Contacts of the helix formed by residues 191 - 213 (chain A) in PDB entry 3J8B
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 191 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A THR 2.7 14.4 + - - +
190A ARG* 1.3 71.4 - - - +
192A ALA* 1.3 62.7 + - - +
194A PHE* 3.3 7.7 + - - +
195A ARG* 3.1 24.3 + - - +
243A MET* 5.2 16.8 - - + +
245A LEU* 6.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ARG 3.4 0.6 - - - -
191A LYS* 1.3 77.8 - - - +
193A GLU* 1.3 61.3 + - - +
195A ARG* 3.7 6.4 + - - +
196A LYS* 3.4 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TRP* 5.2 14.6 - - + -
185A CYS* 6.0 0.9 - - + -
190A ARG* 3.3 19.7 + - + +
191A LYS 3.3 0.2 - - - -
192A ALA* 1.3 76.6 - - - +
194A PHE* 1.3 54.9 + - - +
196A LYS* 3.0 9.1 + - - +
197A LEU* 2.7 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A CYS* 3.9 21.5 - - + +
190A ARG 2.9 18.5 + - - +
191A LYS* 3.5 9.0 - - - +
193A GLU* 1.3 76.9 - - - +
195A ARG* 1.3 62.1 + - - +
197A LEU* 3.1 10.4 + - - +
198A CYS* 3.0 22.9 + - - +
239A SER* 6.3 2.9 - - - -
243A MET* 6.3 3.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
191A LYS 3.1 12.0 + - - +
192A ALA* 3.8 10.3 - - - +
193A GLU 3.3 0.2 - - - -
194A PHE* 1.3 75.8 - - - +
196A LYS* 1.3 61.5 + - - +
198A CYS* 3.3 8.3 + - - +
199A ASP* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ALA 3.4 10.9 + - - +
193A GLU* 3.0 11.7 + - - +
195A ARG* 1.3 74.5 - - - +
197A LEU* 1.3 66.0 + - - +
199A ASP* 3.2 8.7 + - - +
200A ASN* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ALA* 6.0 6.3 - - + -
185A CYS* 6.4 0.4 - - + -
193A GLU 2.7 16.1 + - - +
194A PHE* 3.3 14.1 - - - +
196A LYS* 1.3 73.7 - - - +
198A CYS* 1.3 62.4 + - - +
200A ASN* 3.0 10.5 + - - +
201A LEU* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PHE 3.0 12.3 + - - +
195A ARG* 3.4 12.3 - - - +
196A LYS 3.2 0.2 - - - -
197A LEU* 1.3 76.9 - - - +
199A ASP* 1.3 62.3 + - - +
201A LEU* 3.0 11.5 + - - +
202A ARG* 3.0 20.3 + - - +
236A GLN* 5.8 7.6 - - + -
248A GLU* 6.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ARG 3.2 9.6 + - - +
196A LYS* 3.2 11.2 + - - +
198A CYS* 1.3 78.6 - - - +
200A ASN* 1.3 62.8 + - - +
202A ARG* 3.1 10.5 + - - +
203A MET* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 6.5 1.3 - - + -
196A LYS 3.0 12.7 + - - +
197A LEU* 3.0 13.2 + - - +
199A ASP* 1.3 76.9 - - - +
201A LEU* 1.3 57.8 + - - +
203A MET* 3.2 9.2 + - - +
204A HIS* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU 3.0 11.2 + - - +
198A CYS* 3.0 13.2 + - - +
200A ASN* 1.3 77.3 - - - +
202A ARG* 1.3 62.2 + - - +
204A HIS* 3.4 8.2 + - - +
205A LEU* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A CYS 3.0 10.6 + - - +
199A ASP* 3.1 13.2 + - - +
201A LEU* 1.3 74.7 - - - +
203A MET* 1.3 65.2 + - - +
205A LEU* 3.1 7.2 + - - +
