Contacts of the helix formed by residues 190 - 214 (chain D) in PDB entry 6N0M
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 190 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D LEU* 3.6 5.2 - - - -
188D THR* 4.3 2.6 + - - +
189D TRP* 1.3 75.7 - - - +
191D LEU* 1.3 59.9 + - - +
192D ALA* 3.9 8.8 + - - +
193D GLU* 3.3 37.3 + - - +
194D LEU* 2.9 27.0 + - - +
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Residues in contact with LEU 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D ILE* 5.0 0.9 - - + -
182D LEU* 3.8 28.6 - - + +
190D SER* 1.3 71.0 - - - +
192D ALA* 1.3 69.5 + - - +
194D LEU* 2.9 6.3 + - + -
195D ILE* 2.8 31.3 + - + +
355D LEU* 3.8 33.2 - - + -
475D ILE* 4.2 32.1 - - + -
478D TYR* 5.6 2.5 - - + -
479D MET* 4.0 31.4 - - + -
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Residues in contact with ALA 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D PRO* 3.8 24.5 - - + +
190D SER* 3.9 9.8 - - - +
191D LEU* 1.3 79.6 - - - +
193D GLU* 1.3 62.3 + - + +
195D ILE* 4.1 3.0 - - - +
196D GLN* 3.7 12.1 + - - +
355D LEU* 4.1 20.7 - - - +
356D TYR* 5.4 1.6 - - - +
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Residues in contact with GLU 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D PRO* 4.0 27.4 - - + +
107D LEU* 3.8 13.8 - - + +
155D LYS* 2.7 34.5 + - - -
188D THR 3.9 1.0 - - - +
189D TRP* 3.6 16.0 - - + -
190D SER* 3.3 32.1 + - - +
191D LEU 3.1 0.4 - - - -
192D ALA* 1.3 77.5 - - + +
194D LEU* 1.3 67.1 + - - +
196D GLN* 3.5 5.5 + - - +
197D ALA* 3.1 21.1 + - - +
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Residues in contact with LEU 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D LEU* 4.3 12.3 - - + -
178D ILE* 4.2 22.9 - - + -
181D LEU* 3.3 38.8 - - + -
182D LEU* 4.1 21.1 - - + -
189D TRP* 3.8 12.5 - - + -
190D SER 2.9 21.7 + - - +
191D LEU* 3.6 7.0 - - + +
193D GLU* 1.3 74.6 - - - +
195D ILE* 1.3 57.6 + - - +
197D ALA* 3.0 4.2 + - + +
198D LEU* 2.8 49.9 + - + +
475D ILE* 4.7 7.2 - - + -
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Residues in contact with ILE 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D LEU* 2.8 24.2 + - + +
192D ALA 4.1 4.3 - - - +
194D LEU* 1.3 70.5 - - - +
196D GLN* 1.3 65.7 + - - +
198D LEU* 2.9 21.3 + - + +
199D VAL* 2.9 14.0 + - + +
351D LEU 5.2 0.4 - - - +
352D ILE* 3.8 20.4 - - + -
355D LEU* 3.8 32.5 - - + -
356D TYR* 3.5 31.6 - - + +
472D LEU* 4.3 17.7 - - + -
475D ILE* 3.6 29.4 - - + -
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Residues in contact with GLN 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D LEU* 5.8 0.8 - - - +
100D LEU* 4.6 4.0 - - + +
105D GLY* 3.9 6.7 - - - -
106D PRO* 3.3 29.6 - - + +
107D LEU* 3.1 41.4 + - + +
112D ARG* 3.5 18.4 + - - +
192D ALA 3.7 9.4 + - - +
193D GLU 3.5 8.2 + - - +
195D ILE* 1.3 77.1 - - - +
197D ALA* 1.3 64.0 + - - +
199D VAL* 3.1 3.8 + - - +
200D LEU* 2.9 30.9 + - + +
356D TYR* 3.4 43.3 + - + +
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Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D LEU* 4.0 5.6 - - + +
115D ILE* 4.1 6.0 - - + +
159D LEU* 4.1 14.6 - - + -
189D TRP* 3.8 25.8 - - + -
193D GLU 3.1 10.7 + - - +
194D LEU* 3.0 15.3 + - + +
196D GLN* 1.3 79.0 - - - +
198D LEU* 1.3 56.5 + - - +
200D LEU* 3.2 9.6 + - - +
201D LEU* 2.9 35.2 + - + +
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Residues in contact with LEU 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ILE* 3.9 24.7 - - + -
166D LEU* 4.0 15.9 - - + -
178D ILE* 5.0 0.2 - - + -
194D LEU* 2.8 41.3 + - + +
195D ILE* 2.9 12.8 + - + +
197D ALA* 1.3 72.7 - - - +
199D VAL* 1.3 51.9 + - + +
201D LEU* 3.6 11.9 - - + +
202D THR* 2.6 41.0 + - + +
