Contacts of the helix formed by residues 195 - 220 (chain A) in PDB entry 4P9O
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 ALA 195 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A TYR* 3.9 14.8 - - + +
185A VAL* 4.9 1.1 - - + -
188A VAL* 3.7 27.8 - - + -
189A MET* 3.9 9.8 - - + +
192A HIS 3.0 17.4 + - - +
193A PRO 3.5 1.6 - - - -
194A ASN* 1.4 73.1 - - - +
196A TRP* 1.4 55.5 + - - +
197A VAL 3.2 0.2 - - - -
198A PHE* 3.0 18.4 + - - +
199A PHE* 3.1 30.7 - - + -
301A 2CV 4.3 5.3 - - - -
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Residues in contact with TRP 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL* 4.9 6.1 - - - -
189A MET* 4.0 19.6 - - - +
193A PRO 3.3 26.2 + - - -
194A ASN* 2.9 16.0 + - - -
195A ALA* 1.4 72.0 - - - +
197A VAL* 1.4 84.2 + - + +
198A PHE 3.1 2.7 - - - -
199A PHE 4.0 1.6 - - - +
200A ILE* 3.1 54.3 + - + +
201A PRO* 3.4 1.7 - - - +
300A 2CV 3.4 63.4 + - + -
169B TYR* 4.4 5.2 - - + -
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASN* 2.9 25.7 + - + +
196A TRP* 1.4 112.8 - - + +
198A PHE* 1.3 55.7 + - - +
201A PRO* 3.2 23.3 - - + +
301A 2CV 3.6 36.9 - - + +
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Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ALA* 3.4 37.0 - - + -
148A MET* 3.9 17.3 - - + -
149A ALA* 4.0 13.9 - - + -
152A LEU* 4.4 8.5 - - + -
153A TYR* 3.3 26.7 - - - +
171A LEU* 4.0 13.2 - - + -
194A ASN 4.2 0.2 + - - -
195A ALA 3.0 4.1 + - - +
197A VAL* 1.3 79.1 - - - +
199A PHE* 1.3 88.7 + + - +
201A PRO* 3.4 4.7 - - - +
202A PHE* 3.1 31.6 + - + +
301A 2CV 3.7 50.7 + - + +
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Residues in contact with PHE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TYR* 3.7 29.4 - + - -
161A PHE* 3.6 34.5 - + - -
171A LEU* 4.2 9.4 - - + -
174A VAL* 4.2 18.2 - - + -
180A TRP* 4.9 1.3 - - + -
184A ILE* 4.7 2.5 - - + -
185A VAL* 3.5 42.8 - - + -
188A VAL* 4.3 8.1 - - + -
195A ALA* 3.1 34.1 + - + +
196A TRP* 5.0 0.9 - - - +
198A PHE* 1.3 89.4 - + - +
200A ILE* 1.3 56.0 + - - +
202A PHE* 3.1 5.3 + + - +
203A ILE* 2.8 44.7 + - + +
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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
----------------------------------------------------------
180A TRP* 4.0 10.5 - - + -
196A TRP* 3.1 41.2 + - + +
199A PHE* 1.3 72.8 - - - +
201A PRO* 1.4 63.7 - - + +
203A ILE* 3.1 6.9 + - - +
204A MET* 2.9 41.4 + - + +
300A 2CV 4.1 26.9 - - + -
169B TYR* 3.8 22.0 - - + -
172B PHE* 3.7 42.8 - - + -
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Residues in contact with PRO 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A TRP* 3.4 7.9 - - + +
197A VAL* 3.2 29.6 - - + +
198A PHE 3.4 5.8 - - - +
200A ILE* 1.4 89.0 - - + +
202A PHE* 1.4 51.7 + - - +
204A MET* 3.2 19.4 + - + +
205A LEU* 2.8 37.9 + - - +
301A 2CV 4.7 13.9 - - + -
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Residues in contact with PHE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 5.4 1.8 - - + -
142A PHE* 4.1 13.9 - + - -
145A ALA* 4.0 28.0 - - + -
171A LEU* 3.4 55.2 - - + -
174A VAL* 3.9 22.2 - - + -
175A MET* 4.1 5.4 - - + -
198A PHE* 3.1 23.6 + + + +
199A PHE* 3.1 9.7 + - - +
201A PRO* 1.4 74.1 - - - +
203A ILE* 1.3 54.9 + - - +
205A LEU* 3.9 2.0 - - - +
206A THR* 2.7 71.9 + - + +
