Contacts of the helix formed by residues 189 - 208 (chain A) in PDB entry 4PGF
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 PHE 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A VAL* 3.3 29.2 - - + -
185A THR* 3.4 33.9 - - + +
186A LYS 3.0 1.0 + - - -
187A SER 3.4 0.4 - - - -
188A LYS* 1.3 88.3 - - + +
190A ASP* 1.3 63.4 + - - +
191A ASN 3.4 0.4 - - - -
192A LEU 3.9 0.2 - - - -
193A TYR* 2.7 57.5 + + + +
194A GLY 3.1 5.7 + - - -
357A VAL* 3.5 14.0 - - + +
360A ASN* 4.4 11.9 - - - +
395A ALA* 5.7 4.9 - - + -
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Residues in contact with ASP 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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185A THR 4.6 0.4 + - - +
186A LYS* 2.8 22.2 + - + +
189A PHE* 1.3 74.2 - - - +
191A ASN* 1.3 78.5 + - - +
194A GLY* 3.0 23.4 + - - -
353A HIS* 3.2 15.3 + - - -
357A VAL* 3.4 13.8 - - + +
358A MET* 3.1 20.3 - - - +
361A SER* 2.9 26.3 + - - +
501A NAD 3.9 1.4 - - - -
502A ADN 2.8 33.7 + - - -
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Residues in contact with ASN 191 (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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158A THR* 3.7 3.2 + - - -
181A ASN* 3.2 22.0 + - - +
186A LYS* 2.7 31.8 + - - +
187A SER* 3.4 27.8 + - - +
190A ASP* 1.3 78.7 - - - +
192A LEU* 1.3 61.7 + - - +
195A CYS* 3.3 23.7 - - - +
223A ASP* 3.9 12.9 + - + +
224A VAL* 3.6 12.3 - - + -
501A NAD 3.1 37.9 + - + -
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Residues in contact with LEU 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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187A SER 4.1 2.7 + - - +
188A LYS* 3.7 24.2 - - - +
189A PHE 3.5 2.0 + - - -
190A ASP 3.3 0.4 - - - -
191A ASN* 1.3 80.6 - - - +
193A TYR* 1.3 100.3 + - + +
196A ARG* 3.1 21.9 + - + +
223A ASP* 3.4 24.4 - - + +
226A LYS* 3.4 29.6 - - + -
227A GLY* 3.6 15.4 - - - +
230A GLN* 4.8 10.1 - - - +
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Residues in contact with TYR 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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188A LYS 3.4 14.8 + - - -
189A PHE* 2.7 54.1 + + + +
192A LEU* 1.3 95.7 - - + +
194A GLY* 1.3 66.5 + - - +
196A ARG* 3.3 57.4 + - - +
197A GLU* 3.4 7.6 + - - +
230A GLN* 5.6 0.2 - - - -
357A VAL* 4.9 1.6 - - + -
210B MET* 4.0 20.4 - - + +
212B ALA* 5.0 4.5 - - + -
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Residues in contact with GLY 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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189A PHE 3.1 4.4 + - - -
190A ASP 3.0 16.6 + - - -
193A TYR* 1.3 78.5 - - - +
195A CYS* 1.3 63.2 + - - +
197A GLU* 3.2 3.5 + - - +
198A SER* 3.0 21.1 + - - -
353A HIS* 3.2 23.9 + - - -
354A PRO* 4.3 1.7 - - - +
357A VAL* 4.0 13.7 - - - -
210B MET* 4.4 3.7 - - - +
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Residues in contact with CYS 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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190A ASP 3.5 1.8 + - - -
191A ASN 3.3 21.8 - - - +
192A LEU 3.6 1.7 + - - +
193A TYR 3.4 0.2 - - - -
194A GLY* 1.3 74.6 - - - +
196A ARG* 1.3 63.1 + - - +
