Contacts of the helix formed by residues 192 - 209 (chain A) in PDB entry 2O0K
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 192 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ALA* 3.9 7.8 - - - +
191A HIS* 1.3 99.2 + - + +
193A GLY* 1.3 64.3 + - - +
194A SER* 2.9 25.8 + - - +
195A MET* 3.0 37.1 + - - +
196A SER* 3.5 6.9 + - - -
238A ALA* 4.7 2.0 - - - -
259A PHE* 4.6 10.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LYS* 1.3 72.8 - - - +
194A SER* 1.3 61.4 + - - +
196A SER* 3.3 9.7 + - - -
197A ALA* 3.0 24.8 + - - +
236A ALA* 4.8 2.9 - - - +
237A TYR* 4.6 5.2 - - - -
238A ALA* 4.1 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LYS* 3.3 26.9 - - - +
193A GLY* 1.3 77.6 - - - +
195A MET* 1.3 67.1 + - - +
197A ALA* 3.4 8.1 + - - +
198A GLU* 3.3 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ALA* 3.9 8.5 - - + -
191A HIS* 4.1 5.8 - - - -
192A LYS* 3.0 34.0 + - + +
194A SER* 1.3 75.4 - - - +
196A SER* 1.3 63.8 + - - +
198A GLU* 3.3 20.7 + - - +
199A VAL* 3.2 26.3 + - - +
255A GLU* 3.9 8.7 - - - +
256A ASP* 2.7 36.8 - - - +
259A PHE* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 3.4 21.4 + - - +
189A LEU 3.6 1.2 - - - -
190A ALA* 3.3 21.2 + - - +
192A LYS 3.5 1.8 + - - -
193A GLY 3.3 7.8 + - - -
194A SER 3.2 0.4 - - - -
195A MET* 1.3 78.8 - - - +
197A ALA* 1.3 58.5 + - - +
199A VAL* 3.3 4.6 + - - +
200A LEU* 2.9 27.5 + - - +
236A ALA* 3.6 21.6 - - - +
237A TYR 3.0 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLY 3.0 16.0 + - - +
194A SER* 3.7 8.1 - - - +
195A MET 3.3 0.2 - - - -
196A SER* 1.3 79.3 - - - +
198A GLU* 1.3 51.4 + - - +
200A LEU* 3.7 4.2 - - - +
201A ASP* 2.7 36.1 + - - +
223A LYS* 4.2 23.2 - - + +
224A GLY* 5.7 0.7 - - - -
236A ALA* 4.0 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A THR* 5.4 6.6 + - + +
194A SER 3.3 8.5 + - - +
195A MET* 3.3 31.0 - - - +
196A SER 3.2 0.4 - - - -
197A ALA* 1.3 75.6 - - - +
199A VAL* 1.3 69.7 + - + +
201A ASP* 3.5 8.1 - - - +
202A ARG* 2.9 39.9 + - + +
255A GLU* 5.4 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A THR* 4.5 12.8 - - + -
170A VAL* 4.1 24.9 - - + -
171A ALA* 4.8 1.3 - - - +
174A LEU* 4.5 1.1 - - + -
188A ILE* 3.9 18.4 - - + -
195A MET 3.2 11.2 - - - +
196A SER* 3.3 8.6 + - - +
198A GLU* 1.3 81.8 - - + +
200A LEU* 1.3 55.5 + - - +
202A ARG* 3.5 8.0 + - - +
203A THR* 2.6 37.0 + - - +
253A TYR* 4.2 9.9 - - + +
255A GLU* 2.6 35.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 3.9 10.3 - - + +
196A SER 2.9 16.5 + - - +
197A ALA* 3.7 6.3 - - - +
199A VAL* 1.3 78.9 - - - +
201A ASP* 1.3 60.7 + - - +
203A THR* 3.1 11.2 + - - -
204A LYS* 2.9 43.0 + - + +
222A ASN 4.7 0.9 - - - +
223A LYS 3.9 10.3 - - - +
224A GLY 3.5 10.3 - - - +
225A SER* 3.5 37.5 - - - +
226A ILE* 4.5 8.7 - - + -
234A ILE* 4.2 31.9 - - + +
235A GLY 4.9 0.2 - - - -
236A ALA* 4.5 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ALA 2.7 21.4 + - - +
198A GLU* 3.5 10.8 - - - +
