Contacts of the helix formed by residues 265 - 287 (chain A) in PDB entry 5CRV
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 LYS 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ALA* 2.8 18.8 + - + +
263A GLN* 3.4 43.4 + - + +
264A GLN* 1.3 70.8 - - - +
266A PHE* 1.3 59.2 + - - +
267A GLY 3.4 2.5 - - - -
268A GLU* 3.3 36.0 + - + +
269A ARG* 3.0 25.3 + - - +
322A GLU* 3.9 4.3 - - - -
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Residues in contact with PHE 266 (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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261A GLU* 4.6 11.2 - - + -
264A GLN* 3.5 42.8 - - + -
265A LYS* 1.3 70.5 - - - +
267A GLY* 1.3 63.6 + - - +
269A ARG* 3.3 42.0 - - - +
270A VAL* 3.3 26.9 + - - +
312A ALA 5.0 0.2 - - - +
316A ASN* 4.4 8.1 - - + +
320A TYR* 3.4 62.8 - + + -
322A GLU* 3.1 17.7 + - - +
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Residues in contact with GLY 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 LYS 3.4 0.4 - - - -
266A PHE* 1.3 73.2 - - - +
268A GLU* 1.3 64.9 + - - +
270A VAL* 3.3 6.2 + - - +
271A ALA* 3.2 15.9 + - - +
316A ASN* 4.5 4.5 - - - -
322A GLU* 3.0 25.2 + - - +
323A ALA 3.5 19.3 - - - -
324A VAL* 3.9 4.2 - - - +
325A PRO* 3.5 13.9 - - - +
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Residues in contact with GLU 268 (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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256A MET* 5.2 0.9 - - - +
259A GLN* 5.2 4.7 - - - +
260A ALA* 4.1 9.4 + - + +
263A GLN* 4.6 5.4 - - - +
265A LYS* 3.3 42.7 + - + +
267A GLY* 1.3 75.7 - - - +
269A ARG* 1.3 58.2 + - - +
271A ALA* 3.1 4.2 + - - +
272A TYR* 3.0 59.2 + - + -
325A PRO* 3.8 14.7 - - + +
330A LEU* 3.7 29.7 - - + +
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Residues in contact with ARG 269 (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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257A GLY* 3.9 15.7 - - - +
260A ALA* 3.6 15.4 - - + +
261A GLU* 3.1 38.8 + - + +
265A LYS 3.0 18.1 + - - +
266A PHE* 3.3 42.4 - - - +
268A GLU* 1.3 76.2 - - - +
270A VAL* 1.3 59.5 + - - +
272A TYR* 4.1 0.9 - - - +
273A PHE* 3.1 43.8 + - + -
308A LYS 5.4 0.6 + - - -
311A SER* 4.8 4.9 - - - -
312A ALA* 3.6 33.3 + - + +
315A ASP* 3.7 28.7 + - - +
320A TYR* 4.7 0.2 - - - -
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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
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266A PHE 3.3 11.8 + - - +
267A GLY 3.3 8.6 + - - +
269A ARG* 1.3 73.9 - - - +
271A ALA* 1.3 60.6 + - - +
273A PHE* 3.8 4.6 - - - +
274A GLN* 2.9 33.4 + - - +
309A TYR* 4.4 17.1 - - + +
312A ALA* 3.4 38.4 - - + +
313A LYS* 3.6 17.5 - - + +
316A ASN* 4.1 10.1 - - + +
324A VAL* 4.0 22.4 - - + -
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Residues in contact with ALA 271 (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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267A GLY 3.2 6.0 + - - +
268A GLU* 3.1 10.0 + - - +
270A VAL* 1.3 80.7 - - - +
272A TYR* 1.3 57.6 + - - +
274A GLN* 3.6 5.8 + - - +
275A SER* 3.1 27.0 + - - -
324A VAL* 3.7 15.2 - - + +
325A PRO* 3.5 31.4 - - + +
327A LEU* 3.9 15.3 - - + +
330A LEU* 5.0 2.2 - - + -
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Residues in contact with TYR 272 (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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253A HIS* 3.4 45.4 - + - +
