Contacts of the helix formed by residues 187 - 220 (chain J) in PDB entry 2QJK
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 ASP 187 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I VAL* 5.7 4.3 - - - +
73J VAL* 4.5 9.4 - - - +
151J TRP* 3.6 18.1 - - - -
181J LEU 5.7 0.2 - - - +
185J ALA* 3.1 10.7 + - + +
186J VAL* 1.3 75.6 - - - +
188J ASN* 1.3 87.2 + - - +
189J ALA* 3.4 6.1 - - + +
190J THR* 2.9 17.8 + - - +
191J LEU 3.1 7.4 + - - -
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Residues in contact with ASN 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G THR* 5.1 0.8 + - - -
72J HIS* 3.3 29.4 - - - +
73J VAL* 2.9 52.3 + - + +
187J ASP* 1.3 83.0 + - - +
189J ALA* 1.3 71.1 + - - +
190J THR 2.8 1.6 - - - -
191J LEU* 2.6 17.7 + - - +
192J ASN* 2.8 29.5 + - - +
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Residues in contact with ALA 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G MET 4.5 2.1 - - - +
68G HIS* 6.2 1.8 - - + +
41I SER* 5.4 6.5 - - - +
181J LEU 4.1 8.3 - - - +
182J GLY 4.2 10.8 - - - +
187J ASP* 3.4 4.6 - - + +
188J ASN* 1.3 80.7 - - - +
190J THR* 1.3 60.4 + - - +
192J ASN* 3.7 6.9 + - - +
193J ARG* 2.9 46.4 + - - +
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Residues in contact with THR 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148J VAL* 6.5 0.2 - - + -
151J TRP* 5.4 0.4 - - - -
159J ALA* 5.8 1.1 - - + -
163J THR* 4.8 0.4 - - + -
180J LEU 3.9 13.0 - - - +
181J LEU* 3.0 33.3 + - + -
186J VAL* 3.7 12.4 - - + -
187J ASP* 2.9 28.7 + - - +
188J ASN 2.6 4.4 + - - -
189J ALA* 1.3 71.9 - - - +
191J LEU* 1.3 67.3 + - - -
193J ARG* 2.9 23.9 - - - +
194J PHE* 3.0 40.8 + - + -
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Residues in contact with LEU 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J TYR* 3.6 18.8 - - - +
71J PRO* 4.4 3.4 - - + -
72J HIS* 3.7 15.5 - - - +
73J VAL* 3.4 33.9 - - + +
76J ALA* 4.1 9.0 - - + -
148J VAL* 4.3 5.4 - - + -
149J LEU* 3.8 21.8 - - + -
151J TRP* 3.9 38.1 - - + -
187J ASP 3.1 3.9 + - - +
188J ASN* 2.6 13.5 + - - +
190J THR* 1.3 74.1 - - - +
192J ASN* 1.3 63.5 + - - +
194J PHE* 3.0 17.9 + - + +
195J PHE* 3.0 11.5 + - - +
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Residues in contact with ASN 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G ALA 3.2 10.5 + - - +
67G MET* 3.0 34.6 + - - +
68G HIS* 3.8 8.8 - - - +
69G TYR 3.2 20.0 + - - +
70G THR* 3.6 13.0 + - - -
71J PRO* 3.8 18.8 - - - +
188J ASN* 2.8 29.3 + - - +
189J ALA* 3.8 8.1 - - - +
191J LEU* 1.3 75.0 - - - +
193J ARG* 1.3 61.8 + - - +
195J PHE* 3.2 15.6 + - - +
196J SER* 3.3 9.4 + - - -
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Residues in contact with ARG 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G MET* 3.7 31.3 + - + +
68G HIS* 4.3 15.5 - - - -
37I GLN 5.0 0.2 + - - -
38I MET* 2.9 72.6 + - + +
39I ASN 5.0 1.2 + - - -
179J TRP 3.2 4.9 + - - -
180J LEU 3.1 20.8 + - - -