468D LEU* 4.7 11.4 - - + -
471D ALA* 3.9 23.1 - - + -
472D LEU* 5.3 2.5 - - + +
475D ILE* 3.8 28.5 - - + -
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Residues in contact with VAL 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 4.4 3.4 - - + -
100D LEU* 3.7 27.8 - - + -
195D ILE* 2.9 24.4 + - + +
196D GLN 3.1 6.5 + - - +
198D LEU* 1.3 72.5 - - + +
200D LEU* 1.3 60.5 + - - +
202D THR* 3.0 6.3 + - - -
203D HIS* 2.8 33.5 + - - +
352D ILE* 4.6 2.0 - - + -
356D TYR* 4.0 22.4 - - + -
363D LEU* 3.9 39.5 - - + -
464D MET* 4.4 2.0 - - + -
468D LEU* 4.4 11.4 - - + -
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Residues in contact with LEU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D LEU* 3.9 27.8 - - + +
101D LEU* 3.9 28.5 - - + -
107D LEU* 4.3 4.9 - - + -
112D ARG* 3.7 41.5 - - + +
115D ILE* 3.8 23.6 - - + -
116D ALA 5.2 0.2 - - - +
196D GLN* 2.9 21.4 + - + +
197D ALA* 3.5 7.2 - - - +
199D VAL* 1.3 75.0 - - - +
201D LEU* 1.3 55.4 - - - +
203D HIS* 3.0 6.2 + - + -
204D CYS* 2.9 46.5 + - - -
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Residues in contact with LEU 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ILE* 3.9 13.9 - - + +
118D MET* 5.2 2.0 - - + -
119D ALA* 3.6 16.7 - - + +
159D LEU* 4.1 25.8 - - + +
162D ILE* 4.6 6.3 - - + -
163D ASN* 3.2 44.0 - - + +
166D LEU* 4.2 16.4 - - + -
197D ALA 2.9 26.8 + - - +
198D LEU* 3.6 14.6 - - + +
200D LEU* 1.3 74.7 - - - +
202D THR* 1.3 54.0 + - - +
205D HIS* 2.8 45.6 + - + -
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Residues in contact with THR 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D LEU* 3.8 31.2 - - + -
198D LEU 2.6 25.6 + - - +
199D VAL* 3.0 15.6 + - - -
201D LEU* 1.3 73.9 - - - +
203D HIS* 1.3 58.4 + - - +
205D HIS* 3.6 7.6 - - - +
206D SER* 2.9 32.2 + - - -
464D MET* 3.5 24.4 - - - +
467D ALA* 4.0 16.8 - - + -
468D LEU* 3.9 17.0 - - + +
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Residues in contact with HIS 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D PHE* 4.4 15.3 - + - -
96D LEU* 3.9 18.2 - - + +
97D HIS* 4.2 20.9 + - + -
100D LEU* 3.8 23.8 - - + -
101D LEU* 4.8 9.4 - - + -
199D VAL 2.8 20.1 + - - +
200D LEU* 3.5 3.4 - - + +
202D THR* 1.3 77.3 - - - +
204D CYS* 1.3 62.3 + - - +
206D SER* 2.8 22.0 + - - -
207D LEU* 2.8 62.7 + - + +
366D LYS* 4.9 6.1 - - - -
460D LEU* 5.8 1.2 - - - +
464D MET* 3.9 11.2 - - + +
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Residues in contact with CYS 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LEU* 5.3 1.6 - - - -
116D ALA* 3.6 46.4 - - - +
119D ALA* 4.0 8.3 - - + -
120D ALA* 4.3 5.4 - - + +
128D LEU* 3.7 8.8 - - + +
132D HIS* 4.3 10.5 - - + +
200D LEU* 2.9 27.5 + - - +
201D LEU 3.9 0.2 - - - -
203D HIS* 1.3 85.4 - - - +
205D HIS* 1.3 55.1 + - - +
207D LEU* 4.0 10.1 - - + -
208D SER* 2.5 32.4 + - - -
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Residues in contact with HIS 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ALA* 3.3 22.7 + - - -
123D HIS* 4.3 4.5 - + - -
163D ASN* 2.7 31.8 + - - -
166D LEU* 3.7 13.4 + - + +
167D ALA* 3.4 42.1 + - + +
201D LEU* 2.8 38.2 + - + +
202D THR* 3.6 9.4 - - - +
203D HIS 3.3 0.2 - - - -
204D CYS* 1.3 73.7 - - - +
206D SER* 1.3 61.5 + - - +
208D SER* 2.9 29.9 + - - -
209D SER 3.2 1.2 + - - -
463D ARG* 3.1 26.8 + - - +
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Residues in contact with SER 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D THR 2.9 11.4 + - - -
203D HIS* 2.8 22.7 + - - -
205D HIS* 1.3 80.6 - - - +
207D LEU* 1.3 55.2 + - - +
209D SER* 3.1 8.8 + - - -
210D PHE* 3.0 24.3 + - - +
460D LEU* 3.1 45.1 - - - +
463D ARG* 4.1 11.9 - - - +
