Contacts of the helix formed by residues 266 - 287 (chain A) in PDB entry 1Q8Z
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 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A TYR* 3.3 42.2 - - + +
264A GLY 4.0 0.4 - - - +
265A ILE* 1.3 94.1 - - + +
267A LEU* 1.3 60.3 + - - +
268A ILE* 4.3 8.7 - - + -
269A TYR* 2.9 40.6 + - + +
270A VAL 3.3 6.9 + - - -
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Residues in contact with LEU 267 (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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265A ILE 3.3 4.7 + - - +
266A PRO* 1.3 66.6 - - - +
268A ILE* 1.3 58.8 + - + +
269A TYR 2.8 11.6 + - - -
270A VAL* 4.2 9.2 - - + -
271A LYS* 3.0 39.6 + - - +
598A ILE* 4.2 25.6 - - + +
671A PHE* 4.6 15.0 - - + -
675A GLU* 3.5 24.5 - - - +
679A ILE* 5.0 0.4 - - + -
705A TRP* 3.9 29.4 - - + +
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Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PRO* 4.3 7.6 - - + -
267A LEU* 1.3 75.3 - - + +
269A TYR* 1.3 86.0 + - + +
271A LYS* 4.6 6.0 - - - +
272A GLN* 2.7 35.6 + - - +
542A ASN* 4.1 27.1 - - + +
710A LEU* 4.1 21.9 + - + +
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Residues in contact with TYR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 4.8 6.7 - - + -
260A TYR* 4.0 19.7 + + - -
265A ILE* 3.9 12.6 - - + -
266A PRO* 2.9 35.3 + - + +
267A LEU 2.8 0.4 - - - -
268A ILE* 1.3 98.2 - - + +
270A VAL* 1.3 60.0 + - - +
271A LYS 3.3 1.3 - - - -
272A GLN* 3.1 10.5 + - - +
273A ILE* 2.8 36.3 + - + +
304A ILE* 6.4 0.2 - - + -
542A ASN* 3.4 35.3 + - + -
544A ILE* 3.6 34.3 - - + -
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ILE* 3.7 31.6 - - + +
266A PRO 3.8 2.9 - - - +
267A LEU* 3.1 14.7 + - + +
269A TYR* 1.3 77.7 - - - +
271A LYS* 1.3 52.5 + - - +
273A ILE* 3.0 9.3 + - - +
274A SER* 2.6 51.1 + - - +
594A ILE* 4.4 3.6 - - + -
597A LEU* 3.9 35.2 - - + +
598A ILE* 3.8 22.4 - - + +
705A TRP* 4.0 9.6 - - + -
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Residues in contact with LYS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 3.0 28.9 + - + +
268A ILE* 5.1 3.8 - - - +
270A VAL* 1.3 75.1 - - - +
272A GLN* 1.3 58.2 + - - +
274A SER* 4.3 1.1 - - - -
275A LYS* 2.9 34.5 + - - +
675A GLU* 5.2 1.8 + - - -
678A GLU* 5.6 0.2 + - - -
705A TRP* 3.0 70.2 + - + +
706A LEU* 3.5 9.6 - - + +
708A ASP* 2.9 36.5 + - - +
709A THR* 3.4 22.6 - - + +
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Residues in contact with GLN 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ILE 2.7 22.6 + - - +
269A TYR* 3.1 11.1 + - - +
271A LYS* 1.3 79.5 - - - +
273A ILE* 1.3 62.6 + - - +
275A LYS* 4.1 0.7 - - - +
276A GLN* 3.2 39.0 + - - +
542A ASN 2.9 18.7 - - - +
543A LEU* 3.2 19.8 - - - +
544A ILE* 3.0 47.7 + - + +
709A THR* 3.4 12.1 - - + -
710A LEU* 3.6 27.9 + - - +
712A MET* 4.8 0.2 - - - -
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.8 27.8 - - + -
256A LEU* 3.7 30.1 - - + -
265A ILE* 5.4 0.4 - - + -
269A TYR 2.8 20.5 + - - +
270A VAL* 3.5 8.3 - - - +
272A GLN* 1.3 76.3 - - - +
274A SER* 1.3 57.4 + - - +
276A GLN* 3.5 1.2 + - - +
277A LEU* 2.9 33.2 + - + +
300A VAL* 4.9 2.7 - - + -
302A MET* 4.7 1.1 - - - -
544A ILE* 3.9 13.9 - - + -
546A ILE* 3.8 30.6 - - + +
593A LEU* 5.8 1.6 - - + -
594A ILE* 6.3 0.2 - - + -
597A LEU* 3.7 27.6 - - + -