182J GLY* 3.3 18.6 - - - -
189J ALA* 2.9 29.0 + - - +
190J THR* 2.9 22.6 - - - +
192J ASN* 1.3 77.3 - - - +
194J PHE* 1.3 74.8 + - + +
196J SER* 3.4 2.4 + - - -
197J LEU* 3.1 29.5 + - + +
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Residues in contact with PHE 194 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J PHE* 3.6 31.4 - + - -
145J MET* 3.7 26.4 - - + +
148J VAL* 3.7 27.8 - - + -
149J LEU* 4.6 8.5 - - + -
159J ALA* 4.5 5.6 - - + -
163J THR* 4.4 10.1 - - + -
180J LEU 4.5 4.5 - - - -
190J THR* 3.0 40.6 + - + +
191J LEU* 3.0 10.5 + - - +
193J ARG* 1.3 85.0 - - + +
195J PHE* 1.3 56.0 + - - +
197J LEU* 3.1 4.4 + - + +
198J HIS* 2.6 39.4 + - - +
503J SMA 3.6 31.2 - - + -
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Residues in contact with PHE 195 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G ALA 5.3 3.4 - - - -
69G TYR 6.1 0.2 - - - -
195G PHE* 2.9 43.1 - + - -
199G TYR* 5.7 0.4 - + - -
66J ALA* 4.4 21.5 - - + -
69J TYR* 3.6 33.0 - + - -
71J PRO* 3.7 33.4 - - + -
149J LEU* 4.0 19.2 - - + +
191J LEU 3.0 7.8 + - - +
192J ASN* 3.4 10.3 - - - +
194J PHE* 1.3 77.6 - - - +
196J SER* 1.3 67.0 + - - +
197J LEU 3.1 0.2 + - - -
198J HIS* 3.2 3.6 + - + +
199J TYR* 3.0 35.7 + + - +
502J HEM 3.9 19.1 - - + -
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Residues in contact with SER 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ILE* 2.8 28.2 + - - +
66G ALA* 3.3 13.8 - - - +
67G MET* 3.7 28.7 - - - -
199G TYR* 2.9 34.5 + - - -
192J ASN 3.3 2.2 + - - -
193J ARG 3.7 7.9 - - - -
194J PHE 3.3 0.2 - - - -
195J PHE* 1.3 83.1 - - - +
197J LEU* 1.3 58.1 + - - +
199J TYR* 3.4 1.0 - - - +
200J LEU* 3.2 13.2 + - - +
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Residues in contact with LEU 197 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ILE* 4.8 1.8 - - + -
67G MET* 3.4 28.3 - - + -
38I MET* 5.1 7.6 - - + -
145J MET* 3.7 24.7 - - + -
193J ARG* 3.1 23.1 + - + +
194J PHE* 3.8 2.2 - - + +
195J PHE 3.1 0.2 - - - -
196J SER* 1.3 76.1 - - - +
198J HIS* 1.3 66.3 + - - +
199J TYR 3.0 2.1 + - - -
200J LEU* 3.1 20.8 + - + -
201J LEU* 3.0 33.2 + - + +
503J SMA 4.9 13.2 - - + -
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Residues in contact with HIS 198 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J THR* 3.4 21.6 + - + +
145J MET* 4.2 14.3 - - + -
146J GLY* 3.5 19.1 + - - -
149J LEU* 3.5 17.9 - - + -
194J PHE 2.6 21.5 + - - +
195J PHE* 3.8 4.5 - + + +
197J LEU* 1.3 73.1 - - - +
199J TYR* 1.3 56.3 + - - +
202J PRO* 3.0 25.9 - - - +
502J HEM 2.0 96.9 + + + -
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Residues in contact with TYR 199 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195G PHE* 5.7 0.7 - + - -
196G SER* 2.7 38.7 + - - -
199G TYR* 3.3 52.7 - + + -
200G LEU* 3.7 10.7 - - - +
63J ILE* 3.8 11.3 - - + +
66J ALA* 4.3 7.2 - - + -
195J PHE* 3.0 27.5 + + + +
196J SER 3.4 11.0 - - - +
198J HIS* 1.3 75.7 - - - +
