Contacts of the helix formed by residues 255 - 276 (chain A) in PDB entry 3W0A
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 THR 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A ASP 5.8 0.4 - - - +
254A LEU* 1.4 76.5 - - - +
256A SER* 1.3 59.0 + - - +
257A GLU* 3.5 10.6 + - - +
258A ASP* 3.1 31.3 + - - +
259A GLN* 2.9 27.1 + - - +
347A GLN* 5.8 1.9 - - + +
348A ASP* 5.9 4.5 - - + -
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Residues in contact with SER 256 (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 3.9 0.4 + - - -
255A THR* 1.3 72.0 - - - +
257A GLU* 1.3 59.9 + - - +
259A GLN* 3.8 13.7 + - - +
260A ILE* 3.1 38.4 + - - +
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Residues in contact with GLU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A THR* 3.2 9.5 + - - +
256A SER* 1.3 78.6 + - - +
258A ASP* 1.3 58.4 + - - +
260A ILE* 3.4 5.1 + - - +
261A VAL* 3.0 40.4 + - + +
345A GLY 5.8 1.6 - - - +
347A GLN* 3.3 30.3 - - + +
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Residues in contact with ASP 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU* 4.4 10.3 - - + +
255A THR* 3.1 28.0 + - - +
257A GLU* 1.3 75.7 - - - +
259A GLN* 1.3 63.9 + - - +
261A VAL* 3.3 4.7 + - - +
262A LEU* 3.0 31.9 + - - +
345A GLY 4.5 1.0 - - - +
346A VAL* 3.6 5.9 - - - -
347A GLN* 2.8 33.0 + - - +
348A ASP* 3.0 31.7 + - - +
352A ILE* 3.8 18.9 - - + +
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Residues in contact with GLN 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LYS* 5.1 12.3 - - - +
251A PHE* 3.3 58.5 - - + +
252A ARG* 3.7 14.0 - - - +
254A LEU* 2.9 25.7 - - + +
255A THR 2.9 18.1 + - - +
256A SER* 3.8 11.2 + - - +
257A GLU 3.4 0.2 - - - -
258A ASP* 1.3 75.3 - - - +
260A ILE* 1.3 65.4 + - + +
262A LEU* 3.5 1.0 + - - +
263A LEU* 2.9 34.1 + - - +
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Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 6.5 0.4 - - + -
256A SER* 3.1 24.4 + - - +
257A GLU* 4.0 4.5 - - - +
259A GLN* 1.3 82.0 - - + +
261A VAL* 1.3 64.8 + - + +
263A LEU* 4.0 16.9 - - + +
264A LYS* 3.0 50.8 + - + +
420A GLU* 4.9 3.4 - - - +
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLU* 3.0 28.6 + - + +
258A ASP* 3.8 6.5 - - - +
260A ILE* 1.3 76.8 - - + +
262A LEU* 1.3 52.8 + - - +
264A LYS* 3.9 4.0 - - - +
265A SER* 2.7 38.1 + - - +
343A ARG* 4.7 4.5 - - + -
344A PRO 3.5 23.3 - - - +
345A GLY* 4.0 17.3 - - - +
346A VAL* 3.7 25.8 - - + +
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Residues in contact with LEU 262 (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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251A PHE* 4.2 13.0 - - + -
254A LEU* 3.6 28.5 - - + -
258A ASP 3.0 21.5 + - - +
259A GLN 3.7 4.0 - - - +
261A VAL* 1.3 72.6 - - - +
263A LEU* 1.3 62.7 + - - +
265A SER* 3.3 3.7 + - - -
266A SER* 2.8 32.5 + - - -
338A ILE* 3.6 22.8 - - + +
339A VAL* 4.5 3.1 - - - -
340A SER 3.3 28.0 - - - +
343A ARG* 4.0 7.1 + - + -
346A VAL* 3.8 18.6 - - + -
352A ILE* 4.1 19.3 - - + -
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Residues in contact with LEU 263 (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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238A ILE* 6.0 1.2 - - + +
241A VAL* 4.0 18.1 - - + +
242A ILE* 4.0 43.1 - - + +
245A ALA* 3.7 22.7 - - + -
