Contacts of the helix formed by residues 219 - 239 (chain A) in PDB entry 1C88
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 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ASP 5.7 0.4 - - - +
49A VAL* 3.8 31.9 - - + -
215A CYS* 3.4 3.8 - - - -
217A ALA* 3.9 3.4 - - + -
218A GLY* 1.4 83.3 - - - +
220A GLY* 1.3 71.8 + - - +
221A ARG 3.9 0.2 - - - -
223A GLY* 2.9 19.9 + - - +
257A ARG* 3.6 16.2 - - + +
258A MET* 3.1 21.8 - - + +
259A GLY* 3.6 15.3 - - - +
260A LEU* 3.4 7.1 - - + -
261A ILE 2.9 20.5 + - - -
262A GLN* 3.4 28.7 - - + +
301A OTA 3.4 24.5 - - - +
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Residues in contact with GLY 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ILE* 1.3 77.4 - - - +
221A ARG* 1.3 64.2 + - - +
224A THR* 2.9 23.7 + - - -
261A ILE* 3.8 1.7 - - - -
262A GLN* 3.4 27.1 - - - -
266A GLN* 3.7 9.8 - - - +
301A OTA 2.8 23.6 + - - -
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Residues in contact with ARG 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 3.4 29.8 + - + +
111A ASN* 3.4 15.5 - - - +
115A GLU* 2.8 38.8 + - - -
179A TRP* 2.8 63.4 + - + +
180A PRO 3.6 9.2 - - - +
181A ASP* 3.2 22.7 - - - +
215A CYS* 3.7 8.7 - - + +
216A SER* 3.9 3.0 - - - +
220A GLY* 1.3 71.4 - - - +
222A SER* 1.4 62.2 + - - +
224A THR* 3.1 4.2 + - - -
225A PHE 3.0 19.6 + - - -
266A GLN* 4.2 7.8 - - - +
301A OTA 2.8 41.2 + - - +
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Residues in contact with SER 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.7 22.2 - - - -
110A LEU* 3.7 10.5 - - - +
213A VAL* 3.8 9.5 - - - +
214A HIS* 3.4 12.1 - - - -
215A CYS* 3.1 32.0 + - - -
218A GLY* 3.6 13.3 - - - -
220A GLY 3.3 0.6 - - - -
221A ARG* 1.4 76.4 - - - +
223A GLY* 1.3 64.4 - - - +
225A PHE* 3.4 1.2 + - - +
226A CYS* 3.0 29.3 + - - -
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Residues in contact with GLY 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 4.2 3.0 - - - +
219A ILE 2.9 22.8 + - - -
222A SER* 1.3 77.8 - - - +
224A THR* 1.3 57.3 - - - +
226A CYS* 3.4 2.4 + - - +
227A LEU* 2.8 32.6 + - - +
250A LEU* 5.2 0.2 - - - +
253A MET* 4.6 2.9 - - - +
260A LEU* 4.1 17.9 - - - -
261A ILE* 3.7 13.8 - - - +
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Residues in contact with THR 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A TRP* 3.6 24.0 - - + -
185A PRO* 5.1 0.2 - - + -
191A PHE* 4.6 1.5 - - + -
220A GLY 2.9 15.5 + - - -
221A ARG 3.1 7.4 + - - -
223A GLY* 1.3 76.3 - - - +
225A PHE* 1.4 62.7 + - - +
227A LEU* 3.9 1.2 - - - +
228A ALA* 3.2 25.6 + - + +
261A ILE* 3.7 14.2 - - - +
266A GLN* 3.6 33.4 + - + +
269A PHE* 4.1 18.4 - - + -
270A SER* 3.9 15.3 + - - +
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Residues in contact with PHE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A TYR* 5.2 5.6 - + - -
108A VAL* 4.0 22.9 - - + -
110A LEU* 3.6 35.0 - - + -
179A TRP* 4.0 1.1 - - + -
