Contacts of the helix formed by residues 276 - 298 (chain R) in PDB entry 1HI0
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 PRO 276 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151R THR 4.0 1.1 - - - +
153R ILE* 3.3 28.0 - - + +
194R GLN 4.3 9.4 - - - +
196R GLY 3.3 26.7 - - - +
198R ALA 3.4 21.3 - - - +
199R TYR* 4.6 4.3 - - + -
274R GLY 3.9 0.2 - - - -
275R GLY* 1.3 79.1 - - - +
277R PHE* 1.3 66.0 + - - +
278R ALA 3.4 1.3 - - - -
279R LEU* 3.1 23.9 + - + -
280R ASN* 3.1 12.5 + - - +
363R LEU* 4.0 15.9 - - + -
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Residues in contact with PHE 277 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F C 5.1 10.3 - - - -
143R LEU* 5.5 1.1 - - + -
145R ILE* 4.0 32.8 - - + -
150R SER 5.6 1.3 - - - -
151R THR* 3.2 45.6 + - + +
153R ILE 4.0 2.2 + - - -
163R LYS* 3.8 25.8 - - + -
166R ILE* 3.3 24.5 - - + -
167R ALA* 4.0 13.9 - - + -
275R GLY 3.2 4.1 + - - +
276R PRO* 1.3 68.0 - - - +
278R ALA* 1.3 65.4 + - - +
279R LEU 2.9 0.2 + - - -
280R ASN* 3.1 6.2 + - + +
281R ALA* 2.9 31.2 + - + +
284R MET* 4.0 30.3 - - + -
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Residues in contact with ALA 278 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153R ILE 5.4 0.8 + - - -
154R PRO* 6.4 0.2 - - - +
166R ILE* 4.4 14.2 - - + +
170R ALA* 3.3 20.0 - - + +
193R HIS 3.2 26.9 - - - +
194R GLN* 3.2 23.3 + - + +
195R MET* 3.4 11.5 - - + +
276R PRO 3.4 0.8 + - - -
277R PHE* 1.3 76.5 - - - +
279R LEU* 1.3 56.0 + - - +
282R PRO* 3.0 20.6 - - - +
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Residues in contact with LEU 279 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181R MET* 4.5 3.8 - - + -
195R MET* 4.1 17.0 - - + -
196R GLY* 4.1 16.4 - - - +
199R TYR* 5.7 1.1 - - - +
276R PRO* 3.1 26.1 + - + +
277R PHE 3.0 0.6 - - - -
278R ALA* 1.3 77.1 - - - +
280R ASN* 1.3 67.8 + - - +
281R ALA 3.2 2.0 - - - -
282R PRO* 3.0 18.1 - - - +
283R ILE* 3.6 9.1 - - + +
356R LEU* 4.0 43.3 - - + +
359R THR* 5.0 2.7 - - + -
360R SER* 4.0 30.1 - - - +
363R LEU* 4.4 13.5 - - + -
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Residues in contact with ASN 280 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F C 6.2 0.7 - - - -
199R TYR* 4.2 4.6 + - - -
275R GLY* 3.2 36.9 - - - +
276R PRO* 3.1 6.1 + - - +
277R PHE* 3.1 9.8 + - + +
279R LEU* 1.3 78.3 - - - +
281R ALA* 1.3 51.3 + - - +
283R ILE* 3.1 12.0 + - - +
284R MET* 2.6 53.4 + - - +
360R SER* 4.9 1.8 - - - -
394R GLY 3.4 12.5 - - - +
395R GLN* 3.4 14.5 - - - +
396R GLY* 3.1 23.9 - - - +
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Residues in contact with ALA 281 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143R LEU* 4.1 14.4 - - + +
167R ALA* 4.2 17.7 - - + +
170R ALA* 3.9 16.4 - - + -
171R LEU* 4.3 3.6 - - + -
277R PHE* 2.9 22.2 + - + +
280R ASN* 1.3 75.6 - - - +
282R PRO* 1.3 72.0 - - + +
284R MET* 3.0 12.4 + - - +
285R ALA* 2.9 23.9 + - - +
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Residues in contact with PRO 282 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170R ALA* 4.1 5.6 - - + -
171R LEU* 3.7 6.9 - - + -
174R ALA* 3.8 22.0 - - + -
195R MET* 4.6 2.5 - - + -
278R ALA 3.0 21.8 - - - +
279R LEU* 3.0 17.0 - - + +
281R ALA* 1.3 92.5 - - + +
283R ILE* 1.3 61.7 + - + +
285R ALA* 3.6 4.0 - - - +
286R VAL* 3.6 2.9 - - - +
353R TRP* 3.1 19.3 + - - +
356R LEU* 4.4 15.7 - - + -
657R PHE* 3.5 34.3 - - + -
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Residues in contact with ILE 283 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279R LEU* 3.6 21.1 - - + +
