Contacts of the helix formed by residues 276 - 298 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151P THR 4.0 0.9 - - - +
153P ILE* 3.3 27.6 - - + +
190P TYR* 5.7 0.2 - - + -
194P GLN 4.3 9.4 - - - +
196P GLY 3.3 26.7 - - - +
198P ALA 3.4 21.1 - - - +
199P TYR* 4.6 4.3 - - + -
274P GLY 3.9 0.2 - - - -
275P GLY* 1.3 78.9 - - - +
277P PHE* 1.3 66.3 + - - +
278P ALA 3.4 1.8 - - - -
279P LEU* 3.1 24.7 + - + -
280P ASN* 3.1 12.4 + - - +
363P LEU* 4.0 15.3 - - + -
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Residues in contact with PHE 277 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D C 5.1 10.3 - - - -
143P LEU* 5.5 1.6 - - + -
145P ILE* 4.0 32.1 - - + -
150P SER 5.6 1.6 - - - -
151P THR* 3.2 45.0 + - + +
153P ILE 4.0 2.4 + - - -
163P LYS* 3.8 26.7 - - + -
166P ILE* 3.3 23.8 - - + -
167P ALA* 4.0 13.7 - - + -
275P GLY 3.2 3.7 + - - +
276P PRO* 1.3 69.1 - - - +
278P ALA* 1.3 66.1 + - - +
280P ASN* 3.1 6.2 + - + +
281P ALA* 2.9 29.9 + - + +
284P MET* 4.0 29.8 - - + -
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Residues in contact with ALA 278 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153P ILE 5.4 0.6 + - - -
166P ILE* 4.4 14.2 - - + +
170P ALA* 3.3 19.5 - - + +
193P HIS 3.2 27.8 - - - +
194P GLN* 3.2 23.1 + - + +
195P MET* 3.4 10.7 - - + +
276P PRO 3.4 0.8 + - - -
277P PHE* 1.3 77.8 - - - +
279P LEU* 1.3 56.0 + - - +
282P PRO* 3.0 20.6 - - - +
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Residues in contact with LEU 279 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181P MET* 4.5 3.6 - - + -
194P GLN 4.4 0.2 + - - -
195P MET* 4.0 17.5 - - + +
196P GLY* 4.1 16.4 - - - +
199P TYR* 5.7 0.9 - - - +
276P PRO* 3.1 25.7 + - + +
277P PHE 3.0 0.2 - - - -
278P ALA* 1.3 76.9 - - - +
280P ASN* 1.3 67.1 + - - +
281P ALA 3.2 1.8 - - - -
282P PRO* 3.0 18.2 - - + +
283P ILE* 3.6 9.2 - - + +
356P LEU* 4.0 43.7 - - + +
359P THR* 5.0 2.5 - - + -
360P SER* 4.0 30.3 - - - +
363P LEU* 4.4 12.8 - - + -
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Residues in contact with ASN 280 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D C 6.2 0.9 - - - -
199P TYR* 4.2 5.1 + - - -
275P GLY* 3.2 37.5 + - - +
276P PRO* 3.1 5.3 + - - +
277P PHE* 3.1 10.1 + - + +
279P LEU* 1.3 78.6 - - - +
281P ALA* 1.3 52.0 + - - +
283P ILE* 3.1 11.6 + - - +
284P MET* 2.6 52.8 + - - +
360P SER* 4.9 1.8 - - - -
394P GLY 3.4 12.6 - - - +
395P GLN* 3.4 14.5 - - - +
396P GLY 3.1 24.5 - - - +
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Residues in contact with ALA 281 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143P LEU* 4.1 15.4 - - + +
167P ALA* 4.2 18.2 - - + +
170P ALA* 3.9 15.7 - - + -
171P LEU* 4.3 3.8 - - + -
277P PHE* 2.9 20.9 + - + +
280P ASN* 1.3 75.6 - - - +
282P PRO* 1.3 71.9 - - + +
284P MET* 3.0 12.8 + - - +
285P ALA* 2.9 23.4 + - - +
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Residues in contact with PRO 282 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170P ALA* 4.1 6.1 - - + -
171P LEU* 3.7 7.2 - - + -
174P ALA* 3.8 21.5 - - + -
195P MET* 4.6 1.8 - - + -
278P ALA 3.0 20.6 - - - +
279P LEU* 3.0 17.9 - - + +
281P ALA* 1.3 93.8 - - + +
283P ILE* 1.3 58.9 + - + +
285P ALA* 3.6 4.2 - - - +
286P VAL* 3.6 2.8 - - - +
353P TRP* 3.1 19.9 + - - +
356P LEU* 4.4 15.9 - - + -
657P PHE* 3.5 33.6 - - + -
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Residues in contact with ILE 283 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279P LEU* 3.6 21.1 - - + +
