Contacts of the helix formed by residues 192 - 213 (chain A) in PDB entry 5O5E
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 GLY 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A ILE 3.3 0.8 + - - -
191A ASN* 1.3 72.7 - - - +
193A LEU* 1.3 57.9 + - - +
194A GLU* 3.7 2.7 + - - -
196A GLY* 3.1 26.8 + - - -
239A LEU* 4.0 5.6 - - - -
242A ASN* 3.3 30.6 + - - -
243A TRP* 3.6 24.3 - - - -
380A THR* 3.6 5.4 - - - +
384A LEU* 4.2 0.3 - - - +
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Residues in contact with LEU 193 (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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187A LEU* 3.4 34.1 - - + +
188A ALA* 3.9 2.9 - - - -
190A ILE* 3.1 36.8 + - + +
191A ASN 3.4 0.6 - - - -
192A GLY* 1.3 74.4 - - - +
194A GLU* 1.3 57.3 + - - +
197A GLN* 2.8 50.0 + - + +
364A ILE* 3.8 16.2 - - + -
380A THR* 3.7 14.3 - - + +
383A LEU* 3.6 38.1 - - + -
384A LEU* 4.1 6.0 - - + +
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Residues in contact with GLU 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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184A ILE* 4.0 12.7 - - + +
187A LEU 4.6 0.4 - - - +
188A ALA* 3.4 23.0 - - + +
189A GLY 3.3 24.6 + - - -
190A ILE 3.6 9.2 - - - +
192A GLY 4.1 0.5 + - - -
193A LEU* 1.3 78.7 + - - +
195A ALA* 1.3 61.4 + - - +
197A GLN* 3.4 18.7 - - - +
198A SER* 3.0 22.9 + - - -
242A ASN* 3.6 18.2 + - - +
250A VAL* 3.8 26.1 - - + +
254A PHE* 3.5 6.8 - - + -
255A CYS* 4.6 7.4 - - - -
502A 9LH 3.9 14.6 - - - +
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Residues in contact with ALA 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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192A GLY 4.4 0.2 + - - -
193A LEU 3.6 0.2 - - - -
194A GLU* 1.3 80.2 + - - +
196A GLY* 1.3 56.7 + - - +
198A SER* 3.6 1.7 + - - -
199A LEU* 3.0 24.1 + - - +
235A THR* 3.3 25.3 - - + +
238A LEU* 4.7 2.5 - - + -
239A LEU* 3.7 25.8 - - + -
242A ASN* 4.1 4.7 - - - +
250A VAL* 3.8 22.9 - - + -
254A PHE* 3.6 13.4 - - + -
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Residues in contact with GLY 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 GLY 3.1 23.9 + - - -
195A ALA* 1.3 74.6 - - - +
197A GLN* 1.4 62.9 + - - +
199A LEU* 3.3 9.6 + - - +
200A VAL* 3.2 25.1 + - - +
239A LEU* 3.6 10.9 - - - +
384A LEU* 3.4 17.2 - - - +
501A P6L 5.6 0.9 - - - +
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Residues in contact with GLN 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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184A ILE* 3.7 24.2 - - + +
187A LEU* 3.0 32.5 + - - +
193A LEU* 2.8 42.9 + - + +
194A GLU* 3.4 10.4 - - - +
196A GLY* 1.4 70.5 - - - +
198A SER* 1.4 61.2 + - - +
200A VAL* 3.1 6.8 + - - +
201A ILE* 3.0 35.4 + - + +
282A GLN* 2.8 41.7 + - - +
384A LEU* 3.5 10.4 - - + +
387A GLN* 3.8 13.4 - - - +
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Residues in contact with SER 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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184A ILE* 4.1 9.9 - - - +
194A GLU 3.0 18.7 + - - -
195A ALA 3.6 4.9 - - - -
196A GLY 3.3 0.6 - - - -
197A GLN* 1.4 77.7 - - - +
199A LEU* 1.3 53.5 + - - +
201A ILE* 4.3 2.7 - - - -
202A SER* 2.8 38.6 + - - -
231A PHE* 3.8 17.5 - - - -
254A PHE* 3.7 21.6 - - - -
258A ALA* 3.8 9.9 - - - +
262A PHE* 3.5 14.5 - - - -
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Residues in contact with LEU 199 (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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195A ALA 3.0 10.2 + - - +
