Contacts of the helix formed by residues 257 - 279 (chain B) in PDB entry 1ECX
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 GLU 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B ARG* 3.4 25.7 + - - -
253B ILE* 3.0 24.8 + - + +
254B ALA 3.8 1.8 - - - +
256B GLU* 1.3 84.1 - - + +
258B LEU* 1.3 64.5 + - - +
259B SER* 3.3 2.8 + - - -
260B GLU* 3.4 9.1 + - + +
261B ALA* 2.9 23.7 + - + +
355B LYS* 2.5 42.7 + - - +
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Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B GLY* 3.5 34.5 - - - +
184B LYS* 3.5 20.4 - - - +
185B ILE* 3.6 2.2 - - - +
186B PRO* 3.5 41.3 - - + -
254B ALA 3.1 11.2 + - - +
255B VAL* 3.1 27.0 + - + +
256B GLU 3.4 0.4 - - - -
257B GLU* 1.3 75.1 - - - +
259B SER* 1.3 58.5 + - - +
261B ALA* 3.0 5.0 + - - +
262B ALA* 2.7 39.5 + - + +
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Residues in contact with SER 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B VAL 4.8 0.2 + - - -
256B GLU 5.1 2.4 + - - -
257B GLU 3.4 0.4 - - - -
258B LEU* 1.3 83.3 - - - +
260B GLU* 1.3 63.8 + - - +
262B ALA* 3.4 3.4 + - - +
263B LYS* 3.3 48.5 + - - +
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Residues in contact with GLU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B GLU* 3.4 9.3 + - + +
259B SER* 1.3 79.7 - - - +
261B ALA* 1.3 62.5 + - - +
263B LYS* 3.6 9.8 + - - +
264B HIS* 3.3 22.3 + - + +
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Residues in contact with ALA 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B GLY 4.7 4.5 - - - +
254B ALA 5.7 0.7 - - - +
257B GLU* 2.9 22.4 + - + +
258B LEU* 3.5 5.2 - - - +
260B GLU* 1.3 75.8 - - - +
262B ALA* 1.3 64.7 + - - +
264B HIS* 3.2 7.3 + - - +
265B MET* 3.0 37.3 + - + +
355B LYS* 4.1 32.0 - - + -
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Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LYS 4.1 10.8 - - - +
258B LEU* 2.7 25.6 + - + +
259B SER* 4.0 3.6 - - - +
261B ALA* 1.3 72.5 - - - +
263B LYS* 1.3 60.0 + - + +
265B MET* 3.1 12.0 + - + +
266B GLU* 2.7 33.9 + - - +
292B PRO* 4.0 20.6 - - + +
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Residues in contact with LYS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A PHE* 5.1 4.2 - - + -
259B SER* 3.3 37.0 + - - +
260B GLU* 4.0 7.8 - - - +
262B ALA* 1.3 78.1 - - + +
264B HIS* 1.3 58.1 + - - +
266B GLU* 3.4 7.2 + - - +
267B LYS* 3.0 35.0 + - + +
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Residues in contact with HIS 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B GLU* 3.3 13.0 + - + +
261B ALA* 3.2 11.0 + - - +
262B ALA 3.1 0.8 - - - -
263B LYS* 1.3 77.3 - - - +
265B MET* 1.3 65.6 + - - +
267B LYS* 3.3 15.7 + - + +
268B LEU* 3.1 44.3 + - + +
354B CYS 4.7 2.6 + - - -
355B LYS* 3.6 21.0 + - - -
357B ASN 2.8 30.0 + - - -
358B THR* 4.7 4.0 - - + -
359B GLU 5.1 0.6 + - - -