191A PHE* 3.7 30.7 - + + -
194A PHE* 3.8 25.8 - + - -
195A LEU* 3.6 32.7 - - + +
198A VAL* 4.3 10.5 - - + -
204A LEU* 5.8 2.7 - - + -
211A VAL* 5.7 1.8 - - + -
213A VAL* 4.2 17.5 - - + -
221A ARG 3.0 5.5 + - - +
222A SER 3.6 2.5 - - - +
224A THR* 1.4 77.8 - - - +
226A CYS* 1.3 77.4 + - - +
228A ALA* 3.5 2.6 + - - +
229A ASP* 3.0 26.8 + - + +
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Residues in contact with CYS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 5.9 0.7 - - + -
81A TYR* 3.7 27.6 + - + -
83A LEU* 3.7 30.5 - - + -
213A VAL* 4.0 13.7 - - - -
222A SER 3.0 21.6 + - - +
223A GLY* 4.0 2.9 - - - +
225A PHE* 1.3 78.7 - - - +
227A LEU* 1.3 66.1 + - - +
229A ASP* 3.2 4.9 + - - -
230A THR* 2.9 28.6 + - - -
253A MET* 3.7 19.3 - - + -
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A GLY 2.8 22.2 + - - +
224A THR 3.9 3.8 - - - +
226A CYS* 1.3 74.1 - - - +
228A ALA* 1.3 64.3 + - - +
231A CYS* 2.9 49.6 + - - -
246A ILE* 3.7 21.3 - - + +
249A VAL* 3.8 7.6 - - + -
250A LEU* 3.6 44.4 - - + +
253A MET* 3.8 11.1 - - - -
261A ILE* 3.5 26.5 - - + -
267A LEU* 4.4 2.0 - - + -
270A SER* 3.7 12.3 - - - +
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A PHE* 3.8 28.3 - - + -
195A LEU* 5.0 1.3 - - + -
224A THR* 3.2 15.5 + - + +
227A LEU* 1.3 79.5 - - - +
229A ASP* 1.3 63.9 + - - +
231A CYS* 3.9 0.9 - - - +
232A LEU* 3.0 32.3 + - + +
270A SER* 4.8 6.4 + - - +
273A ALA* 4.3 11.2 - - + -
274A VAL* 3.7 20.9 - - + +
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Residues in contact with ASP 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ARG* 3.0 23.7 + - - -
81A TYR* 2.7 27.7 + - + +
195A LEU* 3.7 24.5 - - + +
199A ARG* 2.8 48.7 + - - +
204A LEU* 4.0 6.0 - - - +
225A PHE* 3.0 21.4 + - + +
226A CYS* 3.2 3.5 + - - +
228A ALA* 1.3 75.8 - - - +
230A THR* 1.3 57.9 + - - +
232A LEU 3.2 1.2 + - - -
233A LEU* 2.9 25.6 + - - +
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Residues in contact with THR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A MET* 3.8 16.7 - - + +
77A ALA* 3.9 21.8 - - + +
79A ARG* 5.1 0.7 - - - +
81A TYR* 2.7 25.8 + - - -
226A CYS 2.9 10.9 + - - -
227A LEU 4.0 1.6 - - - -
229A ASP* 1.3 73.9 - - - +
231A CYS* 1.3 61.4 + - - +
233A LEU* 3.1 8.2 + - - +
234A LEU* 2.8 33.3 + - + +
249A VAL* 3.7 24.9 - - + -
253A MET* 3.2 18.9 - - - +
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Residues in contact with CYS 231 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A LEU* 2.9 47.2 + - - +
230A THR* 1.3 78.2 - - - +
232A LEU* 1.3 57.5 + - - +
234A LEU* 3.5 6.4 + - - +
235A MET* 3.0 30.0 + - - +
244A VAL* 3.9 16.7 - - + +
246A ILE* 3.9 22.0 - - - -
249A VAL* 4.0 15.3 - - - -
274A VAL* 3.6 27.4 - - + -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU* 3.9 28.7 - - + -
195A LEU* 4.1 13.9 - - + -
196A PHE* 4.3 10.5 - - + -
199A ARG* 3.9 10.1 - - - +
228A ALA* 3.0 23.0 + - + +
229A ASP 3.7 3.8 - - - +
231A CYS* 1.3 76.5 - - - +
