Contacts of the helix formed by residues 182 - 204 (chain A) in PDB entry 3JRQ
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 SER 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A GLU* 5.3 1.9 + - - -
141A MET 3.8 22.9 + - - -
142A GLU* 3.8 15.8 - - - +
181A GLY* 1.3 73.1 - - - -
183A GLN* 1.3 68.9 + - - +
184A VAL 3.2 3.1 - - - -
185A ALA* 4.0 2.6 - - - -
186A ASN* 2.9 44.9 + - - +
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Residues in contact with GLN 183 (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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181A GLY* 3.5 12.4 - - - -
182A SER* 1.3 91.9 + - - +
184A VAL* 1.3 58.7 + - - +
186A ASN* 4.0 4.6 - - - +
187A TYR* 3.0 27.5 + - - +
235A VAL* 4.9 7.2 - - + +
236A ALA* 3.7 20.2 - - + -
237A PRO* 3.7 30.2 - - + +
240A VAL* 3.7 8.6 - - + +
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Residues in contact with VAL 184 (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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182A SER 3.2 0.4 - - - -
183A GLN* 1.3 74.3 - - - +
185A ALA* 1.3 61.3 + - - +
187A TYR* 3.2 5.6 + - - +
188A CYS* 2.9 29.5 + - - -
232A ILE* 4.1 22.2 - - + -
236A ALA* 3.8 18.2 - - + -
240A VAL* 3.5 35.4 - - + +
241A GLY 3.9 10.8 - - - +
242A SER* 3.8 9.9 - - - -
315A ILE* 3.6 40.6 - - + +
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Residues in contact with ALA 185 (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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142A GLU 3.3 27.8 - - - +
144A ALA* 3.7 10.4 - - + +
176A TYR* 3.5 23.8 - - - +
178A GLY* 3.6 10.5 - - - +
182A SER* 3.6 6.6 + - - +
183A GLN 3.5 0.2 - - - -
184A VAL* 1.3 78.9 - - - +
186A ASN* 1.3 56.3 + - - +
188A CYS* 3.3 4.2 + - - +
189A ARG* 3.0 27.5 + - - +
241A GLY 4.7 1.4 + - - -
242A SER* 3.7 12.6 - - - +
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Residues in contact with ASN 186 (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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142A GLU 6.0 0.2 - - - -
143A ASP 4.7 3.5 - - - +
144A ALA* 3.8 8.0 - - - +
182A SER* 2.9 40.6 + - - +
183A GLN* 4.1 4.2 - - - +
185A ALA* 1.3 76.4 - - - +
187A TYR* 1.3 61.5 + - - +
189A ARG* 2.6 41.9 + - - +
190A GLU* 3.1 29.0 + - - +
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Residues in contact with TYR 187 (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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183A GLN 3.0 20.9 + - - +
184A VAL* 3.2 6.7 + - - +
186A ASN* 1.3 73.3 - - - +
188A CYS* 1.3 56.2 + - - +
190A GLU* 2.9 23.6 + - - +
191A ARG* 2.6 61.4 + - + +
228A VAL* 4.3 6.7 - - + -
231A GLU* 2.7 37.1 + - + +
232A ILE* 3.6 24.5 - - + -
235A VAL* 3.8 38.4 - - + +
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Residues in contact with CYS 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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176A TYR* 3.4 38.6 + - + -
184A VAL* 2.9 22.7 + - - -
185A ALA 3.6 3.8 - - - +
187A TYR* 1.3 78.7 - - - +
189A ARG* 1.3 61.0 + - - +
191A ARG* 4.8 0.4 - - - -
192A MET* 2.9 52.8 + - + +
193A HIS* 4.7 0.3 + - - -
228A VAL* 4.2 6.5 - - - -
242A SER* 4.8 2.7 - - - -
243A THR 5.2 0.2 - - - -
315A ILE* 4.2 26.0 - - - -
