Contacts of the helix formed by residues 178 - 201 (chain A) in PDB entry 1A16
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 PRO 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LYS 4.6 1.6 - - - +
177A SER* 1.3 86.3 - - - +
179A GLU* 1.3 71.9 + - - +
181A ILE* 3.3 12.5 + - + +
182A ALA* 3.0 26.7 + - - +
185A ARG* 5.2 1.2 + - - -
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SER* 5.2 0.3 - - - -
2A GLU 4.3 11.0 - - - +
3A ILE* 3.9 7.6 - - + -
4A SER 6.3 0.2 - - - +
7A GLU* 3.2 26.6 - - - +
10A ARG* 4.6 10.8 + - - +
177A SER* 3.1 5.1 + - - +
178A PRO* 1.3 93.9 - - - +
180A GLU* 1.3 63.9 + - - +
182A ALA* 3.2 9.7 + - - +
183A VAL* 3.1 25.6 + - - +
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Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.8 7.2 - - + -
7A GLU* 3.8 0.8 - - - +
11A ARG* 3.2 29.7 + - - +
51A TYR* 3.6 19.5 + - - -
173A ARG* 5.1 2.0 - - - +
175A PHE 4.0 4.0 - - - +
176A LYS* 3.4 25.6 - - + +
177A SER* 2.9 36.8 + - - +
179A GLU* 1.3 78.1 - - - +
181A ILE* 1.3 58.5 + - - +
183A VAL* 3.2 5.3 + - - +
184A LEU* 2.9 32.5 + - - +
268A TYR* 2.6 32.8 + - + +
358A LEU* 5.4 0.2 - - - +
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Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LYS* 3.6 32.3 - - + +
177A SER 3.0 16.8 + - - +
178A PRO* 3.7 11.2 - - + +
179A GLU 3.3 0.4 - - - -
180A GLU* 1.3 78.2 - - - +
182A ALA* 1.3 56.0 + - - +
184A LEU* 3.4 7.0 + - + +
185A ARG* 2.8 51.3 + - - +
377A GLY* 4.6 7.2 - - - -
379A VAL* 4.6 3.4 - - + -
410A VAL* 3.9 39.7 - - + -
419A LEU* 5.0 4.3 - - + -
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SER* 4.0 22.2 + - - +
178A PRO 3.0 12.8 + - - +
179A GLU* 3.4 12.3 - - - +
180A GLU 3.2 0.2 - - - -
181A ILE* 1.3 74.5 - - - +
183A VAL* 1.3 64.3 + - - +
185A ARG* 3.3 22.0 + - - +
186A ARG* 3.0 22.0 + - - +
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SER* 3.7 7.0 - - - +
2A GLU* 3.5 39.7 - - - +
3A ILE* 4.0 8.1 - - + -
179A GLU 3.1 14.7 + - - +
180A GLU* 3.2 8.3 + - - +
182A ALA* 1.3 77.2 - - - +
184A LEU* 1.3 56.1 + - - +
186A ARG* 3.1 7.7 + - - +
187A ALA* 2.9 25.3 + - - +
265A TYR* 3.6 21.4 - - + +
266A LYS* 3.9 8.5 - - + -
268A TYR* 3.4 32.1 - - + -
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LYS* 3.9 30.1 - - + -
180A GLU 2.9 20.6 + - - +
181A ILE* 3.8 6.5 - - - +
183A VAL* 1.3 76.3 - - - +
185A ARG* 1.3 56.5 + - - +
187A ALA* 3.3 5.6 + - + +
188A GLY* 2.8 26.2 + - - -
268A TYR* 3.8 32.3 - - + -
269A ALA 3.6 25.8 - - - +
356A LEU* 4.4 13.0 - - + +
357A GLY* 4.5 6.1 - - - -
379A VAL* 4.0 18.6 - - + -
419A LEU* 3.9 18.7 - - + +
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Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PRO 5.2 0.8 + - - -
181A ILE* 2.8 33.9 + - - +
182A ALA* 3.4 33.5 - - - +
183A VAL 3.2 0.2 - - - -
184A LEU* 1.3 75.4 - - - +
186A ARG* 1.3 62.1 + - - +
188A GLY* 3.4 1.2 + - - -
189A GLU* 3.1 26.5 + - - +
417A GLU* 2.7 44.2 + - - +
419A LEU* 4.1 21.4 - - + +
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Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SER* 5.2 8.7 - - - +
182A ALA 3.0 13.8 + - - +
183A VAL* 3.1 8.3 + - - +
185A ARG* 1.3 75.0 - - - +
187A ALA* 1.3 57.7 + - - +
189A GLU* 3.3 28.9 + - - +
190A ILE* 2.8 47.9 + - + +
193A MET* 3.5 23.2 - - - +
222A HIS* 3.6 34.8 + - - +
265A TYR* 3.4 33.9 + - + +
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Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A VAL 2.9 13.4 + - - +
