Contacts of the helix formed by residues 264 - 286 (chain A) in PDB entry 1R1H
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 ASP 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A ARG* 5.6 1.4 - - - +
262A PRO 4.2 1.2 + - - -
263A ILE* 1.3 73.3 - - - +
265A GLU* 1.3 64.9 + - - +
266A ASN* 3.1 19.6 + - - +
267A GLN* 2.8 34.3 + - + +
268A LEU* 2.9 17.3 + - - +
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Residues in contact with GLU 265 (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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249A ILE* 4.4 4.2 - - - +
253A ARG* 3.0 47.1 + - - -
263A ILE* 3.5 15.0 + - + +
264A ASP* 1.3 73.1 + - - +
266A ASN* 1.3 59.4 + - - +
268A LEU* 3.1 11.7 + - - +
269A ALA* 2.8 31.1 + - - +
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Residues in contact with ASN 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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264A ASP* 3.0 11.5 + - - +
265A GLU* 1.3 80.7 - - - +
267A GLN* 1.3 57.8 + - - +
269A ALA* 3.5 7.2 + - - +
270A LEU* 2.9 36.2 + - - +
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Residues in contact with GLN 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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264A ASP* 2.8 28.7 + - + +
266A ASN* 1.3 77.1 - - - +
268A LEU* 1.3 69.6 + - + +
270A LEU* 4.1 18.9 - - - +
271A GLU* 2.8 55.8 + - - +
364A ARG* 5.0 1.9 + - - -
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Residues in contact with LEU 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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168A VAL* 4.8 11.9 - - + +
249A ILE* 3.9 39.7 - - + +
252A ALA* 4.5 15.5 - - + -
253A ARG* 4.0 26.2 - - + +
256A ARG* 4.5 18.4 - - - +
263A ILE* 4.3 8.7 - - + -
264A ASP 2.9 18.5 + - - +
265A GLU* 3.2 18.4 - - - +
267A GLN* 1.3 80.9 - - + +
269A ALA* 1.3 64.0 + - - +
271A GLU* 3.2 4.8 + - - +
272A MET* 3.0 27.8 + - + +
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Residues in contact with ALA 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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249A ILE* 3.8 22.6 - - + +
265A GLU 2.8 18.8 + - - +
266A ASN* 3.7 8.1 - - - +
268A LEU* 1.3 73.6 - - - +
270A LEU* 1.3 58.1 + - + +
272A MET* 4.0 0.5 - - - +
273A ASN* 2.8 43.2 + - - +
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Residues in contact with LEU 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 ASN* 2.9 23.6 + - - +
267A GLN* 3.7 22.2 - - - +
268A LEU 3.1 0.4 - - - -
269A ALA* 1.3 78.3 - - + +
271A GLU* 1.3 62.3 + - + +
273A ASN* 3.6 4.9 + - - +
274A LYS* 3.4 24.7 + - + +
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Residues in contact with GLU 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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168A VAL* 3.4 17.2 - - + +
267A GLN* 2.8 46.5 + - - +
268A LEU* 3.9 4.7 - - - +
270A LEU* 1.3 77.1 - - - +
272A MET* 1.3 70.1 + - + +
274A LYS* 3.3 8.7 + - - +
275A VAL* 3.1 23.0 + - - +
364A ARG* 2.6 41.1 + - - +
365A ASP* 6.1 0.7 - - - +
368A ASN* 2.9 26.3 - - - +
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Residues in contact with MET 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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166A TRP* 4.1 13.2 - - + -
168A VAL* 3.1 43.5 - - + -
245A VAL* 4.2 6.9 - - + +