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Residues in contact with ARG 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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143A ASP 5.4 0.8 + - - -
144A ALA* 3.9 18.5 - - + +
145A VAL 3.5 18.1 - - - +
146A SER* 3.3 27.1 + - - +
176A TYR* 3.8 5.8 - - + -
185A ALA 3.0 12.7 + - - +
186A ASN* 2.6 48.7 + - - +
187A TYR 3.1 0.4 - - - -
188A CYS* 1.3 76.4 - - - +
190A GLU* 1.3 61.6 + - - +
193A HIS* 3.3 14.6 - - - -
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Residues in contact with GLU 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 ASN* 3.1 22.3 + - - +
187A TYR* 2.9 31.1 + - + +
189A ARG* 1.3 79.9 - - - +
191A ARG* 1.3 57.1 + - + +
193A HIS* 3.4 17.0 - - - -
194A LEU* 3.8 16.1 - - - +
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Residues in contact with ARG 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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187A TYR* 2.6 47.2 + - + +
188A CYS* 4.8 0.2 - - - -
190A GLU* 1.3 75.9 - - + +
192A MET* 1.3 66.4 + - - +
193A HIS 3.4 2.0 - - - -
194A LEU* 2.9 33.6 + - - +
195A ALA* 2.8 26.4 + - + +
198A GLU* 2.7 37.5 + - - -
227A ARG* 4.0 7.3 - - - +
228A VAL* 4.1 11.2 - - + -
231A GLU* 2.7 43.3 + - - +
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Residues in contact with MET 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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172A PHE* 3.8 11.7 - - + -
176A TYR* 3.4 18.2 - - + +
188A CYS* 2.9 43.1 + - - +
191A ARG* 1.3 72.2 - - - +
193A HIS* 1.3 59.3 + - - +
195A ALA* 3.1 2.6 + - - +
196A LEU* 2.9 28.7 + - + +
224A SER* 3.9 11.0 - - - +
225A PHE* 3.9 28.5 - - + -
228A VAL* 3.7 31.6 - - + +
244A SER* 3.6 21.3 - - - +
246A VAL* 3.9 9.6 - - + -
315A ILE* 4.3 6.3 - - + -
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Residues in contact with HIS 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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146A SER* 4.6 2.0 + - - -
148A ILE* 3.4 37.2 - - + +
151A PHE* 3.6 17.6 - + + -
172A PHE* 3.6 39.3 - - + -
188A CYS 4.8 0.4 + - - -
189A ARG 3.3 26.6 + - - -
190A GLU* 3.4 16.9 + - - -
192A MET* 1.3 79.1 - - - +
194A LEU* 1.3 76.8 + - + +
196A LEU* 3.9 1.3 - - - -
197A ALA* 3.2 24.4 + - - +
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Residues in contact with LEU 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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154A SER* 4.5 15.9 - - - +
190A GLU 3.8 20.9 - - - +
191A ARG* 2.9 28.0 + - - +
193A HIS* 1.3 93.4 - - + +
195A ALA* 1.3 65.3 + - - +
197A ALA* 3.4 8.1 + - + +
198A GLU* 3.2 26.5 + - - +
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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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191A ARG* 2.8 24.1 + - - +
192A MET 3.5 7.6 - - - +
194A LEU* 1.3 77.5 - - - +
196A LEU* 1.3 56.7 + - - +
198A GLU* 3.2 16.0 + - - +
199A GLU* 3.0 23.6 + - - +
224A SER* 3.9 9.9 - - - +
227A ARG* 3.6 18.5 + - - +
228A VAL* 3.7 23.1 - - + -
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Residues in contact with LEU 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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151A PHE* 3.6 26.7 - - + -
172A PHE* 3.7 25.4 - - + -
192A MET* 2.9 17.1 + - + +
193A HIS 4.1 3.8 - - - +
