Contacts of the helix formed by residues 263 - 286 (chain A) in PDB entry 3PIK
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 ARG 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ILE 4.2 0.6 + - - -
260A LEU* 2.9 23.2 + - - +
262A GLN* 1.3 80.2 - - - +
264A PRO* 1.3 69.6 - - + +
265A ASP* 3.0 36.9 + - - +
266A ILE* 3.3 4.7 + - + +
267A MET* 3.1 19.6 + - - +
355A ASN* 5.1 1.8 + - - -
356A ALA* 3.3 35.1 + - - +
359A GLU* 2.5 34.3 + - - +
436A ALA* 2.9 43.4 + - - +
437A LEU 4.8 1.3 + - - -
438A GLY* 4.4 12.9 - - - +
453A SO4 3.2 24.9 + - - +
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Residues in contact with PRO 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU* 3.3 43.3 - - - +
142A ARG* 3.8 23.8 - - + +
143A ALA* 3.6 9.2 - - - +
146A ILE* 4.1 12.8 - - + -
262A GLN 3.5 4.2 - - - +
263A ARG* 1.3 83.3 - - + +
265A ASP* 1.3 56.4 - - - +
267A MET* 3.1 1.4 + - + -
268A GLU 2.8 26.2 + - - -
438A GLY* 4.9 5.2 - - - +
453A SO4 3.2 24.9 - - - +
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Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ALA* 4.6 7.6 - - + -
263A ARG* 3.0 35.1 + - - +
264A PRO* 1.3 74.1 - - - +
266A ILE* 1.3 82.7 + - - +
268A GLU* 3.4 19.0 - - - +
269A ALA* 3.3 18.4 + - - +
352A LYS* 4.1 20.5 - - + +
355A ASN* 5.4 2.3 - - - +
453A SO4 2.4 41.3 + - - +
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Residues in contact with ILE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 3.6 19.7 - - + +
261A LEU* 4.0 24.2 - - + +
263A ARG* 3.3 11.8 + - - +
264A PRO 3.1 0.4 - - - -
265A ASP* 1.3 93.9 + - - +
267A MET* 1.3 64.4 + - - +
268A GLU 3.1 0.2 - - - -
269A ALA* 3.1 6.6 + - - +
270A GLU* 3.1 20.3 + - - +
349A TYR* 4.1 12.6 - - + +
352A LYS* 3.3 46.4 - - + +
353A ILE* 3.5 25.6 - - + +
356A ALA* 4.6 3.4 - - + -
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Residues in contact with MET 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU* 3.5 31.6 - - + +
142A ARG* 5.6 3.6 - - - -
261A LEU 3.6 15.9 - - - +
262A GLN* 3.2 45.5 - - - +
263A ARG 3.1 9.8 + - - +
264A PRO* 3.1 2.8 + - - +
266A ILE* 1.3 72.7 - - - +
268A GLU* 1.3 65.6 + - - +
270A GLU* 3.1 19.8 + - - +
271A HIS* 3.0 34.1 + - + +
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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
----------------------------------------------------------
136A ALA* 3.3 28.5 - - + +
139A GLU* 3.7 15.0 - - + +
140A ALA* 3.4 33.7 - - - +
143A ALA* 5.1 1.2 - - - +
264A PRO 2.8 12.5 + - - +
265A ASP* 3.4 21.4 - - - +
267A MET* 1.3 78.0 - - - +
269A ALA* 1.3 63.2 + - - +
271A HIS 3.2 2.4 + - - -
272A ALA* 3.0 20.3 + - + +
352A LYS* 6.5 0.9 - - - -
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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
----------------------------------------------------------
265A ASP 3.3 9.2 + - - +
266A ILE* 3.1 12.0 + - - +
268A GLU* 1.3 79.8 - - - +
270A GLU* 1.3 58.1 + - - +
272A ALA* 3.2 10.3 + - - +
273A LEU* 2.9 27.2 + - - +
345A SER 4.9 2.3 - - - +
348A ASN* 4.0 14.6 - - - +
349A TYR* 3.8 34.5 - - + +
352A LYS* 4.5 8.5 - - + -
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 3.2 33.0 + - + +
9A ARG* 5.8 2.9 + - - +
261A LEU 5.2 2.8 - - - +
266A ILE* 3.1 11.6 + - - +
267A MET* 3.1 25.9 + - - +
269A ALA* 1.3 78.0 - - - +
271A HIS* 1.3 65.7 + - + +
273A LEU* 3.0 10.9 + - - +
274A MET* 3.0 43.0 + - + +
349A TYR* 4.2 13.5 - - + -
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Residues in contact with HIS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLN* 2.8 50.4 - - - +