248A MET* 3.3 48.6 - - + +
249A ILE* 3.7 25.4 - - + +
252A ALA* 5.3 2.5 - - + -
268A LEU* 3.0 18.9 + - + +
269A ALA 4.2 0.9 - - - +
271A GLU* 1.3 82.8 - - + +
273A ASN* 1.3 64.2 + - - +
274A LYS 3.3 0.2 - - - -
275A VAL* 3.3 19.6 + - + +
276A MET* 3.1 18.7 + - - +
368A ASN* 4.2 2.7 - - + +
372A TRP* 5.7 0.4 - - - -
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Residues in contact with ASN 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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245A VAL* 4.0 21.3 - - - +
249A ILE* 5.6 0.2 - - - +
269A ALA* 2.8 36.5 + - - +
270A LEU* 4.0 5.3 - - - +
271A GLU 3.2 0.2 - - - -
272A MET* 1.3 79.4 - - - +
274A LYS* 1.3 57.6 + - - +
276A MET* 3.1 9.4 + - - +
277A GLU* 2.8 27.4 + - - +
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Residues in contact with LYS 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 LEU* 3.4 12.3 + - + +
271A GLU* 3.3 10.9 + - - +
272A MET 3.3 0.2 - - - -
273A ASN* 1.3 75.9 - - - +
275A VAL* 1.3 58.3 + - - +
277A GLU* 3.8 13.9 - - + +
278A LEU* 2.9 30.5 + - - +
360A LYS 5.6 3.2 + - - -
361A TYR* 4.3 25.5 - - + -
365A ASP* 4.7 22.1 + - + +
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Residues in contact with VAL 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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248A MET* 3.6 26.0 - - + -
271A GLU 3.1 13.2 + - - +
272A MET* 3.4 19.3 - - + +
273A ASN 3.3 0.2 - - - -
274A LYS* 1.3 75.2 - - - +
276A MET* 1.3 56.7 + - - +
278A LEU* 3.3 9.0 - - - +
279A GLU* 2.9 27.4 + - + +
365A ASP* 4.6 3.1 - - - +
368A ASN* 3.6 35.2 - - + +
369A LEU* 3.8 33.3 - - + +
372A TRP* 4.6 4.0 - - + -
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Residues in contact with MET 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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225A LEU* 3.8 7.2 - - + -
231A TYR* 3.9 16.8 - - + -
233A CYS* 3.7 6.7 - - - -
241A CYS* 3.6 43.7 - - + +
244A TYR* 3.6 33.0 - - + -
245A VAL* 3.8 22.0 - - + -
248A MET* 4.6 2.0 - - + +
272A MET 3.1 6.9 + - - +
273A ASN* 3.1 13.7 + - - +
275A VAL* 1.3 74.9 - - - +
277A GLU* 1.3 61.4 + - - +
279A GLU* 3.2 1.5 + - - +
280A LYS* 2.8 45.6 + - - +
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Residues in contact with GLU 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 ASN 2.8 18.7 + - - +
274A LYS* 3.3 16.8 + - + +
276A MET* 1.3 73.0 - - - +
278A LEU* 1.3 62.8 + - - +
280A LYS* 3.3 30.1 + - - +
281A GLU* 3.2 27.9 + - - +
361A TYR* 3.8 11.7 - - + +
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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
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199A LEU* 5.1 1.3 - - + -
274A LYS 2.9 13.9 + - - +
275A VAL* 3.3 10.3 - - - +
277A GLU* 1.3 77.5 - - - +
279A GLU* 1.3 62.5 + - - +
281A GLU* 3.2 4.7 + - - +
282A ILE* 3.1 31.6 + - + +
357A ILE* 4.3 7.9 - - + -
358A LEU* 4.7 2.5 - - + -
361A TYR* 3.6 45.1 + - + -
365A ASP* 4.1 11.7 - - + +
366A LEU* 4.0 24.9 - - + -
369A LEU* 3.5 35.2 - - + -
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Residues in contact with GLU 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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222A ARG 4.7 0.3 - - - +
223A LEU* 3.7 16.3 - - + +
224A GLY 2.9 21.0 + - - -
231A TYR* 2.7 27.8 + - + +
244A TYR* 2.7 29.9 + - - -