233A LEU* 1.3 58.4 + - - +
235A MET* 3.4 4.5 + - + -
236A ASP* 2.9 28.3 + - - +
273A ALA 4.5 2.7 - - - +
274A VAL* 3.5 36.8 - - + +
277A GLY* 3.6 20.6 - - - -
278A ALA* 3.7 2.2 - - - +
281A ILE* 3.8 22.3 - - + +
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ALA* 3.4 30.5 - - + +
78A GLN 4.4 2.2 - - - +
79A ARG* 3.7 54.1 - - + +
199A ARG* 3.8 10.2 - - - +
229A ASP 2.9 17.6 + - - +
230A THR* 3.5 6.1 - - - +
232A LEU* 1.3 76.6 - - - +
234A LEU* 1.3 59.8 + - - +
236A ASP* 3.1 16.6 + - + +
237A LYS* 2.8 31.1 + - + +
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A MET* 5.9 0.9 - - + -
76A GLU* 3.2 43.1 - - + +
77A ALA* 3.9 19.0 - - + +
230A THR* 2.8 35.4 + - + +
231A CYS* 3.7 5.2 - - - +
233A LEU* 1.3 74.1 - - - +
235A MET* 1.3 60.9 + - - +
237A LYS* 3.3 11.2 + - + +
238A ARG* 2.8 40.1 + - - +
244A VAL* 4.3 10.5 - - + -
249A VAL* 3.8 29.6 - - + -
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Residues in contact with MET 235 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A MET* 3.8 17.9 - - + -
231A CYS 3.0 14.4 + - - +
232A LEU* 4.0 5.4 - - + +
233A LEU 3.3 0.2 - - - -
234A LEU* 1.3 76.5 - - - +
236A ASP* 1.4 52.9 + - - +
238A ARG* 4.0 4.3 - - - -
239A LYS* 2.7 36.9 + - - -
240A ASP 3.3 3.3 + - - -
241A PRO* 3.6 32.5 - - + -
244A VAL* 3.5 15.7 - - + +
274A VAL* 3.8 29.8 - - + +
278A ALA* 3.4 36.6 - - + -
281A ILE* 3.4 21.4 - - + +
282A MET* 4.7 0.4 - - - -
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Residues in contact with ASP 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ARG* 4.9 6.2 + - - -
232A LEU 2.9 18.3 + - - +
233A LEU* 3.3 19.4 - - + +
235A MET* 1.4 72.4 - - - +
237A LYS* 1.3 67.8 + - - +
238A ARG 3.2 0.7 + - - -
239A LYS* 3.1 43.8 + - - +
281A ILE* 3.6 26.2 - - + +
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Residues in contact with LYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A GLU* 4.4 15.6 + - + +
77A ALA* 5.4 5.2 - - - +
78A GLN* 4.4 22.1 + - + +
233A LEU* 2.8 17.8 + - + +
234A LEU* 3.7 11.0 - - + +
235A MET 3.3 0.2 - - - -
236A ASP* 1.3 79.9 - - - +
238A ARG* 1.3 63.6 + - + +
239A LYS* 5.2 0.5 - - - +
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Residues in contact with ARG 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLU* 2.6 48.1 + - - +
234A LEU* 2.8 38.5 + - - +
235A MET* 3.8 5.4 - - - +
237A LYS* 1.3 81.8 - - + +
239A LYS* 1.3 69.4 + - - +
240A ASP* 3.1 13.7 + - + +
243A SER* 2.7 50.6 + - - +
244A VAL* 4.6 4.0 - - - +
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Residues in contact with LYS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A MET 2.7 14.5 + - - -
236A ASP* 3.1 32.4 + - - +
237A LYS 5.2 0.7 - - - +
238A ARG* 1.3 71.8 - - - +
240A ASP* 1.3 58.0 + - - +
241A PRO* 3.7 5.7 - - - +
281A ILE* 2.7 32.6 + - + +
282A MET* 3.5 28.5 - - + +
283A GLY* 5.2 1.6 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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