301A 2CV 4.3 18.9 - - + +
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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
----------------------------------------------------------
174A VAL* 3.8 35.2 - - + +
175A MET* 5.8 0.2 - - - +
177A LEU* 3.9 20.0 - - + -
180A TRP* 3.5 49.1 - - + -
199A PHE 2.8 19.1 + - - +
200A ILE* 3.5 7.0 - - - +
202A PHE* 1.3 73.9 - - + +
204A MET* 1.3 59.9 + - + +
206A THR* 4.0 4.3 - - - -
207A THR* 2.8 44.6 + - + +
172B PHE* 4.0 20.0 - - + -
176B THR* 4.8 2.0 - - + -
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Residues in contact with MET 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ILE* 2.9 35.2 + - + +
201A PRO* 3.7 21.5 - - + +
203A ILE* 1.3 76.0 - - + +
205A LEU* 1.3 57.1 + - - +
207A THR 4.0 3.4 - - - +
208A PHE* 3.2 24.9 - - - +
300A 2CV 5.3 8.7 - - + -
172B PHE* 4.2 22.9 - - + -
214B PHE* 4.2 17.2 - - + -
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 6.0 5.4 - - + -
141A VAL* 3.7 39.3 - - + -
201A PRO 2.8 20.8 + - - +
202A PHE* 3.9 2.9 - - - +
204A MET* 1.3 71.2 - - - +
206A THR* 1.4 56.8 + - + +
208A PHE* 3.5 12.5 - - + +
209A THR* 2.7 43.6 + - - +
301A 2CV 4.6 13.9 - - + -
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Residues in contact with THR 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.3 15.9 - - + -
141A VAL* 4.2 20.9 - - + -
142A PHE* 4.8 5.2 - - + -
175A MET* 3.6 27.4 - - - +
202A PHE* 2.7 56.1 + - + +
203A ILE* 3.6 2.1 + - - -
205A LEU* 1.4 69.2 - - + +
207A THR* 1.3 54.7 + - - +
208A PHE 2.7 17.3 + - - -
209A THR* 3.2 0.4 + - - -
210A VAL* 2.9 30.5 + - - +
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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
----------------------------------------------------------
175A MET* 3.2 30.9 + - + +
177A LEU* 4.3 18.6 - - + +
203A ILE* 2.8 33.6 + - + +
204A MET* 4.0 1.8 - - - +
206A THR* 1.3 71.3 + - - +
208A PHE* 1.3 57.6 + - - +
210A VAL* 5.1 3.8 - - - -
211A LEU* 5.0 6.3 - - - +
214B PHE* 3.6 15.1 - - - -
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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 MET 3.2 21.8 - - - +
205A LEU* 3.5 11.7 - - + +
206A THR 2.7 6.3 + - - -
207A THR* 1.3 70.6 - - - +
209A THR* 1.4 78.9 + - + +
210A VAL 3.2 1.3 - - - +
211A LEU* 3.2 12.8 + - + +
212A ASN* 2.8 61.6 + - - +
214B PHE* 3.6 27.8 - + + -
217B ILE* 4.4 24.9 - - + -
218B ILE* 5.1 5.8 - - + -
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Residues in contact with THR 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 3.9 16.6 - - + +
137A LEU* 3.8 28.8 - - + +
138A LEU* 3.9 27.6 - - + -
205A LEU* 2.7 32.6 + - - +
208A PHE* 1.4 87.8 - - + +
210A VAL* 1.4 54.0 + - - +
212A ASN* 3.4 5.7 + - + +
213A LEU* 2.8 35.9 + - - +
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Residues in contact with VAL 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.8 24.7 - - + -
175A MET* 3.4 37.7 - - + -
206A THR 2.9 20.2 + - - +
207A THR* 5.1 2.9 - - - -
208A PHE 5.0 0.2 - - - +
209A THR* 1.4 74.2 - - - +
211A LEU* 1.4 56.2 + - - +
213A LEU* 3.3 5.7 + - + -
214A PHE* 2.9 57.2 + - + +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A THR 5.0 3.6 - - - +
208A PHE* 3.2 16.7 + - + +
210A VAL* 1.4 77.9 - - - +
212A ASN* 1.3 57.4 + - - +
214A PHE* 4.2 3.9 - - - +
215A ILE* 3.2 48.0 + - + +