135A LEU* 3.5 34.1 - - + +
136A ALA 3.7 6.1 - - - +
139A GLU* 3.9 25.0 - - + +
267A MET* 3.0 26.3 + - + -
268A GLU 3.7 6.1 - - - +
270A GLU* 1.3 78.0 - - + +
272A ALA* 1.3 61.6 + - - +
274A MET* 3.2 13.8 + - + +
275A ALA 3.0 23.6 + - - -
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Residues in contact with ALA 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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132A GLN 5.8 0.2 - - - -
133A ASN* 6.2 0.2 - - - +
136A ALA* 4.3 8.2 - - + +
268A GLU* 3.0 14.6 + - + +
269A ALA* 3.2 12.5 + - - +
271A HIS* 1.3 75.4 - - - +
273A LEU* 1.3 63.3 + - - +
275A ALA* 3.3 9.3 + - - +
276A ALA* 3.0 21.5 + - - +
345A SER* 3.8 12.7 + - - +
348A ASN* 5.3 5.6 - - - +
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 4.2 17.7 - - + +
8A GLN 4.7 3.1 - - - +
10A PRO* 3.7 37.0 - - + -
269A ALA 2.9 12.1 + - - +
270A GLU* 3.0 11.6 + - - +
272A ALA* 1.3 77.0 - - - +
274A MET* 1.3 56.9 + - - +
276A ALA* 3.1 2.3 + - - +
277A ASN* 3.0 34.2 + - - +
342A GLN* 3.7 14.6 - - + +
345A SER* 3.6 24.8 - - - +
346A VAL* 3.6 26.2 - - + -
349A TYR* 4.7 10.3 - - + -
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Residues in contact with MET 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 3.7 40.8 - - + -
128A GLU* 5.5 0.5 - - - +
132A GLN* 3.5 41.3 - - + +
270A GLU* 3.0 36.6 + - + +
271A HIS* 3.2 13.0 + - + +
273A LEU* 1.3 74.1 - - - +
275A ALA* 1.3 64.2 + - - +
277A ASN* 3.2 11.1 + - - +
278A ALA* 3.0 23.0 + - - +
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Residues in contact with ALA 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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129A ALA* 3.6 29.1 - - + +
132A GLN* 3.6 11.1 - - + +
133A ASN* 4.4 7.6 - - + +
271A HIS 3.0 13.1 + - - +
272A ALA* 3.5 13.0 - - - +
273A LEU 3.3 0.2 - - - -
274A MET* 1.3 75.6 - - - +
276A ALA* 1.3 62.8 + - - +
278A ALA* 3.2 3.8 + - - +
279A ASN* 3.0 28.9 + - - +
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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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272A ALA 3.0 12.4 + - - +
273A LEU 3.1 9.6 + - - +
275A ALA* 1.3 74.6 - - - +
277A ASN* 1.3 66.9 + - - +
279A ASN* 3.2 11.0 + - - +
280A ILE* 3.0 25.6 + - - +
338A ALA 4.7 1.8 - - - +
341A ARG* 4.3 4.3 - - + +
342A GLN* 3.6 32.7 - - + +
345A SER* 3.7 11.0 - - - +
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Residues in contact with ASN 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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4A ALA* 3.3 3.9 - - + +
5A PRO* 3.3 37.0 - - + +
6A ASP 4.0 2.0 + - - +
7A TYR* 3.7 34.2 + - - +
8A GLN 4.8 0.5 + - - -
273A LEU* 3.0 20.3 + - - +
274A MET* 3.4 11.0 - - - +
276A ALA* 1.3 77.4 - - - +
278A ALA* 1.3 59.8 + - - +
280A ILE* 3.2 3.2 + - - +
281A GLY 3.2 16.3 + - - -
342A GLN* 2.9 38.8 - - - +
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Residues in contact with ALA 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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4A ALA* 4.1 3.4 - - - -
125A ASN* 3.3 45.8 - - - +
128A GLU* 4.0 11.9 - - + -
129A ALA* 3.7 13.5 - - - +
274A MET 3.0 12.8 + - - +
275A ALA 3.5 9.0 - - - +
276A ALA 3.2 0.2 - - - -
277A ASN* 1.3 76.9 - - - +
279A ASN* 1.3 58.1 + - - +
281A GLY 3.1 2.4 + - - -
282A ALA* 3.0 22.7 + - - +