280R ASN* 3.1 16.1 + - - +
281R ALA 3.0 0.8 - - - -
282R PRO* 1.3 78.1 - - + +
284R MET* 1.3 67.0 + - - +
285R ALA 3.1 1.3 - - - -
286R VAL* 3.0 5.0 + - - +
287R ALA* 2.9 19.6 + - - +
353R TRP* 4.2 11.1 - - + +
356R LEU* 4.4 3.4 - - + +
357R PHE* 4.1 37.9 - - + +
360R SER* 3.4 35.9 - - - +
395R GLN* 4.1 5.4 - - - +
396R GLY* 3.8 24.7 - - - -
397R ALA* 4.2 3.4 - - + +
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Residues in contact with MET 284 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F C 4.7 28.0 - - - +
143R LEU* 3.6 28.7 - - + -
144R LYS 3.8 11.4 - - - +
145R ILE* 5.2 2.2 - - + -
277R PHE* 4.0 24.7 - - + -
280R ASN* 2.6 36.5 + - - +
281R ALA* 3.6 4.0 - - - +
283R ILE* 1.3 73.5 - - - +
285R ALA* 1.3 62.4 + - - +
286R VAL 3.0 1.6 + - - -
287R ALA* 3.9 7.9 - - - -
288R GLN* 3.1 26.7 + - - +
291R ARG* 5.1 0.4 + - - +
396R GLY* 3.9 20.6 - - - +
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Residues in contact with ALA 285 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141R VAL* 5.3 4.5 + - - +
143R LEU* 4.4 14.1 - - + +
171R LEU* 4.1 10.8 - - + -
281R ALA 2.9 14.9 + - - +
282R PRO 3.6 0.4 - - - +
283R ILE 3.1 0.2 - - - -
284R MET* 1.3 77.7 - - - +
286R VAL* 1.3 57.6 + - - +
288R GLN* 5.6 0.2 - - - -
289R PRO* 3.2 20.8 - - - +
654R THR* 5.2 8.4 - - - -
657R PHE* 3.5 34.3 - - + -
658R LEU* 3.4 9.1 - - + +
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Residues in contact with VAL 286 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135R PHE* 4.5 9.2 - - + -
138R LEU* 4.4 11.7 - - + -
282R PRO 3.6 4.0 - - - +
283R ILE 3.0 1.8 + - - +
285R ALA* 1.3 75.6 - - - +
287R ALA* 1.3 67.3 + - - +
288R GLN 3.3 1.8 - - - -
289R PRO* 3.0 14.4 - - - +
290R VAL* 3.1 25.5 + - + +
349R TYR* 4.5 8.1 - - + -
353R TRP* 3.3 53.2 - - + +
657R PHE* 4.4 2.7 - - + -
658R LEU* 3.9 18.4 - - + -
661R VAL* 4.2 10.5 - - + -
662R MET* 5.8 0.4 - - + -
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Residues in contact with ALA 287 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135R PHE* 6.2 0.4 - - - -
283R ILE 2.9 15.9 + - - +
284R MET* 3.7 5.4 - - - +
286R VAL* 1.3 78.5 - - - +
288R GLN* 1.3 57.5 + - - +
290R VAL* 3.0 8.1 + - - +
291R ARG* 2.8 42.5 + - - +
396R GLY 3.6 23.8 - - - +
397R ALA* 4.1 14.1 - - + -
400R LEU* 3.6 8.7 - - + +
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Residues in contact with GLN 288 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141R VAL* 3.8 19.3 - - + -
142R PRO 5.1 4.9 - - - +
143R LEU* 6.4 0.9 - - - -
144R LYS* 6.4 1.6 - - + +
284R MET 3.1 10.8 + - - +
285R ALA* 5.6 0.7 - - - -
287R ALA* 1.3 79.5 - - - +
289R PRO* 1.3 71.8 - - + +
291R ARG* 2.9 45.5 + - - +
292R ASN* 2.9 40.7 + - - +
295R TYR* 5.8 0.2 - - - -
633R THR* 5.0 6.7 + - - -
634R GLU* 5.3 14.4 + - - +
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Residues in contact with PRO 289 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138R LEU* 3.6 31.7 - - + +
139R GLU 3.7 18.6 + - - +
141R VAL* 3.7 16.8 - - + +
285R ALA 3.2 24.0 - - - +
286R VAL* 3.0 19.3 - - - +
288R GLN* 1.3 89.2 - - + +
290R VAL* 1.3 60.9 + - - +
292R ASN* 3.3 12.8 + - + +
293R LYS* 3.1 18.0 + - - +
658R LEU* 4.3 10.8 - - + -
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Residues in contact with VAL 290 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134R MET* 3.7 32.1 - - + +
135R PHE* 3.8 29.4 - - + -
138R LEU* 3.8 24.0 - - + -
286R VAL* 3.1 18.0 + - + +
