Contacts of the helix formed by residues 219 - 236 (chain A) in PDB entry 1O0W
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 THR 219 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLN* 3.0 34.6 + - - +
201A PHE* 3.5 14.5 - - - +
217A GLY 3.2 0.7 - - - -
218A ARG* 1.3 80.2 - - - +
220A LYS* 1.3 64.7 + - - +
221A LYS* 3.6 8.3 + - - +
222A GLU* 3.0 25.0 + - + +
223A ALA* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 4.5 36.8 - - + +
201A PHE* 3.7 24.4 - - + -
203A VAL* 4.3 2.6 - - + +
219A THR* 1.3 72.7 - - - +
221A LYS* 1.3 63.9 + - + +
223A ALA* 3.3 3.4 + - - +
224A GLU* 3.0 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS 6.0 0.4 + - - -
170A LYS* 5.1 2.9 - - - +
219A THR* 3.6 8.0 + - - +
220A LYS* 1.3 79.3 - - - +
222A GLU* 1.3 62.4 + - - +
224A GLU* 3.2 15.8 + - - +
225A LYS* 3.0 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLN* 3.8 10.5 + - - +
152A GLU* 5.2 1.0 - - - -
155A PHE* 3.6 36.6 - - + +
216A LYS 5.2 0.2 - - - +
217A GLY* 3.4 7.5 - - - -
218A ARG* 2.7 64.0 + - - +
219A THR* 3.0 23.2 + - - +
221A LYS* 1.3 77.3 - - - +
223A ALA* 1.3 58.9 + - - +
225A LYS* 3.1 13.9 + - + +
226A GLU* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PHE* 3.2 29.6 - - + +
203A VAL* 3.6 22.7 - - + -
215A GLY 3.9 6.9 - - - +
216A LYS 3.8 3.6 - - - -
217A GLY* 3.6 13.1 - - - +
219A THR 3.0 17.0 + - - +
220A LYS 3.7 1.1 - - - +
222A GLU* 1.3 74.5 - - - +
224A GLU* 1.3 57.2 + - - +
226A GLU* 3.1 2.1 + - - +
227A ALA* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LYS* 2.6 37.8 + - - +
187A TYR* 3.5 35.3 - - + +
203A VAL* 4.0 22.2 - - + -
220A LYS* 3.0 48.0 + - - +
221A LYS* 3.2 14.6 + - - +
223A ALA* 1.3 76.7 - - - +
225A LYS* 1.3 56.2 + - - +
227A ALA* 3.3 2.8 + - - +
228A ALA* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 5.1 18.9 - - - +
152A GLU* 4.5 7.1 + - - +
155A PHE* 4.3 20.4 - - + +
156A TYR* 3.0 36.5 + - + -
169A TYR* 3.5 28.1 - - + +
170A LYS* 4.3 21.5 - - + +
221A LYS* 3.0 24.6 + - - +
222A GLU* 3.4 14.8 - - + +
224A GLU* 1.3 75.8 - - - +
226A GLU* 1.3 57.9 + - - +
228A ALA* 3.3 1.6 + - - -
229A ARG 2.9 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A PHE* 3.6 22.5 - - + -
159A LYS* 2.9 19.4 + - - -
215A GLY* 4.1 2.0 - - - -
216A LYS 3.2 33.8 + - - +
222A GLU 2.9 8.3 + - - +
223A ALA 3.1 7.4 + - - +
225A LYS* 1.3 76.8 - - - +
227A ALA* 1.3 64.4 + - - +
229A ARG* 2.8 46.3 + - - +
230A ILE* 3.0 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 4.6 0.4 - - + -
203A VAL* 3.6 26.9 - - + +
205A VAL* 3.8 21.4 - - + +
213A ALA* 4.0 1.2 - - - +
214A THR 4.4 3.6 - - - -
215A GLY* 3.6 12.0 - - - +
223A ALA 2.8 20.8 + - - +
224A GLU* 3.5 8.5 - - - +
226A GLU* 1.3 73.7 - - - +
228A ALA* 1.3 57.1 + - - +