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Residues in contact with MET 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B GLY 3.6 24.2 - - - +
184B LYS* 4.5 10.8 - - + -
261B ALA* 3.0 33.0 + - + +
262B ALA* 3.8 8.7 - - - +
264B HIS* 1.3 75.9 - - - +
266B GLU* 1.3 67.6 + - - +
267B LYS 3.1 0.2 + - - -
268B LEU* 3.2 8.2 + - + +
269B ARG* 2.8 25.8 + - - +
292B PRO* 3.5 17.4 - - + +
293B ASN* 3.6 27.1 - - + -
353B LEU* 3.7 9.1 - - + +
354B CYS* 3.6 39.3 - - - +
355B LYS* 4.4 5.4 - - + +
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Residues in contact with GLU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A TYR* 4.5 8.4 + - - -
375A PHE* 3.3 40.8 - - + -
262B ALA 2.7 20.9 + - - +
263B LYS* 3.5 9.6 - - - +
265B MET* 1.3 74.1 - - - +
267B LYS* 1.3 60.7 + - - +
269B ARG* 3.4 29.0 + - - +
270B SER* 3.2 21.1 + - - -
287B LEU 5.2 0.7 - - - +
290B SER 5.7 0.3 - - - +
292B PRO* 3.7 24.1 + - + +
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Residues in contact with LYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A SER 5.2 2.9 - - - +
375A PHE* 4.3 37.0 - - + +
263B LYS* 3.0 19.2 + - + +
264B HIS* 3.5 17.7 - - + +
265B MET 3.1 0.2 - - - -
266B GLU* 1.3 73.6 - - - +
268B LEU* 1.3 74.7 + - - +
270B SER* 2.6 26.7 + - - -
271B LYS* 3.2 5.9 + - - +
359B GLU* 5.0 10.3 + - - -
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B HIS* 3.1 31.6 + - + +
265B MET* 3.8 3.8 - - + +
267B LYS* 1.3 85.5 - - - +
269B ARG* 1.3 63.2 + - - +
271B LYS* 3.1 10.9 + - + +
272B LEU* 3.1 23.3 + - - +
353B LEU* 3.7 20.0 - - + -
354B CYS 5.5 0.4 - - - +
357B ASN* 3.6 40.8 - - + +
358B THR 3.9 6.3 - - - +
359B GLU* 3.7 36.3 - - + +
362B VAL* 3.9 13.9 - - + +
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Residues in contact with ARG 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B MET 2.8 17.4 + - - +
266B GLU* 3.4 27.0 + - - +
268B LEU* 1.3 77.6 - - - +
270B SER* 1.3 62.7 + - - +
272B LEU* 3.0 8.3 + - + +
273B VAL* 2.9 33.3 + - + +
285B THR* 3.6 6.7 - - - +
287B LEU* 3.4 32.3 + - - +
290B SER* 3.0 27.1 + - - -
291B LEU 2.9 20.3 + - - -
292B PRO* 3.5 17.8 + - - +
293B ASN 4.5 0.9 - - - -
294B THR 2.6 43.0 + - - +
295B LEU* 4.2 15.7 - - + -
353B LEU* 4.0 10.2 - - + +
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A LEU* 3.7 29.7 - - - +
375A PHE* 3.9 30.5 + - - +
376A LEU* 4.8 7.2 - - - +
266B GLU 3.2 9.1 + - - -
267B LYS* 2.6 21.1 + - - -
269B ARG* 1.3 79.2 - - - +
271B LYS* 1.3 62.4 + - - +
273B VAL* 3.3 3.8 + - - +
274B SER* 3.2 24.8 + - - -
287B LEU* 6.3 0.2 - - - -
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B LYS 3.2 4.7 + - - +
268B LEU* 3.1 13.5 + - + +
270B SER* 1.3 83.2 + - - +
272B LEU* 1.3 60.8 + - - +
274B SER* 3.7 3.0 + - - -
275B GLY* 3.1 20.6 + - - -
359B GLU* 2.8 35.4 + - + +
362B VAL* 4.1 13.9 - - + -
363B ASP* 2.7 33.9 + - - +
366B LEU* 3.8 12.8 - - + +
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 4.5 3.8 - - + -