206A SER* 3.0 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP 3.1 12.4 + - - +
200A ASN* 3.6 10.1 - - - +
202A ARG* 1.3 75.7 - - - +
204A HIS* 1.3 62.0 + - - +
206A SER* 3.3 8.0 + - - -
207A GLN* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ARG* 4.8 19.1 - - + -
166A ASN* 5.1 8.5 - - - +
200A ASN 3.0 12.4 + - - +
201A LEU* 3.6 12.3 - - - +
202A ARG 3.2 0.2 - - - -
203A MET* 1.3 77.3 - - - +
205A LEU* 1.3 61.3 + - - +
207A GLN* 3.3 15.7 + - - +
208A ILE* 3.4 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU 3.1 15.0 + - - +
202A ARG* 3.1 7.6 + - - +
204A HIS* 1.3 73.8 - - - +
206A SER* 1.3 65.6 + - - +
208A ILE* 3.3 19.4 + - - +
209A GLN* 3.8 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ARG 3.0 12.1 + - - -
203A MET* 3.7 11.4 - - - -
205A LEU* 1.3 77.6 - - - +
207A GLN* 1.3 63.2 + - - +
208A ILE 3.4 0.2 + - - -
209A GLN* 3.6 12.6 + - - +
210A ARG* 3.6 9.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
166A ASN* 5.5 6.3 - - + -
203A MET 3.1 12.4 + - - +
204A HIS* 3.4 13.7 - - - +
205A LEU 3.2 0.4 - - - -
206A SER* 1.3 76.0 - - - +
208A ILE* 1.3 53.6 + - - +
210A ARG* 3.0 10.3 + - - +
211A HIS* 2.3 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASN* 5.3 7.2 - - + +
204A HIS 3.4 7.8 + - - +
205A LEU* 3.3 13.4 + - - +
206A SER 3.3 1.0 - - - -
207A GLN* 1.3 78.7 - - - +
209A GLN* 1.3 53.8 + - - +
211A HIS* 3.2 10.7 - - + +
212A HIS* 2.5 37.3 + - - +
217A ALA* 4.5 0.9 - - - +
218A ILE* 4.8 19.6 - - + +
220A LEU* 5.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU 3.8 5.3 + - - +
206A SER* 3.6 10.0 + - - +
207A GLN 3.3 0.4 - - - -
208A ILE* 1.3 79.5 - - - +
210A ARG* 1.3 62.5 + - - +
212A HIS* 3.5 14.8 + - - +
213A ASN* 4.0 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER 3.6 7.3 + - - +
207A GLN* 3.0 13.2 + - - +
209A GLN* 1.3 79.6 - - - +
211A HIS* 1.3 63.5 + - - +
212A HIS 3.4 0.3 + - - -
213A ASN* 3.6 12.2 + - - +
214A GLN* 3.8 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASN* 5.0 11.9 - - + -
207A GLN* 2.3 33.4 + - + +
208A ILE* 3.0 14.6 + - + +
210A ARG* 1.3 68.3 - - - +
212A HIS* 1.3 51.4 + - - +
214A GLN* 2.6 45.6 + - + +
217A ALA* 2.7 17.6 - - + +
218A ILE 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ILE 2.5 18.6 + - - +
209A GLN* 3.7 10.1 - - - +
210A ARG 3.3 0.6 - - - -
211A HIS* 1.3 72.6 - - - +
213A ASN* 1.3 63.7 + - - +
214A GLN 3.1 7.1 - - - +
217A ALA* 3.1 14.1 - - + +
218A ILE 4.5 8.5 - - - +
219A ASN* 6.2 0.7 - - - -
220A LEU* 6.0 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLN 4.0 5.1 + - - +
210A ARG* 3.6 10.2 + - - +
211A HIS 3.2 0.4 - - - -
212A HIS* 1.3 78.4 - - - +
214A GLN* 1.3 61.7 + - - +
215A SER* 3.8 1.0 + - - -
----------------------------------------------------------
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