG* 1.3 79.2 - - - +
202A MET* 1.3 77.7 + - + +
204A GLU* 3.5 5.4 + - - +
205A GLU* 3.4 19.1 + - - +
489A ILE* 3.8 10.4 - - + +
490A ASN* 3.1 27.8 + - - +
1101A ADP 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A THR* 4.3 6.7 - - + -
171A ALA* 5.9 0.2 - - - -
172A GLU* 3.9 25.8 - - + +
175A ILE* 3.7 28.0 - - + -
187A PHE* 5.2 10.3 - - + -
198A LYS* 2.9 27.3 + - + +
199A TYR 4.1 1.3 - - - +
201A GLU* 1.3 106.0 - - + +
203A TYR* 1.3 56.5 + - - +
205A GLU* 3.0 2.3 + - + -
206A PHE* 2.7 51.1 + - + -
209A VAL* 3.5 19.9 - - + +
224A CYS* 5.0 3.1 - - - -
226A VAL* 4.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TYR* 2.7 49.0 + - + +
200A ARG* 3.6 31.6 - - - +
202A MET* 1.3 73.2 - - - +
204A GLU* 1.3 65.4 + - - +
207A GLN* 2.8 71.0 + - + +
209A VAL* 3.7 19.8 - - + +
219A ASN* 6.1 1.1 - - - -
686B LEU* 5.7 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ARG* 2.9 47.8 + - + +
201A GLU* 3.8 6.3 - - - +
203A TYR* 1.3 82.3 - - - +
205A GLU* 1.3 55.7 + - - +
207A GLN* 3.1 11.6 - - - +
685B TYR* 5.4 3.6 - - + -
686B LEU* 3.4 16.4 - - - +
689B ARG* 2.9 32.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
134A LYS* 3.3 32.1 + - - +
172A GLU* 4.3 14.8 - - - +
201A GLU 3.4 11.8 + - - +
202A MET* 3.0 10.1 + - + +
204A GLU* 1.3 79.1 - - - +
206A PHE* 1.3 81.4 + - + +
207A GLN* 3.6 9.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 4.4 8.7 - - + -
172A GLU* 3.4 31.2 - - + -
175A ILE* 3.9 24.5 - - + -
176A ALA* 3.8 26.7 - - + -
179A LEU* 4.3 19.3 - - + +
202A MET* 2.7 46.8 + - + +
205A GLU* 1.3 95.6 - - + +
207A GLN* 1.3 63.6 + - - +
208A ASP* 2.5 23.1 + - - +
209A VAL* 3.8 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A MET 3.9 0.6 + - - -
203A TYR* 2.8 70.3 + - + +
204A GLU* 3.1 18.7 - - - +
205A GLU 3.6 10.3 + - - -
206A PHE* 1.3 82.6 + - - +
208A ASP* 1.3 49.4 + - - +
209A VAL* 2.6 20.5 + - - +
219A ASN* 4.7 3.1 + - - -
----------------------------------------------------------
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