246A LYS* 6.1 0.9 - - + -
251A PHE* 4.0 20.4 - - + -
259A GLN* 2.9 24.7 + - + +
260A ILE* 4.0 18.6 - - + +
262A LEU* 1.3 77.4 - - - +
264A LYS* 1.3 57.2 + - + +
266A SER* 3.6 3.1 + - - +
267A ALA* 3.0 32.1 + - - +
338A ILE* 4.7 5.4 - - + -
421A VAL* 6.1 0.4 - - - -
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Residues in contact with LYS 264 (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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260A ILE* 3.0 38.3 + - + +
261A VAL* 4.0 4.0 - - - +
263A LEU* 1.3 79.3 - - + +
265A SER* 1.3 61.8 + - - +
266A SER 3.5 0.2 + - - -
267A ALA* 3.8 11.4 + - - +
268A ILE 5.3 0.2 + - - -
420A GLU* 2.9 54.8 + - - +
421A VAL* 4.0 37.8 - - + +
422A PHE* 5.4 2.3 - - - -
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Residues in contact with SER 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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261A VAL* 2.7 25.0 + - - -
262A LEU 3.3 4.9 + - - -
264A LYS* 1.3 77.1 - - - +
266A SER* 1.4 58.5 + - - +
268A ILE* 5.2 1.0 + - - +
343A ARG* 3.3 41.2 + - - +
344A PRO* 5.1 10.1 - - - -
394A ASN* 2.8 28.6 + - - +
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Residues in contact with SER 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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241A VAL* 5.3 0.9 - - - +
262A LEU 2.8 22.6 + - - -
263A LEU* 3.6 5.9 + - - +
265A SER* 1.4 75.9 + - - +
267A ALA* 1.4 67.3 + - - +
268A ILE 3.4 2.0 - - - -
269A GLU* 3.0 8.2 + - - +
270A VAL* 2.9 27.3 + - - +
337A CYS* 4.1 1.6 - - - -
338A ILE* 3.8 30.5 - - - +
343A ARG* 3.7 25.1 - - - +
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Residues in contact with ALA 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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238A ILE* 4.3 21.5 - - + -
241A VAL* 5.1 8.0 - - - +
263A LEU 3.0 19.2 + - - +
264A LYS 3.8 3.6 - - - +
265A SER 3.6 1.6 - - - -
266A SER* 1.4 74.5 - - - +
268A ILE* 1.3 57.7 + - - +
270A VAL* 3.4 5.1 + - - +
271A ILE* 3.0 35.0 + - - +
421A VAL* 3.6 29.8 - - + -
422A PHE* 4.3 2.9 - - + -
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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
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234A VAL* 4.9 1.3 - - + -
264A LYS 5.3 0.4 + - - -
265A SER 5.2 0.8 + - - +
267A ALA* 1.3 78.9 - - - +
269A GLU* 1.3 59.7 + - - +
271A ILE* 3.4 23.8 + - + +
272A MET* 3.0 46.4 + - + +
394A ASN* 3.5 42.0 - - - +
397A HIS* 3.7 41.5 - - + +
422A PHE* 3.8 17.8 - - + -
501A DS5 3.9 23.6 - - + -
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Residues in contact with GLU 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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265A SER 4.7 0.2 - - - -
266A SER 3.0 8.5 + - - +
268A ILE* 1.3 78.1 - - + +
270A VAL* 1.4 57.1 - - - +
272A MET* 3.2 2.8 + - - -
273A LEU* 3.0 26.7 + - - +
337A CYS* 3.3 17.3 - - - -
343A ARG* 2.9 38.0 + - - -
387A LEU* 4.7 1.6 - - - +
390A LEU* 3.5 51.7 - - + +
391A ARG* 3.5 14.5 + - - -
394A ASN* 2.9 35.4 + - + +
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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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241A VAL* 3.7 31.4 - - + -
244A PHE* 5.6 0.9 - - + -
266A SER* 2.9 22.1 + - - +
267A ALA 4.0 3.6 - - - +