184A LEU* 3.6 12.1 - - - +
186A ARG* 1.3 75.4 - - - +
188A GLY* 1.3 58.5 + - - +
190A ILE* 4.4 0.7 - - - -
191A THR* 2.9 34.1 + - - -
263A CYS* 3.6 15.5 - - - -
265A TYR* 3.9 20.1 - - + -
268A TYR* 4.2 13.7 - - + +
269A ALA 4.5 1.6 - - - -
270A GLY* 4.3 12.1 - - - +
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Residues in contact with GLY 188 (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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184A LEU 2.8 16.4 + - - -
185A ARG 3.4 0.4 + - - -
187A ALA* 1.3 76.5 - - - +
189A GLU* 1.3 56.3 + - - +
191A THR* 3.5 3.3 + - - -
192A ALA* 3.0 28.4 + - - +
270A GLY* 4.7 1.5 - - - -
272A ILE* 3.7 0.9 - - - +
408A ASP* 4.8 4.7 - - - -
419A LEU* 3.6 13.7 - - - -
420A THR* 3.6 26.6 - - - +
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Residues in contact with GLU 189 (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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185A ARG* 3.1 18.9 + - + +
186A ARG* 3.5 39.8 + - - +
188A GLY* 1.3 74.5 - - - +
190A ILE* 1.3 63.9 + - - +
192A ALA* 3.3 7.1 + - - +
193A MET* 3.1 32.7 + - + +
419A LEU 3.9 4.2 + - - +
422A SER* 4.5 11.2 - - - +
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Residues in contact with ILE 190 (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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186A ARG* 2.8 44.8 + - + +
187A ALA 3.8 3.8 - - - +
189A GLU* 1.3 73.7 - - - +
191A THR* 1.3 62.4 + - - +
193A MET* 3.3 12.4 + - - +
194A ALA* 3.2 19.9 + - - +
218A GLU* 4.7 2.1 - - - +
219A PHE* 4.1 28.0 - - + +
222A HIS* 3.8 33.9 - - + +
224A ALA* 4.5 2.7 - - + -
263A CYS* 3.7 15.9 - - + -
265A TYR* 3.8 34.8 - - + -
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Residues in contact with THR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ALA 2.9 21.5 + - - -
188A GLY* 3.9 1.3 - - - -
190A ILE* 1.3 75.7 - - - +
192A ALA* 1.3 62.4 + - - +
194A ALA* 3.4 2.1 + - - +
195A HIS* 3.0 33.6 + - + +
219A PHE* 4.0 9.4 - - + -
261A ALA 3.1 28.3 - - - +
262A GLY* 3.5 8.1 - - - -
263A CYS* 3.1 23.6 + - - -
270A GLY* 3.7 7.0 - - - -
271A ASP 4.5 0.4 - - - +
272A ILE* 3.5 27.1 - - + +
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Residues in contact with ALA 192 (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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188A GLY 3.0 18.2 + - - +
189A GLU 3.7 3.4 - - - +
190A ILE 3.3 0.2 - - - -
191A THR* 1.3 74.5 - - - +
193A MET* 1.3 64.2 + - - +
195A HIS 3.3 1.4 + - - +
196A THR* 3.0 27.5 + - - -
272A ILE* 3.4 10.3 - - + +
420A THR* 4.4 4.0 - - - +
422A SER* 3.2 28.0 - - - +
423A VAL* 3.5 26.4 - - + +
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Residues in contact with MET 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ARG* 3.5 28.5 - - - +
189A GLU* 3.1 29.4 + - + +
190A ILE* 3.3 9.4 + - - +
192A ALA* 1.3 76.1 - - + +
194A ALA* 1.3 57.7 + - - +
196A THR* 3.4 7.8 + - - -
197A ARG* 3.0 29.8 + - - +
218A GLU* 3.9 16.7 - - + +
221A ARG* 5.3 2.7 - - - -
222A HIS* 3.6 32.8 - - + +
422A SER* 5.9 1.3 - - - +
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Residues in contact with ALA 194 (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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190A ILE 3.2 7.4 + - - +
191A THR 3.6 4.9 - - - +
192A ALA 3.2 0.2 - - - -