256A MET* 3.6 51.0 - - + +
257A GLY* 3.5 12.3 - - - -
260A ALA* 4.8 0.2 - - + -
268A GLU* 3.0 51.1 + - + +
271A ALA* 1.3 74.1 - - - +
273A PHE* 1.3 60.7 + - - +
275A SER* 3.3 4.0 + - - -
276A ALA* 2.9 28.6 + - - +
327A LEU* 4.3 13.5 - - + -
330A LEU* 3.8 26.5 - - + +
331A GLN 3.9 13.2 + - - -
332A PRO* 5.6 0.5 - - - +
333A VAL* 5.3 2.2 - - + +
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Residues in contact with PHE 273 (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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254A LEU* 3.2 41.7 - - + -
257A GLY* 3.6 24.5 - - - -
258A LYS* 4.2 5.4 - - + -
261A GLU* 4.4 9.0 - - - -
269A ARG* 3.1 32.7 + - + +
270A VAL* 3.9 3.6 - - - +
272A TYR* 1.3 76.5 - - - +
274A GLN* 1.3 57.4 + - - +
276A ALA* 3.4 5.2 + - + +
277A LEU* 3.0 28.2 + - - +
305A ILE* 3.8 7.7 - - + +
308A LYS* 3.3 49.1 - - + -
309A TYR* 4.0 18.6 - - + +
312A ALA* 3.6 12.6 - - + -
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Residues in contact with GLN 274 (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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270A VAL* 2.9 24.6 + - - +
271A ALA* 3.8 5.7 - - - +
273A PHE* 1.3 73.6 - - - +
275A SER* 1.3 60.0 + - - +
277A LEU* 3.2 4.1 + - + +
278A ASP* 3.0 49.6 + - - +
309A TYR* 3.6 36.0 + - + -
324A VAL* 4.9 9.0 - - - +
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Residues in contact with SER 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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253A HIS* 2.5 35.9 + - - -
271A ALA 3.1 17.9 + - - -
272A TYR* 3.5 3.8 - - - -
274A GLN* 1.3 77.4 - - - +
276A ALA* 1.3 56.9 + - - +
278A ASP* 3.3 9.1 + - - +
279A LYS* 2.9 43.3 + - - +
327A LEU* 3.4 19.9 - - - +
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Residues in contact with ALA 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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250A ALA* 3.3 39.7 - - - +
253A HIS* 4.1 3.3 - - + +
254A LEU* 3.8 12.8 - - - +
272A TYR 2.9 18.0 + - - +
273A PHE* 3.6 6.5 - - - +
275A SER* 1.3 75.6 + - - +
277A LEU* 1.3 57.8 + - - +
279A LYS 3.4 0.2 + - - -
280A LEU* 2.8 27.7 + - - +
305A ILE* 3.9 17.5 - - + -
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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
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273A PHE 3.0 16.2 + - - +
274A GLN* 3.2 5.8 + - + +
276A ALA* 1.3 73.1 - - - +
278A ASP* 1.3 67.8 + - - +
280A LEU* 3.5 9.1 + - + +
281A ASN* 3.1 46.7 + - - +
302A MET* 5.1 10.1 - - + +
305A ILE* 3.7 17.0 - - + +
306A GLY* 4.4 17.0 - - - +
309A TYR* 4.0 37.5 - - + -
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Residues in contact with ASP 278 (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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274A GLN* 3.0 37.1 + - - +
275A SER* 3.6 8.1 - - - +
277A LEU* 1.3 80.0 - - - +
279A LYS* 1.3 62.6 + - + +
281A ASN* 3.5 10.5 + - - +
282A GLU* 3.2 21.0 + - - +
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Residues in contact with LYS 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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246A TYR* 3.5 36.0 - - + +
249A ALA* 3.6 35.2 - - + +
250A ALA* 3.9 3.6 - - + -
253A HIS* 3.5 18.8 - - - +
275A SER* 2.9 38.7 + - - +
276A ALA 3.7 3.4 - - - +
278A ASP* 1.3 74.5 - - + +
280A LEU* 1.3 65.8 + - - +
282A GLU* 3.2 8.7 + - - +