230A ILE* 3.4 2.5 + - - +
231A ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TYR* 3.7 28.0 - - + +
170A LYS* 3.8 3.8 - - + +
173A LEU* 3.8 15.8 - - + +
187A TYR* 3.4 24.4 - - - +
224A GLU 2.9 15.1 + - - +
225A LYS 3.6 4.7 - - - +
227A ALA* 1.3 76.3 - - - +
229A ARG* 1.3 58.0 + - - +
231A ALA* 3.9 0.5 - - - +
232A TYR* 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LYS* 3.6 12.2 - - - +
164A GLU* 3.5 31.6 + - - +
165A MET 4.6 0.2 - - - -
167A PHE* 5.8 0.7 - - + -
169A TYR* 3.4 49.9 - - + +
225A LYS 2.9 13.5 + - - +
226A GLU* 2.8 43.4 + - - +
228A ALA* 1.3 78.0 - - - +
230A ILE* 1.3 75.9 + - - +
232A TYR* 3.6 3.5 - - - +
233A GLU* 2.8 81.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ALA* 3.6 18.8 - - + -
214A THR 3.4 22.9 - - - +
215A GLY* 4.2 4.5 - - - -
226A GLU* 3.0 32.2 + - - +
227A ALA 3.8 4.3 - - - +
229A ARG* 1.3 92.7 - - - +
231A ALA* 1.3 61.2 + - - +
233A GLU* 3.4 6.2 + - - +
234A LYS* 2.9 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU* 4.0 14.4 - - + -
205A VAL* 3.4 24.7 - - + -
212A ILE* 3.7 17.5 - - + -
213A ALA* 3.6 8.2 - - + +
227A ALA 2.9 17.5 + - - +
228A ALA 3.9 2.9 - - - +
230A ILE* 1.3 75.0 - - - +
232A TYR* 1.3 58.6 + - - +
234A LYS* 4.3 1.6 - - - -
235A LEU* 2.8 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PHE* 3.8 30.1 - + + -
169A TYR* 5.4 1.3 - - + +
172A ALA* 3.6 45.2 - - + +
173A LEU* 3.9 13.7 - - + +
175A GLU* 5.7 2.2 + - - -
176A ILE* 4.4 17.4 - - + +
228A ALA 2.8 23.2 + - - +
229A ARG* 3.6 5.6 - - - +
231A ALA* 1.3 74.2 - - - +
233A GLU* 1.3 69.1 + - + +
235A LEU* 3.8 3.2 - - - +
236A LEU* 3.0 58.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLU* 4.4 10.6 - - - +
165A MET* 4.9 4.9 + - - +
167A PHE* 6.1 2.6 - - + -
229A ARG* 2.8 60.6 + - + +
230A ILE* 3.9 5.4 - - - +
232A TYR* 1.3 85.3 - - + +
234A LYS* 1.3 62.0 + - - +
236A LEU* 3.6 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A THR 4.6 3.6 + - - -
212A ILE* 2.8 44.2 + - + +
213A ALA* 5.2 2.0 - - + -
230A ILE* 2.9 21.5 + - + +
231A ALA 3.6 4.3 - - - +
233A GLU* 1.3 73.5 - - - +
235A LEU* 1.3 72.1 + - + +
236A LEU 3.0 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU* 3.8 24.7 - - + -
176A ILE* 4.3 6.3 - - + -
177A VAL* 4.2 10.8 - - + -
180A GLU* 3.9 25.6 - - - +
181A HIS* 5.9 3.1 - - - +
207A VAL* 5.4 2.2 - - + -
212A ILE* 3.9 34.3 - - + -
231A ALA 2.8 23.9 + - - +
232A TYR* 3.9 3.6 - - - +
234A LYS* 1.3 79.0 - - + +
236A LEU* 1.3 69.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE* 4.0 29.6 - - + -
232A TYR* 3.0 58.1 + - + +
233A GLU* 3.7 14.6 - - - +
234A LYS 3.0 14.5 - - - +
235A LEU* 1.3 85.1 - - + +
----------------------------------------------------------
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