200J LEU* 1.3 65.5 + - - +
202J PRO* 3.0 15.4 - - - +
203J PHE* 3.5 33.4 - + - -
502J HEM 3.1 34.1 - - + +
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Residues in contact with LEU 200 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ILE* 3.2 46.0 - - + -
199G TYR* 3.7 8.0 + - - +
203G PHE* 3.9 20.6 - - + -
196J SER 3.2 12.7 + - - +
197J LEU* 3.1 17.0 + - + +
199J TYR* 1.3 80.3 - - - +
201J LEU* 1.3 69.3 + - + +
203J PHE* 3.1 23.9 + - + +
204J VAL* 3.5 19.1 + - + -
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Residues in contact with LEU 201 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J ALA* 3.9 13.0 - - + +
141J ALA* 3.7 12.6 - - + -
142J THR* 3.3 37.0 - - + +
145J MET* 3.7 16.6 - - + -
197J LEU* 3.0 22.4 + - + +
200J LEU* 1.3 75.3 - - + +
202J PRO* 1.3 72.0 - - + +
204J VAL* 2.7 35.0 + - + +
205J ILE* 2.8 15.3 + - + +
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Residues in contact with PRO 202 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J LEU* 4.5 5.3 - - + +
59J ILE* 4.3 12.7 - - + +
142J THR* 4.0 2.5 - - + +
198J HIS 3.0 30.3 - - - +
199J TYR 3.0 12.3 - - - +
201J LEU* 1.3 82.9 - - + +
203J PHE* 1.3 58.0 + - + +
205J ILE* 3.2 15.1 - - + +
206J ALA* 2.8 27.2 + - - +
502J HEM 3.5 55.9 - - + -
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Residues in contact with PHE 203 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200G LEU* 3.9 24.7 - - + -
203G PHE* 3.2 59.5 - + + -
59J ILE* 4.6 26.5 - - + -
63J ILE* 4.9 1.6 - - + -
199J TYR* 3.5 34.3 - + - -
200J LEU* 3.1 15.2 + - - +
202J PRO* 1.3 73.7 - - - +
204J VAL* 1.3 62.1 + - + +
206J ALA* 3.1 10.2 - - + +
207J ALA* 2.8 28.6 + - - +
502J HEM 5.5 4.0 - - + -
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Residues in contact with VAL 204 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200J LEU* 3.7 26.2 - - + +
201J LEU* 2.7 34.7 + - + +
203J PHE* 1.3 72.4 - - + +
205J ILE* 1.3 65.1 + - + +
207J ALA* 3.1 10.8 + - + +
208J LEU* 2.9 34.6 + - + +
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Residues in contact with ILE 205 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J LEU* 4.1 12.8 - - + -
104J PHE* 5.2 1.1 - - + -
135J ILE* 4.3 8.3 - - + -
138J ALA* 3.9 16.4 - - + -
139J MET* 3.8 32.1 - - + +
142J THR* 3.9 6.5 - - - +
201J LEU 2.8 17.6 + - - +
202J PRO* 3.2 6.7 - - + +
204J VAL* 1.3 77.7 - - - +
206J ALA* 1.3 65.8 + - - +
208J LEU* 2.7 14.0 + - - +
209J VAL* 2.7 39.9 + - + +
501J HEM 4.2 12.1 - - + -
502J HEM 3.8 29.8 - - + -
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Residues in contact with ALA 206 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J LEU* 3.7 21.1 - - + +
59J ILE* 4.9 7.6 - - + -
202J PRO 2.8 15.5 + - - +
203J PHE* 3.1 17.5 - - + +
205J ILE* 1.3 72.0 - - - +
207J ALA* 1.3 63.9 + - - +
209J VAL* 3.2 5.1 + - - +
210J ALA* 3.0 18.2 + - - +
505J ANJ 3.9 19.9 - - + +