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Residues in contact with ASN 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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125A ASN 4.7 1.0 - - - +
126A MET* 4.7 6.2 - - - +
129A ALA* 3.5 20.4 - - - +
275A ALA* 3.0 19.1 + - - +
276A ALA* 3.2 11.4 + - - +
278A ALA* 1.3 74.5 - - - +
280A ILE* 1.3 63.8 + - - +
282A ALA* 3.7 10.9 - - - +
283A ALA* 3.1 24.3 + - - +
338A ALA* 3.8 13.9 - - + +
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Residues in contact with ILE 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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5A PRO* 3.8 11.2 - - + -
276A ALA 3.0 14.4 + - - +
277A ASN* 3.5 7.4 - - - +
278A ALA 3.2 0.2 - - - -
279A ASN* 1.3 74.6 - - - +
281A GLY* 1.3 65.1 + - - +
283A ALA* 3.3 3.2 + - - +
284A ARG* 2.9 55.6 + - - +
335A LEU* 4.2 9.0 - - + -
338A ALA* 3.7 24.7 - - + +
339A GLU* 4.0 17.7 - - + +
342A GLN* 3.5 46.4 - - + +
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Residues in contact with GLY 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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3A LEU* 3.6 9.9 - - - +
4A ALA* 3.4 31.1 - - - +
120A PHE 4.7 0.2 - - - +
125A ASN* 3.9 9.7 + - - -
277A ASN 3.2 4.9 + - - -
278A ALA 3.1 7.4 + - - -
280A ILE* 1.3 79.3 - - - +
282A ALA* 1.3 61.2 + - - +
284A ARG* 3.3 3.6 + - - +
285A ALA* 3.0 22.3 + - - +
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Residues in contact with ALA 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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122A ARG* 3.7 36.9 - - + +
125A ASN* 3.9 7.3 - - + +
126A MET* 3.9 18.4 - - + +
278A ALA 3.0 12.5 + - - +
279A ASN* 3.7 13.5 - - - +
281A GLY* 1.3 76.5 - - - +
283A ALA* 1.3 61.7 + - - +
285A ALA* 3.3 15.8 + - - +
286A ALA* 3.5 5.4 + - - +
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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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279A ASN 3.1 17.0 + - - +
280A ILE 3.7 3.4 - - - +
282A ALA* 1.3 74.1 - - - +
284A ARG* 1.3 64.2 + - - +
286A ALA* 3.2 19.6 + - - +
287A PHE* 3.8 11.3 - - - -
331A ASN 4.9 1.6 - - - +
334A ASN* 3.9 17.9 - - - +
335A LEU* 3.8 31.4 - - + +
338A ALA* 4.1 8.1 - - + -
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Residues in contact with ARG 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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3A LEU* 2.9 44.4 + - + -
4A ALA 4.2 0.2 - - - -
5A PRO* 3.9 22.2 - - - +
280A ILE* 2.9 35.8 + - - +
281A GLY 3.3 5.1 + - - +
283A ALA* 1.3 75.3 - - - +
285A ALA* 1.3 63.3 + - - +
287A PHE* 3.0 24.5 + - + -
288A PHE* 3.3 14.7 - - + -
335A LEU* 3.8 19.9 - - + +
339A GLU* 4.5 10.3 + - - -
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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
----------------------------------------------------------
3A LEU* 3.6 10.9 - - - +
120A PHE* 3.3 30.8 - - + +
122A ARG* 3.7 24.2 - - + +
281A GLY 3.0 9.9 + - - +
282A ALA 3.4 11.9 - - - +
284A ARG* 1.3 77.0 - - - +
286A ALA* 1.3 62.6 + - - +
288A PHE* 3.0 23.5 + - - +
289A PRO 5.2 0.3 - - - +
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 5.0 11.2 - - - +
282A ALA 3.5 5.3 + - - +
283A ALA* 3.2 17.1 + - - +
284A ARG 3.0 1.2 + - - -
285A ALA* 1.3 79.2 - - - +
287A PHE* 1.3 60.2 + - - +
288A PHE 3.1 2.9 + - - +
324A PRO* 3.4 17.8 - - - +
331A ASN* 3.8 26.5 + - + +
334A ASN* 5.8 2.9 - - + +
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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