193A MET* 1.3 76.8 - - - +
195A HIS* 1.3 56.6 + - - +
197A ARG* 3.3 4.8 + - - +
198A ALA* 2.9 27.9 + - - +
215A ILE* 3.8 26.3 - - + +
218A GLU* 3.7 15.0 - - + +
219A PHE* 3.5 38.4 - - + -
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Residues in contact with HIS 195 (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 THR* 3.0 27.3 + - + +
192A ALA 3.3 5.1 + - - +
194A ALA* 1.3 76.0 - - - +
196A THR* 1.3 65.9 + - - +
198A ALA* 3.5 7.3 + - - +
199A MET* 3.1 27.4 + - - +
215A ILE* 5.2 2.7 - - + +
259A ILE* 3.2 34.1 + - + +
261A ALA* 3.0 42.1 + - + -
272A ILE* 3.0 38.7 + - + +
274A ARG* 4.0 16.2 - - + -
276A PHE* 5.2 1.9 - + - -
423A VAL* 3.8 16.6 - - + -
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Residues in contact with THR 196 (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 ALA 3.0 18.2 + - - -
193A MET* 3.6 8.6 - - - -
195A HIS* 1.3 73.2 - - - +
197A ARG* 1.3 66.6 + - - +
199A MET* 3.1 7.4 + - - +
200A GLU* 3.0 48.6 + - - +
422A SER 4.2 4.9 + - - -
423A VAL* 3.5 23.5 - - - +
424A VAL 5.1 0.3 + - - -
433A LEU* 4.3 16.1 - - + +
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Residues in contact with ARG 197 (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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193A MET 3.0 17.6 + - - +
194A ALA* 3.4 6.3 - - - +
196A THR* 1.3 78.1 - - - +
198A ALA* 1.3 62.1 + - - +
200A GLU* 3.2 12.2 + - - +
201A LYS* 2.9 44.4 + - + +
214A GLU* 2.8 54.2 + - + +
217A HIS* 2.8 43.6 + - - +
218A GLU* 3.0 38.4 + - - +
221A ARG* 4.9 1.2 - - - +
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Residues in contact with ALA 198 (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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194A ALA 2.9 16.2 + - - +
195A HIS* 3.6 8.7 - - - +
196A THR 3.2 0.2 - - - -
197A ARG* 1.3 76.5 - - - +
199A MET* 1.3 56.1 + - - +
201A LYS* 4.5 1.8 - - - +
202A CYS* 3.0 32.2 + - - +
211A LEU* 3.7 14.2 - - + +
214A GLU* 5.0 4.5 - - - -
215A ILE* 4.0 15.3 - - + -
259A ILE* 3.7 28.7 - - + -
276A PHE* 4.3 2.0 - - - -
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Residues in contact with MET 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A HIS 3.1 13.3 + - - +
196A THR 3.1 8.5 + - - +
198A ALA* 1.3 75.5 - - - +
200A GLU* 1.3 61.4 + - - +
201A LYS 3.5 0.5 + - - -
202A CYS 3.9 2.9 + - - +
203A ARG* 4.7 0.9 + - - -
274A ARG* 3.8 23.1 - - + -
276A PHE* 3.5 34.5 - - + -
423A VAL* 3.8 20.9 - - + -
424A VAL* 3.7 23.1 - - - +
430A ILE* 4.1 28.5 - - + -
433A LEU* 3.8 25.1 - - + -
434A MET* 3.4 33.3 - - + +
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Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A THR* 3.0 30.6 + - - +
197A ARG* 3.7 9.8 - - - +
199A MET* 1.3 79.1 - - - +
201A LYS* 1.3 65.7 + - + +
203A ARG* 3.1 19.0 + - - -
433A LEU* 3.5 33.4 - - + +
437A ALA* 3.3 28.8 - - + +
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Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG* 2.9 33.9 + - + +
198A ALA 3.3 2.2 + - - +
200A GLU* 1.3 85.5 - - + +
202A CYS* 1.3 65.4 + - - +
203A ARG* 3.3 11.7 + - - +
206A MET* 3.3 19.6 - - + +
211A LEU* 4.6 3.6 - - + -
214A GLU* 3.2 46.7 + - + +
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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
------------------------------------------------------------
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