197A GLU 2.9 1.6 + - - -
198A SER* 3.4 7.9 - - - -
199A LEU* 3.0 27.7 + - - +
224A VAL* 3.9 18.8 - - - +
227A GLY 4.8 1.3 - - - -
228A CYS* 4.3 18.1 - - - +
299A ILE* 4.2 8.7 - - + -
353A HIS* 3.1 21.0 - - - -
501A NAD 3.8 24.7 - - - -
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Residues in contact with ARG 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 LEU* 3.1 15.7 + - - +
193A TYR* 3.4 48.2 + - - +
194A GLY 3.2 0.4 - - - -
195A CYS* 1.3 76.1 - - - +
197A GLU* 1.3 59.5 + - - +
199A LEU 4.9 0.2 - - - -
200A ILE* 4.4 1.4 - - - +
227A GLY* 3.5 25.1 - - - +
230A GLN* 3.0 43.3 - - - +
231A ALA* 3.0 32.3 - - + +
212B ALA* 3.5 14.1 - - - +
234B GLY 4.4 9.0 + - - -
235B PHE* 2.9 50.8 + - + +
236B GLY* 4.1 5.7 - - - +
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Residues in contact with GLU 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 TYR 3.4 5.1 + - - +
194A GLY 3.2 7.2 + - - +
195A CYS 3.0 0.4 - - - -
196A ARG* 1.3 82.2 + - + +
198A SER* 1.3 62.5 + - - +
199A LEU 3.5 0.7 - - - -
200A ILE* 4.0 5.4 + - - +
201A ASP* 3.7 18.4 + - - +
354A PRO* 3.7 6.4 - - + +
204B LYS* 2.6 38.8 + - - +
210B MET* 3.6 14.9 - - - +
211B ILE* 2.9 26.0 + - - +
212B ALA* 3.0 32.7 + - - +
235B PHE* 3.6 34.6 - - + +
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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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194A GLY 3.0 10.1 + - - -
195A CYS* 3.4 3.6 - - - -
197A GLU* 1.3 77.4 - - - +
199A LEU* 1.3 66.7 + - - +
201A ASP* 3.3 7.3 + - - +
202A GLY* 2.9 19.2 + - - -
346A ASN* 3.5 19.7 - - - +
350A ALA* 4.7 0.8 - - - +
352A GLY* 3.0 36.8 - - - -
353A HIS* 3.0 24.5 + - - -
354A PRO* 4.8 1.1 - - - -
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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 CYS* 3.0 17.9 + - - +
196A ARG 5.5 0.2 - - - -
198A SER* 1.3 78.5 + - - +
200A ILE* 1.3 67.8 + - + +
202A GLY* 3.1 3.5 + - - -
203A ILE* 3.1 40.1 + - + +
228A CYS* 3.6 35.9 - - + +
231A ALA* 5.3 0.7 - - + -
232A LEU* 4.3 22.0 - - + -
273A VAL* 4.1 22.2 - - + -
297A CYS* 4.5 0.2 - - - -
299A ILE* 4.0 21.3 - - + -
345A VAL* 3.8 22.5 - - + +
346A ASN* 4.2 2.9 - - - +
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Residues in contact with ILE 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 ARG 4.4 3.6 - - - +
197A GLU 4.0 6.4 + - - +
199A LEU* 1.3 82.3 - - + +
201A ASP* 1.3 57.8 + - - +
203A ILE* 3.2 7.3 + - + +
204A LYS* 2.8 48.0 + - + +
211A ILE* 4.7 12.1 - - + -
231A ALA* 3.8 28.7 - - + -
232A LEU* 3.8 31.0 - - + -
235A PHE* 3.8 41.3 - - + -
200B ILE* 6.3 1.1 - - + -
235B PHE* 4.5 3.4 - - + -
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Residues in contact with ASP 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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197A GLU 3.7 13.4 + - - +
198A SER* 3.3 11.9 + - - +
199A LEU 3.1 0.4 - - - -
200A ILE* 1.3 77.6 - - - +
202A GLY* 1.3 65.1 + - - +
204A LYS* 3.3 3.5 + - - -
205A ARG* 2.6 67.0 + - - +
350A ALA* 3.9 7.3 - - + +
351A MET 5.0 0.5 + - - -
352A GLY 5.5 2.3 - - - +
201B ASP* 3.7 16.5 - - - +
204B LYS* 3.8 23.4 - - + +
205B ARG* 4.6 0.2 - - - +
208B ASP* 3.9 4.0 - - - +