269A GLU* 1.4 71.7 - - - +
271A ILE* 1.3 55.6 + - - +
273A LEU* 3.2 6.1 + - + +
274A ARG* 2.8 36.7 + - - +
334A MET* 4.1 28.0 - - + +
337A CYS* 3.8 16.6 - - + -
338A ILE* 3.4 33.9 - - + -
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Residues in contact with ILE 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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234A VAL* 3.8 23.6 - - + +
237A SER* 3.8 23.1 - - - -
238A ILE* 3.5 31.6 - - + -
241A VAL* 4.8 2.7 - - + -
267A ALA 3.0 24.6 + - - +
268A ILE* 3.5 21.3 - - + +
269A GLU 3.3 0.2 - - - -
270A VAL* 1.3 76.6 - - - +
272A MET* 1.3 58.5 + - - +
274A ARG* 3.5 9.1 - - - +
275A SER* 2.9 32.7 + - - -
422A PHE* 5.3 0.2 - - + -
501A DS5 3.6 35.1 - - + +
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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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268A ILE* 3.0 40.6 + - + +
269A GLU* 3.2 7.4 + - - +
271A ILE* 1.3 76.6 - - + +
273A LEU* 1.3 61.8 + - - +
275A SER* 2.8 22.1 + - - -
276A ASN* 3.5 2.4 + - - +
309A LEU* 4.2 14.8 - - + -
313A LEU* 4.0 31.4 - - + -
316A PHE* 4.4 4.2 - - + -
317A GLN* 3.0 19.6 + - - +
390A LEU* 3.9 12.6 - - + -
393A LEU* 3.8 42.6 - - + +
394A ASN 5.3 0.7 - - - -
397A HIS* 4.7 1.1 - - + -
501A DS5 4.1 15.3 - - + -
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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
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269A GLU 3.0 15.4 + - - +
270A VAL* 3.5 8.5 - - - +
272A MET* 1.3 76.6 - - - +
274A ARG* 1.3 63.2 + - - +
276A ASN* 3.1 20.8 + - - +
316A PHE* 3.9 6.3 - - + -
320A LEU* 3.8 25.0 - - + +
330A HIS* 3.4 14.5 - - + +
333A LEU* 3.9 25.8 - - + +
334A MET* 3.9 38.6 - - + +
337A CYS* 4.0 16.2 - - + -
386A LYS* 5.5 0.4 - - + -
390A LEU* 3.6 27.8 - - + -
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Residues in contact with ARG 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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139A HIS* 4.8 3.5 - - - +
142A THR* 3.0 34.1 + - - -
143A TYR* 3.8 19.8 + - + +
237A SER* 4.4 4.7 + - - -
240A LYS* 3.5 8.2 - - - +
241A VAL* 3.7 36.0 - - - +
244A PHE* 4.8 9.1 - - - +
270A VAL* 2.8 25.6 + - - +
271A ILE* 3.5 12.1 - - + +
273A LEU* 1.3 73.6 - - - +
275A SER* 1.3 64.3 + - - +
276A ASN 3.2 1.0 + - - -
277A GLU* 3.3 20.1 + - - +
330A HIS* 4.2 9.9 + - - +
334A MET* 3.8 29.2 - - + +
501A DS5 2.7 44.3 + - + +
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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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271A ILE 2.9 15.8 + - - -
272A MET 2.8 18.5 + - - -
274A ARG* 1.3 76.0 - - - +
276A ASN* 1.4 60.6 + - - +
277A GLU 3.1 0.4 - - - -
278A SER* 3.0 25.0 + - - -
279A PHE 3.2 4.7 + - - -
286A TRP* 3.1 28.7 + - - -
317A GLN* 3.3 5.9 + - - -
501A DS5 3.6 37.2 - - - +
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Residues in contact with ASN 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 MET 3.5 0.6 + - - +
273A LEU 3.1 16.5 + - - +
274A ARG 3.1 1.0 - - - -
275A SER* 1.4 80.7 + - - +
277A GLU* 1.3 58.1 + - - +
279A PHE* 3.2 11.0 + - - +
317A GLN* 2.9 51.5 + - - +
320A LEU* 3.6 30.5 - - + +
321A LYS* 2.9 45.8 + - - +
330A HIS* 5.0 5.3 + - + -
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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