Contacts of the helix formed by residues 218 - 239 (chain A) in PDB entry 2IWR
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 ASN 218 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A TYR* 5.2 5.8 - - + +
210A GLU 2.9 28.6 + - - +
211A THR* 4.0 5.6 - - + -
216A GLY 3.2 2.6 + - - -
217A LEU* 1.3 90.6 - - - +
219A VAL* 1.3 62.2 + - - +
220A ASP 3.6 1.8 - - - -
221A ARG* 3.5 38.2 + - + +
222A VAL* 3.2 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.8 30.1 - - + +
89A ARG* 4.0 10.5 - - + -
90A PHE* 3.7 38.1 - - + +
211A THR* 4.5 2.0 - - - -
213A ALA* 3.9 24.0 - - - +
216A GLY* 3.3 19.9 + - - +
217A LEU 3.1 11.4 - - - +
218A ASN* 1.3 73.4 - - - +
220A ASP* 1.3 70.9 + - - +
221A ARG 3.2 0.3 + - - -
222A VAL* 3.2 11.0 + - - +
223A PHE* 3.3 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ARG 5.4 0.3 - - - +
90A PHE* 3.3 36.5 - - + +
108A LYS* 4.7 3.4 + - - -
216A GLY 4.7 1.8 + - - -
219A VAL* 1.3 80.0 - - - +
221A ARG* 1.3 57.9 + - - +
223A PHE* 3.3 4.0 + - - +
224A GLN* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A TYR* 4.0 17.2 - - + -
218A ASN* 3.5 36.0 + - - +
219A VAL 3.1 0.4 - - - -
220A ASP* 1.3 76.6 - - - +
222A VAL* 1.3 67.9 + - - +
224A GLN* 4.5 4.7 - - - -
225A GLU* 2.8 63.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 5.1 2.7 - - + -
140A ILE* 4.1 22.9 - - + -
175A ALA* 4.5 0.7 - - + -
177A VAL* 3.9 21.5 - - + -
209A TYR* 3.7 36.3 + - + -
211A THR* 3.7 19.1 - - + -
218A ASN 3.3 15.9 - - - +
219A VAL* 3.2 7.5 + - - +
221A ARG* 1.3 77.3 - - - +
223A PHE* 1.3 67.5 + - + +
225A GLU* 4.0 0.5 - - - +
226A VAL* 3.0 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 4.0 16.2 - - + +
75A VAL* 4.7 2.2 - - + -
86A LEU* 3.9 33.0 - - + -
87A ILE* 4.2 19.5 - - + -
90A PHE* 3.5 46.2 - + + -
110A MET* 4.2 4.3 - - + +
119A VAL* 5.9 0.2 - - + -
121A ILE* 3.7 37.9 - - + -
140A ILE* 3.6 25.1 - - + -
219A VAL 3.3 17.0 - - - -
220A ASP 3.3 1.2 + - - +
222A VAL* 1.3 77.2 - - + +
224A GLN* 1.3 60.4 + - - +
226A VAL* 4.7 0.7 - - - -
227A ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 6.1 0.2 - - + -
110A MET* 4.0 19.8 - - + +
111A LEU 5.6 3.6 - - - +
112A VAL* 4.9 2.3 - - - +
220A ASP* 2.9 20.7 + - + +
221A ARG* 4.0 4.3 - - - +
223A PHE* 1.3 76.9 - - - +
225A GLU* 1.3 61.4 + - + +
227A ALA* 3.3 4.0 + - - +
228A GLN* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A SER* 5.5 0.3 - - - -
209A TYR* 2.7 35.9 + - - +
221A ARG* 2.8 58.9 + - + +
224A GLN* 1.3 74.6 - - + +
226A VAL* 1.3 60.8 + - - +
228A GLN* 3.3 7.8 + - - +
229A LYS* 2.9 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 4.1 15.7 - - + -
138A ALA* 3.4 29.8 - - + -
140A ILE* 4.3 13.5 - - + -
173A ALA* 5.0 6.3 - - + +
174A LEU 4.7 4.7 - - - +
175A ALA* 3.6 31.9 - - + +
207A SER* 6.2 0.2 - - - -
209A TYR* 4.9 5.6 - - - +
222A VAL* 3.0 23.7 + - + +
223A PHE 4.0 2.9 - - - +
225A GLU* 1.3 72.9 - - - +
227A ALA* 1.3 68.6 + - - +
229A LYS* 3.1 11.0 + - + +
230A VAL* 3.1 20.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
71A LEU* 3.7 24.0 - - + +
73A LEU* 4.6 7.6 - - + +
110A MET* 3.7 20.9 - - - -
112A VAL* 4.0 6.3 - - + -
119A VAL* 4.4 4.9 - - + -
223A PHE 2.9 19.6 + - - +
224A GLN 3.5 4.9 - - - +
226A VAL* 1.3 77.6 - - - +
228A GLN* 1.3 63.1 + - - +
230A VAL* 3.1 9.1 + - - +