248A MET* 5.0 0.3 - - - +
275A VAL 2.9 16.8 + - - +
276A MET* 4.1 4.3 - - - +
278A LEU* 1.3 73.9 - - - +
280A LYS* 1.3 61.4 + - - +
282A ILE* 4.2 8.5 - - + -
283A ALA* 2.8 29.3 + - - +
369A LEU* 4.1 22.1 - - + +
373A ARG* 3.5 14.0 + - - -
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Residues in contact with LYS 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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231A TYR* 3.8 42.8 - - + +
232A GLU 5.4 0.4 + - - -
233A CYS* 3.8 22.9 - - - +
276A MET* 2.8 29.6 + - + +
277A GLU* 3.3 35.4 + - - +
278A LEU 3.2 0.2 - - - -
279A GLU* 1.3 76.5 - - - +
281A GLU* 1.3 56.1 + - + +
283A ALA* 3.1 3.6 + - - +
284A ASN* 2.9 30.6 + - - +
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Residues in contact with GLU 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 GLU* 3.2 22.9 + - - +
278A LEU 3.2 8.4 + - - +
280A LYS* 1.3 76.1 - - - +
282A ILE* 1.3 58.0 + - - +
284A ASN* 3.3 7.7 + - - +
285A ALA* 2.9 30.1 + - - +
357A ILE* 3.6 32.0 - - + +
360A LYS* 2.9 34.6 + - - -
361A TYR* 2.7 25.2 + - - +
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Residues in contact with ILE 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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199A LEU* 3.2 37.0 - - + +
221A PRO* 4.3 10.8 - - + -
223A LEU* 4.2 14.4 - - + -
278A LEU* 3.1 22.1 + - + +
279A GLU* 3.6 10.1 - - + +
281A GLU* 1.3 72.7 - - + +
283A ALA* 1.3 68.0 + - - +
285A ALA* 3.0 8.7 + - - +
286A THR* 3.0 27.3 + - + +
350A TYR* 3.6 25.3 - - + +
354A LEU* 4.9 8.1 - - + -
357A ILE* 4.8 4.7 - - + -
358A LEU* 5.4 0.4 - - + -
369A LEU* 3.9 18.4 - - + -
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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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223A LEU* 3.9 19.5 - - + -
228A ARG* 3.6 15.3 + - - +
231A TYR* 3.6 35.2 - - + -
279A GLU 2.8 18.7 + - - +
280A LYS 3.1 5.4 + - - +
282A ILE* 1.3 75.7 - - - +
284A ASN* 1.3 63.9 + - - +
286A THR* 2.6 27.3 + - - -
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Residues in contact with ASN 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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228A ARG* 3.2 25.4 + - - +
280A LYS 2.9 16.4 + - - +
281A GLU* 3.7 7.0 - - - +
283A ALA* 1.3 76.4 - - - +
285A ALA* 1.3 59.5 + - - +
286A THR 3.7 0.5 - - - +
353A LYS* 5.1 4.5 + - - +
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Residues in contact with ALA 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 GLU 2.9 17.5 + - - +
282A ILE* 3.0 5.8 + - - +
284A ASN* 1.3 78.3 + - - +
286A THR* 1.3 63.3 - - - +
287A ALA 3.7 0.3 + - - -
350A TYR* 3.6 26.7 - - + +
353A LYS* 3.7 40.5 - - + -
354A LEU 5.1 0.2 - - - +
357A ILE* 3.8 19.3 - - + -
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Residues in contact with THR 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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220A GLN* 3.4 28.7 - - + +
221A PRO 4.6 9.2 - - - +
223A LEU* 4.7 8.0 - - + +
228A ARG* 2.9 43.3 + - - +
282A ILE* 3.0 22.4 + - + +
283A ALA* 2.6 19.8 + - - +
284A ASN 3.7 0.3 - - - +
285A ALA* 1.3 80.6 - - - +
287A ALA* 1.3 62.1 + - - +
288A LYS 3.8 0.2 + - - -
350A TYR* 3.9 15.0 - - + -
353A LYS* 5.4 2.0 + - - -
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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