280P ASN* 3.1 16.4 + - - +
281P ALA 3.0 0.4 - - - -
282P PRO* 1.3 77.4 - - + +
284P MET* 1.3 66.1 + - - +
285P ALA 3.1 1.6 - - - -
286P VAL* 3.0 5.5 + - - +
287P ALA* 2.9 19.8 + - - +
353P TRP* 4.2 10.0 - - + +
356P LEU* 4.4 3.8 - - + +
357P PHE* 4.1 38.6 - - + +
360P SER* 3.4 36.8 - - - +
395P GLN* 4.1 5.8 - - - +
396P GLY* 3.8 24.5 - - - -
397P ALA* 4.2 3.4 - - + +
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Residues in contact with MET 284 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D C 4.7 28.5 - - - +
143P LEU* 3.6 31.4 - - + -
144P LYS 3.8 11.7 - - - +
145P ILE* 5.2 2.9 - - + -
277P PHE* 4.0 23.6 - - + -
280P ASN* 2.6 36.6 + - - +
281P ALA* 3.6 4.5 - - - +
283P ILE* 1.3 72.1 - - - +
285P ALA* 1.3 61.9 - - - +
286P VAL 3.0 1.2 + - - -
287P ALA* 3.9 7.9 - - - -
288P GLN* 3.1 27.0 + - - +
291P ARG* 5.1 0.6 + - - +
396P GLY* 3.9 21.5 - - - +
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Residues in contact with ALA 285 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141P VAL* 5.3 4.5 + - - +
143P LEU* 4.4 14.3 - - + +
171P LEU* 4.1 11.0 - - + -
281P ALA 2.9 15.2 + - - +
282P PRO 3.6 0.4 - - - +
283P ILE 3.1 0.2 - - - -
284P MET* 1.3 76.7 - - - +
286P VAL* 1.3 58.1 + - - +
288P GLN* 5.6 0.4 - - - -
289P PRO* 3.2 20.8 - - - +
654P THR* 5.2 7.9 - - - -
657P PHE* 3.5 34.1 - - + -
658P LEU* 3.4 9.7 - - + +
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Residues in contact with VAL 286 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135P PHE* 4.5 9.9 - - + -
138P LEU* 4.4 11.7 - - + -
282P PRO 3.6 3.6 - - - +
283P ILE 3.0 1.6 + - - +
285P ALA* 1.3 77.0 - - - +
287P ALA* 1.3 67.6 + - - +
288P GLN 3.3 1.3 - - - -
289P PRO* 3.0 13.7 - - - +
290P VAL* 3.1 25.6 + - + +
349P TYR* 4.5 7.9 - - + -
353P TRP* 3.3 53.2 - - + +
657P PHE* 4.4 2.7 - - + -
658P LEU* 3.9 17.9 - - + -
661P VAL* 4.2 9.9 - - + -
662P MET* 5.8 0.4 - - + -
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Residues in contact with ALA 287 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135P PHE* 6.2 0.7 - - - -
283P ILE 2.9 16.3 + - - +
284P MET* 3.7 4.9 - - - +
286P VAL* 1.3 78.5 - - - +
288P GLN* 1.3 56.7 + - - +
290P VAL* 3.0 8.1 + - - +
291P ARG* 2.8 43.0 + - - +
396P GLY 3.6 23.8 - - - +
397P ALA* 4.1 14.4 - - + -
400P LEU* 3.6 9.6 - - + +
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Residues in contact with GLN 288 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141P VAL* 3.8 19.5 - - + -
142P PRO 5.1 5.4 - - - +
143P LEU* 6.4 1.3 - - - -
144P LYS* 6.4 1.3 - - + +
284P MET 3.1 10.2 + - - +
285P ALA* 5.6 0.2 - - - -
287P ALA* 1.3 79.1 - - - +
289P PRO* 1.3 71.3 - - + +
291P ARG* 2.9 46.2 + - - +
292P ASN* 2.9 40.0 + - - +
295P TYR* 5.8 0.2 - - - -
633P THR* 5.0 7.9 + - - -
634P GLU* 5.3 14.7 + - - +
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Residues in contact with PRO 289 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138P LEU* 3.6 30.9 - - + +
139P GLU 3.7 17.6 + - - +
141P VAL* 3.7 17.7 - - + +
285P ALA* 3.2 23.3 - - - +
286P VAL* 3.0 18.4 - - - +
288P GLN* 1.3 90.7 - - + +
290P VAL* 1.3 61.6 + - - +
292P ASN* 3.3 12.4 + - - +
293P LYS* 3.1 18.5 + - - +
658P LEU* 4.3 10.5 - - + -
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Residues in contact with VAL 290 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134P MET* 3.7 31.6 - - + +
135P PHE* 3.8 31.0 - - + -
138P LEU* 3.8 24.7 - - + -
286P VAL* 3.1 18.2 + - + +
287P ALA* 3.0 9.3 + - - +
289P PRO* 1.3 75.2 - - - +