214B PHE* 4.5 25.6 - - + -
215B ILE* 5.5 7.0 - - + -
218B ILE* 3.8 25.1 - - + -
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Residues in contact with ASN 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.6 11.9 - - + +
208A PHE* 2.8 53.9 + - + +
209A THR* 3.5 10.1 - - + +
211A LEU* 1.3 72.0 - - - +
213A LEU* 1.4 58.9 + - - +
215A ILE* 3.6 5.7 + - - +
216A GLY* 3.0 26.2 + - - -
218B ILE* 3.5 29.0 - - - +
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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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131A VAL* 3.4 34.2 - - + +
134A VAL* 3.8 13.6 - - + +
135A ALA* 3.7 31.4 - - + +
138A LEU* 4.4 20.9 - - + -
209A THR* 2.8 20.9 + - + +
210A VAL* 3.7 4.9 - - - +
212A ASN* 1.4 69.4 - - - +
214A PHE* 1.3 79.7 + - + +
216A GLY 3.5 5.5 + - - -
217A ILE* 3.4 25.4 + - + +
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Residues in contact with PHE 214 (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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210A VAL* 2.9 38.9 + - + +
211A LEU* 4.2 4.5 - - - +
213A LEU* 1.3 93.5 - - + +
215A ILE* 1.4 63.2 + - + +
216A GLY 3.5 0.2 + - - -
217A ILE* 3.6 23.0 + - + +
218A ILE* 3.3 24.8 + - + +
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Residues in contact with ILE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.2 44.8 + - + +
212A ASN* 4.0 4.5 - - - +
213A LEU 3.5 0.2 - - - -
214A PHE* 1.4 72.9 - - + +
216A GLY* 1.3 65.7 + - - +
218A ILE* 3.1 18.8 + - + +
219A VAL* 3.1 34.4 + - + +
215B ILE* 5.6 5.2 - - + -
218B ILE* 4.1 34.3 - - + -
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Residues in contact with GLY 216 (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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131A VAL* 3.4 29.6 - - - +
212A ASN 3.0 17.6 + - - -
213A LEU 3.8 3.8 - - - -
214A PHE 3.3 0.8 - - - -
215A ILE* 1.3 78.2 - - - +
217A ILE* 1.4 58.4 + - - +
219A VAL* 3.7 7.3 + - - +
220A ASP* 3.3 16.3 + - - +
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A VAL* 3.8 13.5 - - + -
213A LEU* 3.4 24.9 - - + +
214A PHE* 3.6 24.2 + - + +
215A ILE 3.3 0.4 - - - -
216A GLY* 1.4 71.7 - - - +
218A ILE* 1.4 65.0 + - + +
220A ASP* 3.2 23.9 + - + +
221A ALA* 3.7 6.4 + - - +
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Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A PHE* 3.3 26.5 - - + +
215A ILE* 3.1 18.8 + - + +
217A ILE* 1.4 77.0 - - + +
219A VAL* 1.3 62.8 + - + +
221A ALA* 3.4 19.3 + - - +
222A MET* 3.7 6.9 + - - +
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Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ILE* 3.1 28.5 + - + +
216A GLY* 4.0 7.2 - - - +
218A ILE* 1.3 72.6 - - + +
220A ASP* 1.4 54.3 + - - +
221A ALA 2.9 15.4 + - - -
222A MET* 3.0 26.9 + - + +
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Residues in contact with ASP 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A VAL* 5.0 7.2 - - + -
216A GLY 3.3 14.5 + - - +
217A ILE* 3.2 21.2 + - + +
219A VAL* 1.4 72.4 - - - +
221A ALA* 1.3 55.1 + - - +
222A MET 5.2 0.4 - - - -
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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
------------------------------------------------------------
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