231A VAL* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL* 3.6 11.3 - - + +
113A ASP* 3.4 40.3 + - - +
224A GLN 3.0 14.4 + - - +
225A GLU* 3.6 11.4 - - - +
226A VAL 3.2 0.2 - - - -
227A ALA* 1.3 75.8 - - - +
229A LYS* 1.3 58.1 + - - +
231A VAL* 3.2 16.6 + - - +
232A THR* 2.8 53.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ALA* 3.8 21.2 - - + +
174A LEU 2.9 15.7 + - - +
205A ARG* 2.9 28.7 + - + +
206A CYS 3.5 1.4 - - - -
207A SER* 2.7 34.8 + - - +
209A TYR* 5.6 1.3 - - - -
225A GLU* 2.9 17.3 + - - +
226A VAL* 3.1 16.1 + - + +
228A GLN* 1.3 78.2 - - + +
230A VAL* 1.3 56.6 + - - +
232A THR* 3.8 5.9 - - - -
233A LEU* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 3.6 24.5 - - + -
73A LEU* 4.6 7.9 - - + -
137A ASP* 3.7 29.8 - - + +
138A ALA* 3.6 27.1 - - + -
173A ALA* 4.2 5.8 - - + -
226A VAL 3.1 14.4 + - - +
227A ALA* 3.1 7.8 + - - +
229A LYS* 1.3 75.7 - - - +
231A VAL* 1.3 62.9 + - - +
233A LEU* 3.3 6.9 + - - +
234A ARG* 3.0 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 4.0 15.3 - - + -
112A VAL* 4.0 14.6 - - + +
113A ASP* 6.1 2.0 - - + -
115A GLN* 6.0 0.7 - - - +
117A HIS* 3.6 30.3 - - + +
227A ALA 3.1 13.6 + - - +
228A GLN* 3.7 18.6 - - - +
230A VAL* 1.3 76.9 - - - +
232A THR* 1.3 62.4 + - - +
234A ARG* 3.4 8.7 + - - +
235A LYS* 3.1 22.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLN* 2.8 40.9 + - - +
229A LYS* 3.8 6.3 - - - -
231A VAL* 1.3 72.0 - - - +
233A LEU* 1.3 63.2 + - - +
235A LYS* 3.2 8.0 + - + +
236A GLN* 3.1 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASP 5.8 2.2 - - - +
171A GLY* 3.4 34.5 - - - +
172A LEU 4.6 0.2 - - - +
173A ALA* 4.7 11.0 - - + +
205A ARG* 3.5 38.6 - - - +
229A LYS 2.9 18.5 + - - +
230A VAL* 3.7 4.9 - - - +
232A THR* 1.3 78.1 - - - +
234A ARG* 1.3 62.5 + - + +
236A GLN* 3.2 15.3 + - + +
237A GLN* 3.0 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO* 4.7 12.3 - - - +
70A GLU 3.0 28.7 + - - +
71A LEU* 3.7 14.6 - - - +
72A ARG* 5.2 2.8 - - - +
117A HIS* 5.6 0.2 - - - -
137A ASP* 3.1 28.1 + - - -
230A VAL* 3.0 31.7 + - + +
231A VAL* 3.8 6.7 - - - +
233A LEU* 1.3 75.9 - - + +
235A LYS* 1.3 63.3 + - - +
237A GLN* 3.3 16.8 + - - +
238A GLN* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A VAL* 3.1 17.1 + - + +
232A THR* 3.5 11.2 - - - +
233A LEU 3.2 0.2 - - - -
234A ARG* 1.3 77.9 - - - +
236A GLN* 1.3 61.8 + - + +
238A GLN* 3.3 8.8 + - - +
239A LEU* 3.3 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ARG* 4.5 9.5 + - - -
232A THR* 3.1 30.8 + - + +
233A LEU* 3.2 25.2 + - + +
235A LYS* 1.3 76.9 - - + +
237A GLN* 1.3 64.1 + - + +
239A LEU* 3.4 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ARG 4.7 4.6 + - - -
170A GLY* 4.5 7.1 - - - -
171A GLY 4.3 14.5 + - - +
233A LEU* 3.0 47.8 + - + +
234A ARG* 3.7 18.8 - - - +
235A LYS 3.3 0.2 - - - -
236A GLN* 1.3 78.9 - - + +
238A GLN* 1.3 61.9 + - - +
239A LEU 3.3 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ARG 3.0 17.0 + - - +
235A LYS* 3.6 8.9 - - - +
236A GLN 3.3 0.2 - - - -
237A GLN* 1.3 77.5 - - - +
239A LEU* 1.3 67.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LYS 3.3 10.2 + - - +
236A GLN* 3.6 17.9 - - - +
237A GLN 3.2 8.0 - - - +
238A GLN* 1.3 89.0 + - - +
----------------------------------------------------------
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