291P ARG* 1.3 64.2 + - - +
293P LYS* 3.1 4.2 + - - +
294P ILE* 3.1 23.8 + - + +
400P LEU* 3.7 26.5 - - + -
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Residues in contact with ARG 291 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D C 4.4 10.3 + - - -
284P MET* 5.1 0.4 + - - +
287P ALA* 2.8 17.2 + - - +
288P GLN* 3.1 58.6 + - - +
290P VAL* 1.3 76.9 - - - +
292P ASN* 1.3 63.9 + - - +
294P ILE* 3.5 6.6 + - - +
295P TYR* 2.9 53.9 + - + -
396P GLY 3.3 23.0 + - - -
397P ALA* 4.3 0.2 - - - +
399P ASP* 2.7 38.8 + - - -
400P LEU* 4.2 14.4 - - + -
633P THR* 5.3 2.5 - - - -
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Residues in contact with ASN 292 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139P GLU 4.9 1.0 + - - -
141P VAL* 3.7 27.3 - - - +
288P GLN* 2.9 42.3 + - - +
289P PRO* 3.6 13.8 - - + +
291P ARG* 1.3 74.5 - - - +
293P LYS* 1.3 54.8 + - - +
295P TYR* 3.8 5.8 - - - +
296P SER* 2.6 36.0 + - - -
633P THR* 5.7 0.2 + - - -
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Residues in contact with LYS 293 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133P LEU 3.1 21.1 + - - +
134P MET 4.1 3.1 - - - +
136P SER* 2.4 30.5 + - - +
137P ASP* 2.7 42.4 + - - +
138P LEU* 4.0 13.9 - - + -
289P PRO 3.1 13.7 + - - +
290P VAL 3.1 8.0 + - - +
292P ASN* 1.3 77.2 - - - +
294P ILE* 1.3 65.3 + - + +
296P SER* 2.7 20.6 + - - +
297P LYS* 2.9 40.9 + - + +
298P TYR* 4.7 4.5 - - + -
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Residues in contact with ILE 294 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134P MET* 3.9 51.8 - - + -
290P VAL* 3.1 12.4 + - + +
291P ARG 3.5 9.9 - - - +
293P LYS* 1.3 77.7 - - + +
295P TYR* 1.3 74.3 - - + +
298P TYR* 3.0 49.7 + - + +
302P PHE* 3.7 31.5 - - + +
400P LEU* 4.0 18.2 - - + -
403P THR* 5.0 4.3 - - + +
440P TRP* 5.3 0.2 - - + -
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Residues in contact with TYR 295 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288P GLN* 5.8 0.2 - - - -
291P ARG* 2.9 47.7 + - + +
292P ASN* 4.0 6.3 - - - +
294P ILE* 1.3 86.5 - - + +
296P SER* 1.3 57.8 + - - +
299P ALA* 3.1 22.2 - - - +
302P PHE* 3.5 37.2 - - + -
303P HIS* 3.2 30.7 + + + +
399P ASP* 4.1 12.1 + - - -
400P LEU* 5.7 0.9 - - + +
451P LYS* 3.1 32.7 + - + +
633P THR* 3.8 29.2 - - + -
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Residues in contact with SER 296 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292P ASN 2.6 23.9 + - - -
293P LYS* 2.7 16.5 + - - -
295P TYR* 1.3 75.3 - - - +
297P LYS* 1.3 68.0 + - - +
298P TYR 3.1 0.4 - - - -
299P ALA* 2.9 22.1 + - - +
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Residues in contact with LYS 297 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133P LEU* 5.5 1.8 - - - +
137P ASP* 5.8 1.4 + - - -
293P LYS* 2.9 27.9 + - + +
296P SER* 1.3 80.9 + - - +
298P TYR* 1.3 101.3 + - + +
299P ALA 3.7 0.9 + - - -
437P ASP* 3.4 14.2 + - - -
441P GLN* 3.9 21.4 - - - +
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Residues in contact with TYR 298 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133P LEU* 3.4 41.7 + - + +
293P LYS* 4.6 4.6 - - + -
294P ILE* 3.0 32.8 + - + +
297P LYS* 1.3 113.0 + - + +
299P ALA* 1.3 64.8 + - - +
300P TYR 3.0 4.9 + - - +
301P THR* 3.1 4.2 + - - -
302P PHE* 3.1 31.0 + - + +
437P ASP* 2.8 43.4 + - - -
440P TRP* 3.5 42.2 - + + -
441P GLN* 4.0 8.7 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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