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Residues in contact with ALA 207 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203J PHE 2.8 11.6 + - - +
204J VAL* 3.2 13.9 - - + +
206J ALA* 1.3 75.6 - - - +
208J LEU* 1.3 67.2 + - + +
210J ALA* 3.0 23.1 - - - +
211J ILE* 3.3 10.2 + - + +
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Residues in contact with LEU 208 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131J VAL* 4.0 11.8 - - + +
134J LEU* 3.9 35.7 - - + +
135J ILE* 3.8 25.1 - - + +
138J ALA* 5.2 4.7 - - + -
204J VAL* 2.9 27.9 + - + +
205J ILE* 2.7 16.6 + - - +
207J ALA* 1.3 74.1 - - + +
209J VAL* 1.3 52.6 + - - +
211J ILE* 2.8 23.0 + - + +
212J HIS* 2.7 32.2 + - - +
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Residues in contact with VAL 209 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J ALA* 6.0 0.2 - - - -
55J LEU* 3.9 10.5 - - + -
135J ILE* 4.0 4.0 - - + +
205J ILE* 2.7 33.8 + - + +
206J ALA* 3.3 7.4 - - - +
208J LEU* 1.3 71.9 - - - +
210J ALA* 1.3 66.1 + - - +
212J HIS* 3.2 10.5 - - + +
213J ILE* 3.0 33.1 + - + +
501J HEM 3.5 51.4 - - + -
505J ANJ 4.2 23.3 - - + +
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Residues in contact with ALA 210 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206J ALA 3.0 10.7 + - - +
207J ALA* 3.0 15.4 + - - +
208J LEU 2.9 0.6 + - - -
209J VAL* 1.3 74.4 - - - +
211J ILE* 1.3 53.9 + - + +
213J ILE* 2.7 28.4 + - - +
214J TRP* 2.8 16.3 + - - +
505J ANJ 4.3 22.4 + - + -
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Residues in contact with ILE 211 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G LEU* 3.9 26.9 - - + -
25G ILE* 4.7 16.4 - - + -
131J VAL* 4.2 18.4 - - + -
207J ALA 3.9 11.4 - - - +
208J LEU* 2.8 24.7 + - + +
210J ALA* 1.3 73.2 - - + +
212J HIS* 1.3 52.8 + - - +
214J TRP* 3.4 19.7 - - + +
215J ALA* 2.7 34.5 + - + +
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Residues in contact with HIS 212 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J THR* 3.6 30.3 + - + +
131J VAL* 3.9 13.4 - - + +
132J GLY* 4.0 7.4 + - - -
135J ILE* 4.1 5.4 - - + -
208J LEU 2.7 15.4 + - - +
209J VAL* 3.2 16.4 - - + +
211J ILE* 1.3 73.0 - - - +
213J ILE* 1.3 64.2 + - + +
215J ALA* 3.2 5.4 + - - +
216J PHE* 3.1 24.7 + + - +
501J HEM 2.0 98.3 + + + -
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Residues in contact with ILE 213 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J THR* 5.7 2.9 - - + -
209J VAL* 3.0 15.2 + - + +
210J ALA* 2.7 12.8 + - - +
212J HIS* 1.3 71.2 - - + +
214J TRP* 1.3 67.1 + - - +
216J PHE* 3.2 25.6 + - + -
217J HIS* 2.9 49.2 + - + +
501J HEM 5.5 2.0 - - + -
505J ANJ 2.8 73.8 - - + +
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Residues in contact with TRP 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G LEU* 3.6 13.5 - - + -
24G PRO* 4.1 24.2 - - + +
25G ILE* 3.4 47.1 - - + -
28G LEU* 3.7 33.4 - - + -
210J ALA 2.8 15.0 + - - +
211J ILE* 3.4 23.3 - - + +
213J ILE* 1.3 73.9 - - - +