287R ALA* 3.0 10.4 + - - +
289R PRO* 1.3 75.2 - - - +
291R ARG* 1.3 63.9 + - - +
293R LYS* 3.1 4.0 + - - +
294R ILE* 3.1 23.8 + - + +
400R LEU* 3.7 27.4 - - + -
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Residues in contact with ARG 291 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F C 4.4 10.3 + - - -
284R MET* 5.1 0.6 + - - +
287R ALA* 2.8 16.8 + - - +
288R GLN* 2.9 56.6 + - - +
290R VAL* 1.3 78.3 - - - +
292R ASN* 1.3 62.2 - - - +
294R ILE* 3.5 6.0 + - - +
295R TYR* 2.9 55.6 + - + -
396R GLY 3.3 23.4 + - - -
397R ALA* 4.3 0.4 - - - +
399R ASP* 2.7 38.8 + - - -
400R LEU* 4.2 13.7 - - + -
633R THR* 5.3 2.9 - - - -
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Residues in contact with ASN 292 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139R GLU 4.9 1.0 + - - +
141R VAL* 3.7 27.5 - - - +
288R GLN* 2.9 41.7 + - - +
289R PRO* 3.6 13.6 - - + +
290R VAL 3.3 0.2 - - - -
291R ARG* 1.3 75.1 - - - +
293R LYS* 1.3 53.8 + - - +
295R TYR* 3.8 6.0 - - - +
296R SER* 2.6 36.4 + - - -
633R THR* 5.7 0.5 + - - -
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Residues in contact with LYS 293 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133R LEU 3.1 20.4 + - - +
134R MET 4.1 3.6 - - - +
136R SER* 2.4 30.7 + - - +
137R ASP* 2.7 42.4 + - - +
138R LEU* 4.0 15.0 - - + -
289R PRO 3.1 13.1 + - - +
290R VAL 3.6 7.0 - - - +
292R ASN* 1.3 76.7 - - - +
294R ILE* 1.3 65.7 + - + +
296R SER* 2.7 19.2 + - - -
297R LYS* 2.9 41.3 + - + +
298R TYR* 4.7 3.8 - - + -
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Residues in contact with ILE 294 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134R MET* 3.9 53.2 - - + -
290R VAL* 3.1 11.5 + - + +
291R ARG 3.5 9.4 - - - +
293R LYS* 1.3 77.0 - - + +
295R TYR* 1.3 74.7 + - + +
298R TYR* 3.0 49.2 + - + +
302R PHE* 3.7 30.8 - - + +
400R LEU* 4.0 18.4 - - + -
403R THR* 5.0 4.7 - - + +
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Residues in contact with TYR 295 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291R ARG* 2.9 47.8 + - + +
292R ASN* 4.0 6.7 - - - +
294R ILE* 1.3 87.8 - - + +
296R SER* 1.3 58.8 + - - +
299R ALA* 3.1 21.1 - - - +
302R PHE* 3.5 37.9 - - + -
303R HIS* 3.2 30.7 - + + +
399R ASP* 4.1 12.1 + - - -
400R LEU* 5.7 0.9 - - - +
451R LYS* 3.1 34.0 + - + +
633R THR* 3.8 29.8 - - + -
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Residues in contact with SER 296 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292R ASN 2.6 23.5 + - - -
293R LYS* 2.7 16.5 + - - -
295R TYR* 1.3 74.8 - - - +
297R LYS* 1.3 68.1 + - - +
298R TYR 3.1 0.4 - - - -
299R ALA* 2.9 21.8 + - - +
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Residues in contact with LYS 297 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133R LEU* 5.5 1.4 - - - +
137R ASP* 5.8 1.6 + - - -
293R LYS* 2.9 28.0 + - + +
296R SER* 1.3 80.1 + - - +
298R TYR* 1.3 99.3 + - + +
299R ALA 3.4 0.9 + - - -
437R ASP* 3.4 14.7 + - - -
441R GLN* 3.9 22.0 - - - +
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Residues in contact with TYR 298 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133R LEU* 3.4 42.0 + - + +
293R LYS* 4.7 4.4 - - + -
294R ILE* 3.0 34.2 + - + +
297R LYS* 1.3 111.5 + - + +
299R ALA* 1.3 63.6 + - - +
300R TYR 3.0 5.2 + - - +
301R THR 3.1 4.0 + - - -
302R PHE* 3.1 31.4 + - + +
437R ASP* 2.8 43.7 + - - -
440R TRP* 3.5 41.5 - + + -
441R GLN* 4.0 9.4 - - + -
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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