283A ALA* 3.0 16.8 + - - +
327A LEU* 5.5 1.6 - - - +
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Residues in contact with LEU 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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247A TYR* 4.0 15.3 - - + -
250A ALA* 3.8 10.5 - - + +
276A ALA 2.8 18.9 + - - +
277A LEU* 3.8 9.9 - - + +
279A LYS* 1.3 76.6 - - - +
281A ASN* 1.3 58.4 + - - +
283A ALA* 3.0 8.4 + - + +
284A ILE* 2.8 34.0 + - + +
298A LEU* 3.6 29.4 - - + +
301A THR* 3.6 19.3 - - + +
302A MET* 3.4 43.5 - - + +
305A ILE* 4.2 7.4 - - + -
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Residues in contact with ASN 281 (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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277A LEU* 3.1 37.9 + - - +
278A ASP* 3.7 10.6 + - - +
280A LEU* 1.3 76.3 - - - +
282A GLU* 1.3 56.7 + - - +
284A ILE* 3.3 9.9 + - - +
285A LYS* 3.0 27.5 + - - +
302A MET* 3.6 26.2 - - - +
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Residues in contact with GLU 282 (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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246A TYR* 3.5 36.9 - - + -
278A ASP 3.2 13.4 + - - +
279A LYS* 3.4 9.9 - - - +
280A LEU 3.2 0.8 - - - -
281A ASN* 1.3 72.6 - - - +
283A ALA* 1.3 65.8 + - - +
285A LYS* 3.5 25.6 + - - +
286A LEU* 3.1 37.7 + - + +
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Residues in contact with ALA 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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243A MET* 3.6 26.4 - - + +
246A TYR* 3.9 6.2 - - + +
247A TYR* 3.8 17.3 - - - +
279A LYS 3.0 11.9 + - - +
280A LEU* 3.0 11.5 + - - +
282A GLU* 1.3 74.9 - - - +
284A ILE* 1.3 58.9 + - - +
286A LEU* 3.1 7.6 + - - +
287A ALA* 2.8 30.2 + - - +
298A LEU* 4.3 13.2 - - + -
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Residues in contact with ILE 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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280A LEU* 2.8 28.5 + - + +
281A ASN* 3.5 15.3 - - - +
283A ALA* 1.3 74.4 - - - +
285A LYS* 1.3 66.0 + - - +
287A ALA* 3.2 10.9 + - - +
288A LYS* 3.6 8.5 + - - +
295A GLN* 5.3 5.0 - - - +
298A LEU* 4.0 31.6 - - + +
299A ARG* 6.1 0.2 - - - -
302A MET* 3.7 37.5 - - + -
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Residues in contact with LYS 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 ASN 3.0 13.8 + - - +
282A GLU* 3.6 32.6 + - - +
284A ILE* 1.3 78.6 - - - +
286A LEU* 1.3 63.3 + - + +
287A ALA 3.3 0.5 + - - -
288A LYS* 3.4 18.5 + - - +
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Residues in contact with LEU 286 (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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239A LYS* 4.6 4.8 - - - +
242A GLN* 4.0 36.8 - - + +
243A MET* 4.3 9.4 - - - +
246A TYR* 3.7 33.4 - - + -
282A GLU* 3.1 33.8 + - - +
283A ALA* 3.1 8.5 + - - +
285A LYS* 1.3 80.6 - - + +
287A ALA* 1.3 57.0 + - - +
288A LYS 3.2 5.0 + - - +
290A GLN* 3.4 13.2 + - - -
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A MET* 3.7 10.5 - - + -
283A ALA 2.8 15.5 + - - +
284A ILE 3.2 6.3 + - - +
286A LEU* 1.3 75.9 - - - +
288A LYS* 1.3 60.5 + - - +
290A GLN* 3.0 18.7 + - - +
294A VAL* 3.9 11.4 - - + -
295A GLN* 2.7 32.5 + - - +
298A LEU* 3.5 26.0 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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