464D MET* 3.9 15.1 - - - -
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Residues in contact with LEU 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LEU* 3.7 28.5 - - + -
83D MET* 4.2 23.6 - - + -
93D PHE* 4.3 7.2 - - + -
97D HIS* 4.9 6.1 - - + +
101D LEU* 6.1 0.9 - - + -
128D LEU* 3.7 20.2 - - + -
132D HIS* 6.1 1.3 - - - +
203D HIS* 2.8 62.6 + - + +
204D CYS* 4.2 4.7 - - - +
206D SER* 1.3 69.0 + - - +
208D SER* 1.3 60.5 + - - +
210D PHE* 3.3 4.9 + - + +
211D VAL* 2.8 32.6 + - - +
460D LEU* 4.4 12.6 - - + -
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Residues in contact with SER 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ALA* 4.0 5.7 - - - -
123D HIS* 3.9 24.2 - - - -
125D CYS* 3.9 23.6 - - - +
128D LEU* 3.5 12.0 - - - +
204D CYS 2.5 24.4 + - - -
205D HIS* 2.9 13.4 + - - -
207D LEU* 1.3 76.2 - - - +
209D SER* 1.3 65.1 + - - +
211D VAL* 3.3 0.3 + - - +
212D PHE* 3.1 30.0 + - - -
432D PRO* 4.5 0.7 - - - -
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Residues in contact with SER 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D HIS 3.2 1.6 + - - -
206D SER* 3.1 12.8 + - - -
208D SER* 1.3 77.6 - - - +
210D PHE* 1.3 53.6 + - - +
212D PHE* 3.7 0.9 - - - +
213D GLY 2.8 31.7 + - - -
428D VAL* 2.8 44.5 + - - +
429D ALA* 3.9 0.2 - - - -
432D PRO* 3.9 5.3 - - - +
459D LEU* 4.1 12.6 - - - -
460D LEU* 5.1 2.0 - - - -
463D ARG* 3.1 30.4 + - - -
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Residues in contact with PHE 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LEU* 3.6 33.0 - - + -
82D VAL* 4.2 5.6 - - + -
83D MET* 3.6 35.2 - - + -
206D SER 3.0 12.3 + - - +
207D LEU* 3.4 11.2 - - + +
208D SER 3.2 0.2 - - - -
209D SER* 1.3 76.9 - - - +
211D VAL* 1.3 62.4 + - - +
214D CYS* 3.1 43.5 + - - +
216D ILE* 3.5 23.3 - - + -
453D VAL* 4.2 12.1 - - + -
456D ASN* 4.2 17.3 - - + -
457D LEU* 4.3 10.8 - - + -
460D LEU* 3.6 26.8 - - + +
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Residues in contact with VAL 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LEU* 4.3 20.4 - - + -
125D CYS* 4.0 12.3 - - - -
127D TYR* 3.8 41.3 - - + -
128D LEU* 4.3 6.5 - - + -
207D LEU 2.8 25.1 + - - +
208D SER 3.3 3.6 + - - +
210D PHE* 1.3 72.0 - - - +
212D PHE* 1.3 72.0 + - + +
215D GLY* 3.0 4.2 + - - -
216D ILE* 3.0 51.3 + - + +
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Residues in contact with PHE 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D HIS* 3.3 21.3 - - + -
124D GLN* 3.5 21.1 - - + -
125D CYS* 3.7 23.6 - - + -
126D SER 5.0 1.6 - - - -
208D SER* 3.1 26.7 + - - +
211D VAL* 1.3 79.8 - - + +
213D GLY* 1.3 65.3 + - - +
215D GLY* 3.3 9.3 + - - -
237D GLN* 3.3 8.7 - - - +
432D PRO* 3.3 39.9 - - + +
433D GLU* 3.7 21.8 - - + -
435D THR* 3.6 15.5 - - - +
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Residues in contact with GLY 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D SER 2.8 16.2 + - - -
211D VAL 3.2 0.2 - - - -
212D PHE* 1.3 76.6 - - - +
214D CYS* 1.3 56.2 + - - +
237D GLN* 3.3 11.4 - - - +
424D TYR* 2.7 26.6 + - - -
428D VAL* 3.7 14.1 - - - +
435D THR* 4.3 0.7 - - - -
440D TYR* 3.6 6.8 - - - -
456D ASN* 3.4 20.4 - - - -
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Residues in contact with CYS 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D VAL* 4.3 13.9 - - + -
210D PHE* 3.1 38.4 + - - +
213D GLY* 1.3 72.2 - - - +
215D GLY* 1.3 55.5 + - - +
216D ILE* 3.3 9.1 + - + -
235D SER* 2.7 28.9 + - - -
237D GLN* 3.5 10.8 - - - +
238D SER* 4.2 4.8 + - - +
440D TYR* 4.8 5.4 - - - -
453D VAL* 4.1 16.8 - - - -
456D ASN* 3.7 28.5 - - - +
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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