195A ALA* 1.3 76.0 - - - +
197A ALA* 1.3 52.5 + - - +
199A GLU* 3.3 1.6 + - - +
200A ILE* 2.8 51.0 + - + +
217A TRP* 4.2 5.2 - - + -
220A ALA* 3.8 3.8 - - + +
221A LEU* 3.8 36.6 - - + +
224A SER* 3.0 26.8 + - - +
248A VAL* 3.8 16.2 - - + -
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Residues in contact with ALA 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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151A PHE* 4.0 4.5 - - + +
152A LEU* 3.9 26.9 - - + +
154A SER* 4.5 16.8 - - - +
193A HIS 3.2 20.6 + - - +
194A LEU* 3.7 10.3 - - + +
195A ALA 3.3 0.2 - - - -
196A LEU* 1.3 76.3 - - - +
198A GLU* 1.3 61.0 + - + +
200A ILE* 3.5 3.3 + - - +
201A ALA* 3.1 21.5 + - - +
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Residues in contact with GLU 198 (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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191A ARG* 2.7 38.5 + - - -
194A LEU* 3.2 15.0 + - - +
195A ALA* 3.2 12.5 + - - +
197A ALA* 1.3 74.5 - - + +
199A GLU* 1.3 66.1 + - - +
201A ALA* 3.1 16.8 + - - +
202A LYS* 3.1 17.9 + - - +
227A ARG* 3.9 20.7 + - - +
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Residues in contact with GLU 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 8.8 + - - +
196A LEU 3.5 7.2 - - - +
198A GLU* 1.3 76.1 - - - +
200A ILE* 1.3 58.0 + - - +
202A LYS* 2.8 36.3 + - - +
203A GLU* 3.1 25.8 + - - +
220A ALA* 3.7 25.9 - - + +
223A ASN* 3.7 32.0 + - + +
224A SER* 3.6 13.5 - - - +
227A ARG* 3.2 35.6 + - - +
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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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152A LEU* 3.9 29.2 - - + -
167A GLN* 5.3 1.8 - - - +
196A LEU* 2.8 30.9 + - + +
197A ALA 3.7 5.6 - - - +
198A GLU 3.2 0.2 - - - -
199A GLU* 1.3 73.6 - - - +
201A ALA* 1.3 56.3 + - - +
203A GLU 4.7 0.2 - - - +
204A LYS* 3.0 28.2 + - - +
205A PRO* 3.6 19.2 - - + +
217A TRP* 3.6 46.2 - - + -
220A ALA* 3.5 23.8 - - + -
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Residues in contact with ALA 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 ALA 3.1 12.0 + - - +
198A GLU* 3.1 12.2 + - - +
200A ILE* 1.3 75.9 - - - +
202A LYS* 1.3 61.6 + - - +
204A LYS* 4.1 18.7 - - - +
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Residues in contact with LYS 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 GLU* 3.1 13.6 + - - +
199A GLU* 2.8 29.2 + - - +
201A ALA* 1.3 80.7 - - + +
203A GLU* 1.3 67.2 + - - +
204A LYS* 3.2 12.1 - - - -
227A ARG* 2.5 37.6 - - - +
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Residues in contact with GLU 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 GLU* 3.1 26.3 + - - +
202A LYS* 1.3 80.8 - - - +
204A LYS* 1.3 73.3 + - - +
205A PRO* 4.2 11.7 - - + -
216A LYS* 3.2 53.4 + - + +
219A LYS* 3.5 39.3 + - + +
220A ALA* 4.3 9.4 - - + -
223A ASN* 4.1 1.6 + - - -
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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* 3.0 14.9 + - - +
201A ALA* 4.1 13.7 - - - +
202A LYS 3.2 14.5 - - - -
203A GLU* 1.3 83.1 - - - +
205A PRO* 1.4 72.8 - - - +
206A MET* 3.3 16.9 + - + +
216A LYS* 4.0 5.2 + - - +
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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