196A GLY* 3.3 12.1 - - - +
197A GLN 3.2 0.4 - - - -
198A SER* 1.3 77.0 - - - +
200A VAL* 1.4 56.2 + - - +
202A SER* 3.3 3.6 + - - +
203A ALA* 3.2 26.9 + - - +
232A PHE* 3.4 52.2 - - + +
235A THR* 3.7 19.3 - - + -
236A LEU* 3.8 23.6 - - + +
239A LEU* 3.7 33.9 - - + -
501A P6L 4.4 19.3 - - + +
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Residues in contact with VAL 200 (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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196A GLY 3.2 12.9 + - - +
197A GLN 3.1 8.1 + - - +
199A LEU* 1.4 74.0 - - - +
201A ILE* 1.4 52.8 + - + +
203A ALA* 3.4 3.1 + - - +
204A SER* 2.7 47.3 + - - +
384A LEU* 3.9 24.5 - - + +
387A GLN* 3.7 38.4 - - + +
388A ILE* 3.9 14.8 - - + +
391A SER* 4.1 2.5 - - - +
501A P6L 3.9 31.7 - - + +
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Residues in contact with ILE 201 (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 ILE* 5.3 1.3 - - + -
197A GLN* 3.0 25.6 + - + +
198A SER* 3.8 8.3 - - - +
200A VAL* 1.4 73.6 - - - +
202A SER* 1.4 56.2 + - - +
204A SER* 3.1 10.0 + - - -
205A ILE* 3.0 38.9 + - + +
262A PHE* 3.6 24.9 - - + -
278A PHE* 4.1 16.4 - - + +
279A PHE* 3.9 31.9 - - + -
282A GLN* 3.7 19.1 - - + +
387A GLN* 3.6 26.9 - - + +
391A SER* 5.4 0.7 - - - +
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Residues in contact with SER 202 (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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198A SER 2.8 23.7 + - - -
199A LEU* 3.3 9.2 + - - -
201A ILE* 1.4 71.0 - - - +
203A ALA* 1.3 53.9 + - - +
205A ILE* 3.2 3.6 + - - +
206A ILE* 2.8 39.9 + - - +
228A MET* 3.8 14.6 - - - +
231A PHE* 3.6 26.2 - - - -
232A PHE* 3.4 19.9 - - - +
262A PHE* 3.7 12.0 - - - -
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Residues in contact with ALA 203 (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 LEU 3.2 17.8 + - - +
200A VAL 3.6 4.3 - - - +
202A SER* 1.3 79.5 + - - +
204A SER* 1.4 56.7 + - - +
206A ILE* 3.2 12.8 + - - +
207A VAL* 2.9 35.9 + - + +
232A PHE* 4.0 10.7 - - + -
501A P6L 3.7 34.1 - - + -
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Residues in contact with SER 204 (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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200A VAL* 2.7 23.7 + - - +
201A ILE* 3.1 9.8 + - - -
203A ALA* 1.4 75.0 - - - +
205A ILE* 1.4 56.9 + - - +
208A PHE* 3.1 24.1 + - - +
278A PHE* 3.6 23.5 - - - -
391A SER* 2.7 33.9 + - - -
395A PHE* 3.2 15.8 - - - -
501A P6L 4.2 11.7 - - - +
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Residues in contact with ILE 205 (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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201A ILE* 3.0 26.8 + - + +
202A SER 3.7 5.2 - - - +
204A SER* 1.4 74.2 - - - +
206A ILE* 1.4 52.9 + - - +
208A PHE* 3.3 4.2 + - + +
209A ASN* 2.8 43.9 + - - +
224A SER* 3.8 16.6 - - - +
228A MET* 3.9 12.6 - - + -
262A PHE* 3.7 30.1 - - + -
265A VAL* 4.7 5.2 - - + -
271A PHE* 3.7 27.6 - - + -
275A MET* 4.0 18.4 - - + -
278A PHE* 3.7 22.2 - - + -
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Residues in contact with ILE 206 (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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202A SER 2.8 27.3 + - - +
203A ALA* 3.2 9.8 + - - +
205A ILE* 1.4 70.9 - - - +
207A VAL* 1.4 63.9 + - + +
209A ASN* 3.2 4.6 + - - +
210A LEU* 3.0 38.0 + - + +