215J ALA* 1.3 56.5 + - - +
217J HIS* 3.3 8.0 + - + +
218J SER* 2.9 33.1 + - - -
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Residues in contact with ALA 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G ARG 4.0 2.1 - - - +
23G LEU* 3.6 23.6 - - + -
127J VAL* 4.7 9.4 - - + -
128J THR* 3.9 24.9 - - - +
131J VAL* 5.7 0.9 - - + -
211J ILE* 2.7 21.3 + - + +
212J HIS* 3.5 5.4 - - - +
214J TRP* 1.3 70.3 - - - +
216J PHE* 1.3 58.8 + - - +
217J HIS 3.0 4.9 - - - -
218J SER* 3.0 18.9 + - - -
219J THR* 3.5 15.8 + - - +
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Residues in contact with PHE 216 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J THR* 4.0 8.1 - - + +
212J HIS* 3.1 29.3 + + - +
213J ILE* 3.2 35.4 - - + -
215J ALA* 1.3 76.3 - - - +
217J HIS* 1.3 72.2 + + - +
218J SER 3.3 0.2 - - - -
219J THR* 4.0 8.3 - - - -
220J GLY* 3.2 26.9 + - - -
221J ASN* 2.9 31.3 + - - +
501J HEM 3.5 66.2 - + + +
505J ANJ 3.5 25.8 - - - -
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Residues in contact with HIS 217 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J ILE* 6.0 1.4 - - - +
31J ASP 4.0 3.2 + - - -
32J THR* 3.3 43.9 + - + +
35J ILE* 3.6 46.0 - - + +
213J ILE* 2.9 39.9 + - + +
214J TRP* 3.4 11.2 - - + +
216J PHE* 1.3 95.9 - + - +
218J SER* 1.3 61.0 + - - +
219J THR 3.3 1.2 + - - -
220J GLY 3.8 5.0 + - - -
505J ANJ 4.5 7.7 + - - -
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Residues in contact with SER 218 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G SER 4.5 6.8 - - - +
22G ARG 3.1 25.6 + - - +
23G LEU* 4.2 1.2 - - - +
24G PRO* 3.9 13.9 - - - +
3J GLY* 5.8 4.2 - - - -
4J ILE* 6.4 0.7 - - - -
214J TRP* 2.9 33.5 + - - -
215J ALA 3.0 5.3 + - - -
217J HIS* 1.3 78.4 - - - +
219J THR* 1.3 59.1 + - - +
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Residues in contact with THR 219 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G SER 4.6 3.1 - - - +
22G ARG* 3.7 28.7 - - + +
4J ILE* 5.2 3.8 - - - -
124J PRO* 4.3 34.4 - - + +
125J ARG* 4.2 13.8 + - - +
128J THR* 4.8 2.7 + - - +
215J ALA 3.5 11.1 + - - +
216J PHE* 3.9 6.6 + - - -
217J HIS 3.3 0.2 - - - -
218J SER* 1.3 82.5 - - - +
220J GLY* 1.3 73.0 + - - +
228J GLU* 4.2 4.5 - - - +
231J ARG* 3.4 22.8 + - - +
501J HEM 4.3 0.3 + - - -
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Residues in contact with GLY 220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J ILE* 4.7 14.7 - - - +
35J ILE* 4.8 7.9 - - - -
36J PRO 6.0 0.9 - - - -
125J ARG* 3.8 5.1 + - - -
216J PHE 3.2 13.2 + - - +
217J HIS 3.8 7.2 + - - -
218J SER 3.7 0.8 - - - -
219J THR* 1.3 94.7 + - - +
221J ASN* 1.3 67.8 + - - -
228J GLU* 5.6 0.2 - - - -
231J ARG* 4.9 2.2 - - - -
501J HEM 3.6 5.7 - - - +
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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) + - + + + + + -
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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