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Residues in contact with GLY 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 2.9 13.5 + - - -
199A LEU 3.1 4.0 + - - -
201A ASP* 1.3 76.6 - - - +
203A ILE* 1.3 59.3 + - - +
205A ARG* 3.6 0.5 + - - +
206A ALA* 3.2 24.8 + - - +
345A VAL* 3.7 22.0 - - - -
349A CYS* 3.4 10.3 - - - +
350A ALA* 3.6 18.7 - - - +
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Residues in contact with ILE 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* 3.1 40.6 + - + +
200A ILE* 3.6 10.1 - - + +
202A GLY* 1.3 72.6 - - - +
204A LYS* 1.3 62.0 + - + +
206A ALA 3.3 0.5 + - - -
207A THR* 2.8 49.5 + - + +
209A VAL* 4.2 14.8 - - + -
211A ILE* 4.5 11.7 - - + -
232A LEU* 4.9 9.2 - - + -
271A ILE* 4.6 17.7 - - + -
273A VAL* 4.6 1.8 - - + -
295A ILE* 5.0 7.4 - - + -
297A CYS* 4.3 19.1 - - - -
339A LEU* 4.4 13.7 - - + -
345A VAL* 4.8 1.8 - - + -
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Residues in contact with LYS 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 ILE* 2.8 33.4 + - + +
201A ASP* 3.8 4.3 - - - +
203A ILE* 1.3 76.5 - - + +
205A ARG* 1.3 63.7 + - - +
207A THR* 4.7 0.4 - - - -
208A ASP* 2.7 38.6 + - - +
209A VAL 3.2 23.6 + - - +
211A ILE* 4.4 10.8 - - + -
235A PHE* 6.0 0.7 - - - -
197B GLU* 2.6 53.7 + - - +
198B SER* 5.6 0.6 - - - +
201B ASP* 3.6 30.0 - - + +
205B ARG* 3.5 2.5 - - - +
354B PRO* 3.4 15.8 - - - +
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Residues in contact with ARG 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 ASP* 2.6 51.2 + - - +
202A GLY 4.0 0.2 - - - +
204A LYS* 1.3 77.0 - - - +
206A ALA* 1.3 53.8 + - - +
207A THR 3.6 0.2 + - - -
208A ASP* 4.1 5.4 - - - +
322A LYS* 2.5 31.3 + - - -
349A CYS 3.3 26.7 - - - +
350A ALA* 3.6 11.4 - - - +
351A MET* 3.9 18.4 - - - +
204B LYS 3.6 12.7 + - - -
205B ARG* 3.5 51.9 + - + +
208B ASP* 2.9 22.0 + - - -
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Residues in contact with ALA 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 GLY 3.2 16.6 + - - +
203A ILE 3.7 4.0 - - - +
204A LYS 3.1 0.8 - - - -
205A ARG* 1.3 81.7 - - - +
207A THR* 1.3 58.7 + - - +
208A ASP* 5.2 0.4 - - - -
321A ILE* 5.8 0.9 - - - +
322A LYS* 3.5 23.1 + - - +
325A VAL* 3.5 20.3 - - + +
339A LEU* 3.8 28.0 - - + -
349A CYS* 3.9 15.0 - - - -
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Residues in contact with THR 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 ILE* 2.8 20.4 + - + +
206A ALA* 1.3 83.9 - - - +
208A ASP* 1.3 76.0 + - - +
209A VAL* 3.2 25.5 + - - +
295A ILE* 4.2 21.1 - - + -
325A VAL* 5.2 1.1 - - + -
337A ILE* 4.5 12.1 - - + -
339A LEU* 3.8 28.5 - - + -
24B ILE* 5.5 6.6 - - - +
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Residues in contact with ASP 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 LYS* 2.7 31.3 + - - +
205A ARG 4.1 8.3 - - - +
207A THR* 1.3 76.3 + - - +
209A VAL* 1.3 61.1 + - - +
322A LYS* 5.0 2.3 + - - -
59B GLU* 5.1 6.3 - - - +
201B ASP* 4.1 3.3 - - - +
205B ARG* 2.9 24.4 + - - -
351B MET* 3.3 39.1 - - + +
354B PRO* 3.9 19.0 - - + +
355B SER* 4.4 6.1 + - - -
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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