225A LEU* 3.9 22.6 - - + +
228A MET* 3.4 40.6 - - + +
229A ILE* 4.1 9.9 - - + +
232A PHE* 3.8 22.0 - - + -
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Residues in contact with VAL 207 (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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203A ALA* 2.9 24.4 + - + +
204A SER 3.9 0.2 - - - +
206A ILE* 1.4 71.2 - - + +
208A PHE* 1.4 63.1 + - - +
210A LEU* 3.2 13.9 + - + +
211A VAL* 3.1 30.2 + - + +
395A PHE* 3.6 25.6 - - + -
501A P6L 3.8 25.6 - - + -
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Residues in contact with PHE 208 (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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204A SER 3.1 19.6 + - - +
205A ILE* 3.5 4.5 - - - +
207A VAL* 1.4 74.5 - - - +
209A ASN* 1.4 67.1 + - - +
211A VAL* 3.2 5.1 + - - +
212A GLU* 3.0 38.2 + - + +
221A HIS* 3.2 27.1 - + - -
271A PHE* 3.7 33.7 - + + -
274A THR* 3.9 18.8 - - + -
278A PHE* 4.1 8.1 - + + -
395A PHE* 3.5 17.1 - + + -
398A ARG* 3.8 32.5 - - - -
399A TYR* 3.2 32.8 - + - -
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Residues in contact with ASN 209 (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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205A ILE* 2.8 30.8 + - - +
206A ILE* 3.4 6.0 - - - +
208A PHE* 1.4 75.9 - - - +
210A LEU* 1.3 51.9 + - - +
212A GLU 3.5 2.1 + - - -
213A LEU* 2.8 36.7 + - - +
221A HIS* 2.8 39.9 + - - +
224A SER* 3.1 34.5 + - - -
225A LEU* 3.5 32.4 - - + +
228A MET* 4.5 1.8 - - - +
271A PHE* 3.8 5.9 - - - -
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Residues in contact with LEU 210 (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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11A LEU* 6.0 1.6 - - + -
206A ILE* 3.0 35.7 + - + +
207A VAL* 3.2 12.5 + - + +
209A ASN* 1.3 72.3 - - - +
211A VAL* 1.4 66.5 + - + +
213A LEU* 3.4 22.6 - - + +
214A GLU* 3.7 14.4 - - - +
225A LEU* 3.8 22.7 - - + -
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Residues in contact with VAL 211 (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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207A VAL* 3.1 29.6 + - + +
208A PHE* 3.5 8.7 - - - +
210A LEU* 1.4 79.7 - - + +
212A GLU* 1.3 57.0 + - - +
213A LEU 3.2 4.0 + - - -
214A GLU* 3.4 20.5 + - - +
215A GLY 4.7 0.7 + - - -
395A PHE* 5.1 3.8 - - + -
399A TYR* 3.5 38.6 - - + +
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Residues in contact with GLU 212 (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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208A PHE* 3.0 25.8 + - + +
209A ASN 3.5 0.9 - - - -
211A VAL* 1.3 71.5 - - - +
213A LEU* 1.4 57.4 + - - +
214A GLU 3.2 2.7 - - - -
215A GLY 2.8 29.3 - - - +
216A ASP* 5.4 4.9 - - - +
217A CYS* 3.0 20.9 + - - +
221A HIS* 3.4 28.2 + - + +
398A ARG* 3.6 24.1 + - - -
399A TYR* 2.7 38.6 + - - +
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Residues in contact with LEU 213 (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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8A PRO* 6.1 3.6 - - + -
11A LEU* 4.2 12.8 - - + -
209A ASN 2.8 14.0 + - - +
210A LEU* 3.4 19.1 - - + +
211A VAL 3.2 1.0 - - - -
212A GLU* 1.4 76.0 - - - +
214A GLU* 1.4 67.2 + - - +
215A GLY 3.4 0.4 - - - -
218A ARG* 3.2 51.1 + - + +
221A HIS* 4.4 4.0 - - - +
222A VAL* 3.8 27.6 - - + +
225A LEU* 3.6 31.4 - - + -
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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