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Residues in contact with SER 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL* 2.6 36.3 + - - +
271A LYS* 3.7 4.0 - - - -
273A ILE* 1.3 73.1 - - - +
275A LYS* 1.3 61.3 + - - +
277A LEU* 3.2 5.3 + - - +
278A LEU* 2.9 36.4 + - - +
594A ILE* 3.3 39.0 - - - +
597A LEU* 5.1 0.9 - - - +
682A PHE* 4.4 5.8 - - - -
705A TRP* 4.5 1.3 - - - -
706A LEU* 4.0 12.8 - - - -
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Residues in contact with LYS 275 (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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271A LYS 2.9 20.5 + - - +
274A SER* 1.3 73.0 - - - +
276A GLN* 1.3 57.1 + - - +
278A LEU* 3.6 3.2 + - - +
279A LEU* 3.1 33.1 + - - +
701A VAL* 3.6 29.2 + - + +
706A LEU* 2.9 47.6 + - + +
707A LYS* 4.6 0.6 - - - +
709A THR* 3.7 11.4 - - + +
712A MET* 3.0 42.0 + - + -
713A GLU 3.7 6.7 + - - -
715A ILE* 2.9 34.6 + - - -
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Residues in contact with GLN 276 (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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224A HIS* 3.0 40.5 + - + +
272A GLN* 3.2 27.2 + - - +
273A ILE* 5.3 0.2 - - - -
274A SER 3.2 0.2 - - - -
275A LYS* 1.3 75.7 - - - +
277A LEU* 1.3 65.4 + - - +
279A LEU* 3.1 7.6 + - - +
280A GLY* 2.9 22.2 + - - -
544A ILE* 3.1 22.8 + - - +
545A GLN* 3.1 4.3 - - - +
546A ILE* 2.8 42.1 + - + -
712A MET* 3.6 24.6 - - + +
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ILE* 2.9 23.0 + - + +
274A SER* 3.5 6.3 - - - +
276A GLN* 1.3 75.5 - - - +
278A LEU* 1.3 58.1 + - - +
280A GLY* 3.3 1.9 + - - -
281A LEU* 2.9 38.4 + - + +
295A ILE* 4.6 10.3 - - + -
300A VAL* 4.8 13.2 - - + -
546A ILE* 3.8 10.4 - - + +
548A ILE* 3.6 28.0 - - + -
590A THR* 3.3 38.6 - - + +
593A LEU* 4.2 20.9 - - + -
594A ILE* 5.3 4.3 - - + -
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A SER* 2.9 21.5 + - - +
275A LYS 3.9 1.6 - - - +
277A LEU* 1.3 74.5 - - - +
279A LEU* 1.3 60.1 + - - +
281A LEU* 4.5 3.6 - - + -
282A ASP* 2.9 27.7 + - - +
587A ILE* 5.3 2.0 - - + -
590A THR* 4.1 25.6 - - + -
594A ILE* 5.3 0.4 - - + -
682A PHE* 3.9 13.5 - - + -
686A MET* 4.8 4.7 - - + -
697A ALA* 3.2 30.6 - - + +
700A LEU* 3.9 29.4 - - + -
701A VAL* 3.6 15.5 - - + -
706A LEU* 3.7 27.8 - - + -
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Residues in contact with LEU 279 (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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220A MET* 4.1 37.0 - - + +
221A GLY* 3.4 12.0 - - - +
224A HIS* 4.6 4.3 - - + +
275A LYS 3.1 17.3 + - - +
276A GLN* 3.6 6.5 - - - +
278A LEU* 1.3 75.9 - - - +
280A GLY* 1.3 61.7 + - - +
282A ASP* 3.5 6.2 + - - +
283A TYR* 3.3 15.1 + - - +
701A VAL* 3.9 15.2 - - + +
712A MET* 3.4 34.1 - - + -
715A ILE* 4.2 15.7 - - + -
716A ARG 4.9 1.6 - - - +
717A VAL* 3.9 26.5 - - + -
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Residues in contact with GLY 280 (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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221A GLY* 3.6 21.3 - - - -
224A HIS* 4.3 4.7 - - - +
225A ILE* 3.8 3.0 - - - +
276A GLN 2.9 14.3 + - - -
277A LEU 3.7 2.9 - - - -
279A LEU* 1.3 74.3 - - - +
281A LEU* 1.3 64.8 + - - +
283A TYR* 3.0 14.4 + - - +
284A MET* 3.1 15.1 + - - +
548A ILE* 3.9 15.5 - - - -
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 2.9 32.1 + - + +