200A LEU* 1.3 73.9 - - - +
202A ARG* 1.3 66.4 + - - +
204A LYS* 3.2 20.4 + - - +
205A GLN* 2.9 47.6 + - - +
223A LYS 5.7 0.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
127A ILE* 5.3 12.3 - - - +
167A THR* 2.9 36.2 - - + -
168A THR* 2.8 42.2 + - - +
171A ALA* 3.8 16.3 - - + +
198A GLU* 2.9 28.7 + - + +
199A VAL 3.6 5.6 - - - +
201A ASP* 1.3 82.0 + - - +
203A THR* 1.3 62.6 + - - +
205A GLN* 3.5 20.7 + - - +
206A ALA* 3.3 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA* 3.5 33.8 - - - +
174A LEU* 3.9 20.6 - - + +
175A ALA* 3.8 17.9 - - - +
188A ILE* 5.0 0.2 - - - +
199A VAL 2.6 20.6 + - - -
200A LEU* 3.1 14.9 + - + -
202A ARG* 1.3 76.8 - - - +
204A LYS* 1.3 62.7 + - - +
206A ALA* 3.4 3.5 + - - +
207A ILE* 3.0 33.6 + - + +
234A ILE* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LEU* 2.9 28.3 - - + +
201A ASP* 3.2 17.2 + - - +
203A THR* 1.3 74.4 - - - +
205A GLN* 1.3 54.6 + - + +
207A ILE* 2.9 7.9 + - - +
208A GLU* 2.7 40.2 + - - +
221A TRP* 3.2 51.3 + - + +
222A ASN 2.7 28.2 + - - +
223A LYS* 4.3 5.6 - - - +
226A ILE* 3.5 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA 5.4 0.7 - - - -
128A THR* 5.7 4.3 + - - -
201A ASP* 2.9 37.8 + - - +
202A ARG* 3.7 22.1 + - - +
203A THR 3.4 0.2 - - - -
204A LYS* 1.3 78.8 - - + +
206A ALA* 1.3 62.0 + - - +
207A ILE 3.5 0.2 + - - -
208A GLU* 4.3 15.5 - - - +
209A LEU* 3.5 34.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
125A CYS* 5.4 9.5 - - + -
126A ALA 4.7 15.1 + - - +
171A ALA* 4.6 11.4 - - + +
172A ILE* 5.1 8.5 - - + -
175A ALA* 4.5 13.4 - - + +
202A ARG 3.3 11.3 + - - +
203A THR 3.7 9.0 - - - +
204A LYS 3.1 0.8 - - - -
205A GLN* 1.3 80.4 - - - +
207A ILE* 1.3 59.1 + - - +
209A LEU* 3.9 3.6 + - - +
210A LEU* 3.3 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 5.5 0.4 - - + -
175A ALA* 3.8 22.2 - - + +
178A VAL* 4.4 10.5 - - + -
179A CYS* 4.9 2.9 - - - -
203A THR* 3.0 29.8 - - + +
204A LYS* 2.9 9.1 + - + +
206A ALA* 1.3 76.0 - - - +
208A GLU* 1.3 67.8 + - - +
209A LEU 3.1 1.8 - - - -
210A LEU* 3.1 26.8 + - + +
215A GLN* 2.9 30.4 + - + +
216A PRO* 5.0 8.3 - - + -
218A ILE* 5.7 1.6 - - + -
221A TRP* 4.2 16.4 - - + -
226A ILE* 4.2 24.5 - - + -
228A LEU* 5.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 2.9 30.1 + - - -
92A ASN* 3.2 27.4 + - + +
93A LEU* 3.5 26.2 - - + -
204A LYS* 2.7 26.5 + - - +
205A GLN* 4.0 16.9 + - - +
207A ILE* 1.3 71.8 - - - +
209A LEU* 1.3 66.2 + - + +
215A GLN* 3.5 7.4 - - - +
221A TRP* 3.7 20.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 4.0 7.5 - - - +
92A ASN* 4.7 14.8 - - - +
124A TYR 4.7 5.7 - - - +
126A ALA* 3.9 37.6 - - + +
127A ILE* 4.5 1.1 - - - -
128A THR 3.4 24.9 - - - +
129A HIS* 4.8 14.4 - - + +
134A VAL* 4.3 15.7 - - + +
205A GLN* 3.5 22.1 + - + +
206A ALA 4.3 4.9 - - - +
207A ILE 3.1 1.4 - - - -
208A GLU* 1.3 87.9 - - + +
210A LEU* 1.3 64.6 + - - +
211A PRO* 3.7 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