268B LEU 3.1 16.7 + - - +
269B ARG* 3.0 9.5 + - - +
271B LYS* 1.3 76.4 - - - +
273B VAL* 1.3 53.4 + - - +
275B GLY 3.7 0.2 - - - -
276B LEU* 2.7 44.0 + - + +
295B LEU* 3.7 14.6 - - + -
351B ILE* 3.9 28.3 - - + -
353B LEU* 4.2 22.9 - - + -
362B VAL* 3.3 28.7 - - + +
365B PHE* 3.9 31.4 - - + -
366B LEU* 4.3 8.2 - - + +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ASN 4.4 1.8 - - - +
310A LEU* 4.2 14.6 - - + -
269B ARG* 2.9 24.8 + - + +
270B SER* 3.6 8.1 - - - +
272B LEU* 1.3 75.7 - - - +
274B SER* 1.3 64.6 + - - +
276B LEU* 3.9 1.4 - - - +
277B MET* 3.0 50.6 + - + +
283B ILE* 4.4 12.7 - - + +
287B LEU* 4.2 24.7 - - + -
295B LEU* 3.7 30.1 - - + -
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A THR* 3.5 23.3 + - - +
309A ASN* 3.2 28.8 + - - +
310A LEU* 4.0 16.6 - - - -
270B SER 3.2 12.6 + - - -
271B LYS* 4.3 3.1 - - - -
273B VAL* 1.3 80.6 - - - +
275B GLY* 1.3 62.8 + - - +
278B ASN* 2.8 36.9 + - - -
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Residues in contact with GLY 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B LYS 3.1 16.1 + - - -
272B LEU 3.7 2.2 - - - -
274B SER* 1.3 77.6 - - - +
276B LEU* 1.3 60.7 + - - +
278B ASN* 3.3 11.2 + - - +
279B LEU* 3.3 25.1 + - - +
366B LEU* 3.8 21.8 - - - -
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU* 2.7 25.7 + - + +
273B VAL* 3.9 3.1 - - - +
275B GLY* 1.3 69.4 - - - +
277B MET* 1.3 67.3 + - - +
279B LEU* 2.9 16.4 + - + +
280B GLY 3.1 0.7 + - - -
281B ALA* 3.0 27.0 + - + +
283B ILE* 5.0 3.1 - - + -
295B LEU* 4.3 7.2 - - + -
297B VAL* 3.9 24.9 - - + -
299B PHE* 4.0 20.0 - - + -
351B ILE* 3.8 28.3 - - + -
365B PHE* 4.0 18.8 - - + -
366B LEU* 4.1 12.1 - - + -
369B ILE* 4.1 13.7 - - + -
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Residues in contact with MET 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ASN* 2.7 68.0 - - + +
312A SER* 4.6 12.1 - - - -
313A GLY 4.7 1.8 - - - +
273B VAL* 3.0 34.0 + - + +
276B LEU* 1.3 75.8 - - - +
278B ASN* 1.3 56.9 + - - +
280B GLY* 2.7 25.1 + - - -
281B ALA 3.9 15.6 - - - +
283B ILE* 3.7 26.5 - - + -
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Residues in contact with ASN 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A SER* 4.5 14.0 + - - -
306A THR* 5.2 2.6 + - - -
309A ASN* 3.0 17.2 + - - +
274B SER* 2.8 33.3 + - - +
275B GLY* 3.6 9.6 - - - +
276B LEU 3.2 0.2 - - - -
277B MET* 1.3 77.0 - - - +
279B LEU* 1.3 63.5 + - + +
280B GLY 3.3 0.8 + - - -
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B GLY 3.3 13.4 + - - +
276B LEU* 2.9 14.3 + - + +
278B ASN* 1.3 82.3 - - + +
280B GLY* 1.3 57.4 + - - +
281B ALA 3.7 0.2 - - - -
299B PHE* 3.6 13.1 - - + -
366B LEU* 4.0 12.6 - - + +
369B ILE* 3.9 27.6 - - + -
370B GLU* 3.6 45.5 - - + +
373B LEU* 4.1 19.7 - - + +
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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