278A LEU* 3.9 4.7 - - + +
280A GLY* 1.3 74.8 - - - +
282A ASP* 1.3 59.4 + - - +
284A MET* 3.0 14.6 + - - +
285A HIS* 2.8 43.1 + - + +
292A HIS* 5.0 0.2 - - + -
295A ILE* 4.1 17.9 - - + -
548A ILE* 3.8 14.5 - - + +
586A ASP* 4.3 25.1 - - + +
587A ILE* 4.6 9.9 - - + -
590A THR* 3.2 29.8 - - + +
697A ALA* 4.0 9.9 - - + -
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Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLU* 5.1 3.1 - - - +
278A LEU 2.9 19.3 + - - +
279A LEU* 3.7 8.4 - - - +
281A LEU* 1.3 76.4 - - - +
283A TYR* 1.3 63.6 + - - +
285A HIS* 4.8 4.2 - - - +
286A ARG* 2.7 72.5 + - - +
287A ARG* 5.6 0.2 - - - -
696A ASP* 4.5 1.6 - - - +
697A ALA* 3.9 4.6 - - - +
698A GLY* 3.4 28.3 + - - +
717A VAL* 4.0 10.5 - - + +
729A ILE* 5.2 0.9 - - - +
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Residues in contact with TYR 283 (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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209A VAL* 2.6 34.4 + - + -
212A ALA* 3.1 8.8 - - + +
213A ASP* 2.8 19.9 + - - -
218A ASP* 3.7 38.1 - - + -
221A GLY* 3.9 9.0 - - - -
222A ALA* 3.8 21.3 - - + -
225A ILE* 3.6 19.3 - - + -
279A LEU 3.3 10.3 + - - +
280A GLY 3.0 9.7 + - - +
282A ASP* 1.3 80.9 - - - +
284A MET* 1.3 62.1 + - - +
287A ARG* 3.2 32.4 + - + +
288A CYS* 3.0 38.7 + - - -
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Residues in contact with MET 284 (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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209A VAL* 5.2 5.8 - - + -
225A ILE* 3.4 30.5 - - + -
280A GLY 3.1 7.0 + - - +
281A LEU* 3.0 16.9 + - - +
283A TYR* 1.3 78.2 - - + +
285A HIS* 1.3 59.8 + - + +
288A CYS* 3.3 9.4 - - - +
289A GLY 2.8 26.5 + - - -
290A ILE* 2.9 44.4 + - + +
292A HIS* 3.8 20.0 - - + +
548A ILE* 4.3 24.5 - - - -
551A LEU* 3.6 26.7 - - + -
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Residues in contact with HIS 285 (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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281A LEU* 2.8 35.4 + - + +
282A ASP* 4.2 3.8 - - - +
284A MET* 1.3 78.2 - - + +
286A ARG* 1.3 65.0 + - + +
289A GLY* 3.3 15.2 + - - -
290A ILE 3.3 15.9 + - - +
291A ILE* 4.5 0.4 - - - -
292A HIS 5.0 0.2 - - - -
583A CYS* 3.3 48.2 + - + +
586A ASP* 3.0 35.5 + - + +
587A ILE* 4.3 13.4 - - + +
696A ASP* 5.9 0.2 - - + -
697A ALA* 5.3 2.9 - - + -
729A ILE* 4.2 19.6 - - + +
730A PRO* 5.2 1.6 - - - +
732A TRP* 3.8 15.5 - + + -
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLU* 4.2 8.1 + - - -
282A ASP* 2.7 51.1 + - - +
285A HIS* 1.3 82.6 - - + +
287A ARG* 1.3 98.4 + - - +
289A GLY* 4.5 1.4 + - - -
717A VAL* 3.6 2.6 - - - +
719A ASP* 2.7 38.1 + - - +
720A ARG* 3.1 39.1 - - - +
729A ILE* 3.5 35.2 - - + -
730A PRO* 5.7 4.6 - - + +
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Residues in contact with ARG 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ARG* 4.1 11.8 + - - -
212A ALA* 4.7 11.0 - - + +
217A GLU* 5.8 3.8 - - - -
218A ASP* 3.3 28.3 - - - +
282A ASP 4.0 1.1 + - - -
283A TYR* 3.2 30.3 + - + +
286A ARG* 1.3 120.5 + - - +
288A CYS* 1.3 63.5 + - - +
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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) + - + + + + + -
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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