Contacts of the helix formed by residues 261 - 282 (chain B) in PDB entry 3ELP
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 261 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ASN* 5.6 0.9 - - - +
261A THR* 5.7 5.4 - - - +
265A ARG* 4.6 10.8 - - + -
344A PHE* 3.4 37.9 - - + -
380A LEU* 4.8 1.8 - - + -
215B ASN* 3.9 5.4 + - - -
257B ARG 5.0 1.7 + - - +
258B GLY* 3.1 7.7 + - - -
260B LYS* 1.3 80.4 - - + +
262B LEU* 1.3 65.1 + - - +
263B HIS* 3.2 3.8 - - - -
264B VAL* 3.0 32.3 - - + +
265B ARG* 3.0 31.3 + - - +
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PHE* 3.9 26.9 - - + -
78B LEU* 4.6 6.5 - - + -
192B SER* 4.5 4.5 - - - +
193B PRO* 4.3 18.8 - - + -
194B TYR* 4.5 6.1 - - + -
208B TYR* 4.6 14.6 - - + +
214B MET* 5.7 2.5 - - + -
258B GLY 3.4 3.0 + - - +
259B LEU* 3.2 27.8 + - + +
261B THR* 1.3 78.3 - - - +
263B HIS* 1.3 58.2 + - - +
265B ARG* 3.5 24.0 - - - +
266B MET* 2.9 66.1 + - + +
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Residues in contact with HIS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LYS* 4.4 11.9 + - - -
380A LEU* 2.8 37.6 + - + +
18B PHE* 4.4 10.5 - + + -
19B ALA* 3.1 25.4 - - + +
22B ALA* 6.2 1.6 - - + -
23B ILE* 4.8 1.0 - - + +
194B TYR* 3.4 36.4 - - + +
259B LEU 4.7 0.8 + - - -
260B LYS 3.7 23.7 + - - -
261B THR* 3.9 2.9 - - - -
262B LEU* 1.3 79.7 - - - +
264B VAL* 1.3 94.1 + - + +
266B MET* 3.8 1.6 - - - +
267B GLU* 3.0 33.1 + - - +
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Residues in contact with VAL 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A VAL* 3.8 35.5 - - + +
265A ARG* 4.9 4.9 - - + -
268A LYS* 3.8 31.4 - - + -
380A LEU* 4.6 5.6 - - + -
261B THR* 3.0 39.9 - - + +
263B HIS* 1.3 104.4 - - + +
265B ARG* 1.3 60.7 + - + +
267B GLU* 3.5 7.0 + - - +
268B LYS* 3.3 21.7 + - - +
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Residues in contact with ARG 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A THR* 4.4 9.4 - - + -
264A VAL* 4.8 2.5 - - + -
214B MET* 3.0 37.9 - - + +
215B ASN* 3.6 19.0 + - - +
258B GLY 3.0 27.9 + - - -
261B THR* 3.0 29.2 + - - +
262B LEU* 3.5 27.8 - - - +
264B VAL* 1.3 77.7 - - + +
266B MET* 1.3 63.4 + - - +
268B LYS* 3.3 1.5 + - - -
269B HIS* 2.9 34.1 + - + -
344B PHE* 3.4 30.5 - - - -
380B LEU* 3.5 23.4 - - + +
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Residues in contact with MET 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B MET 3.8 22.4 - - - +
192B SER* 3.8 13.9 - - - +
194B TYR* 3.6 21.1 - - + -
195B PHE* 3.4 18.9 - - + -
214B MET* 5.5 3.1 - - - +
262B LEU* 2.9 49.7 + - + +
263B HIS 3.8 0.2 - - - +
265B ARG* 1.3 81.6 - - - +
267B GLU* 1.3 57.5 + - - +
269B HIS* 3.2 20.9 + - + +
270B PHE* 2.9 30.3 + - - +
311B THR* 4.4 19.1 - - + +
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Residues in contact with GLU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B HIS* 2.8 37.5 + - - -
194B TYR* 3.1 23.1 + - + +
195B PHE* 4.4 1.1 - - - -
263B HIS 3.0 15.1 + - - +
264B VAL* 3.7 7.9 - - - +
265B ARG 3.2 0.2 - - - -
266B MET* 1.3 77.6 - - - +
268B LYS* 1.3 57.4 + - - +
270B PHE* 3.3 21.0 + - - +
271B LYS* 2.9 35.7 + - + +
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Residues in contact with LYS 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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263A HIS* 4.2 10.3 - - + -
264A VAL* 3.5 33.0 - - + -
267A GLU* 6.5 0.9 - - - -
264B VAL 3.3 4.8 + - - +
266B MET 3.3 0.2 - - - -
267B GLU* 1.3 75.6 - - - +
269B HIS* 1.3 66.7 + - - +
271B LYS* 3.5 37.2 - - + +
272B ASN* 2.9 48.2 + - - +
380B LEU* 3.6 26.9 - - + +
381B GLU 4.7 3.3 + - - +
383B GLU* 6.1 1.2 - - - +
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Residues in contact with HIS 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B MET* 3.5 25.6 - - - +
265B ARG* 2.9 29.0 + - + -
266B MET* 3.2 26.4 + - + +
268B LYS* 1.3 76.1 - - - +
270B PHE* 1.3 54.0 + - - +
272B ASN* 3.9 1.0 - - - +
273B GLY* 2.7 34.3 + - - -
311B THR* 4.6 3.6 - - + -
312B GLY* 3.8 22.2 - - - +
342B GLY* 4.2 5.8 - - - -
343B GLY 3.4 21.5 - - - -
377B SER* 6.0 0.7 - - - -
378B VAL 2.8 26.6 + - - +
379B GLY* 3.9 5.4 + - - -
380B LEU* 3.6 20.0 - - + +
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Residues in contact with PHE 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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9B GLN* 6.3 2.7 - - + -
11B PHE* 4.0 21.5 - + - -
14B HIS* 5.8 2.0 - + - -
195B PHE* 3.6 9.4 - + + -
266B MET 2.9 16.0 + - - +
267B GLU* 3.4 21.3 - - - +
269B HIS* 1.3 74.2 - - - +
271B LYS* 1.3 62.3 + - + +
273B GLY* 3.3 0.5 + - - -
274B MET* 2.8 44.6 + - + +
291B TYR* 3.5 10.1 - - - -
308B THR 4.8 4.0 - - - -
309B GLY* 3.8 12.8 - - - -
310B CYS* 3.0 56.3 + - + +
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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
----------------------------------------------------------
267B GLU* 2.9 23.8 + - + +
268B LYS* 3.5 33.9 - - + +
269B HIS 3.3 0.2 - - - -
270B PHE* 1.3 76.8 - - + +
272B ASN* 1.3 66.5 + - - +
274B MET* 2.9 17.9 + - - +
275B ALA* 3.0 13.6 + - - +
383B GLU* 4.9 14.7 + - - -
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Residues in contact with ASN 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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268B LYS* 2.9 38.3 + - - +
269B HIS 4.0 0.7 - - - +
271B LYS* 1.3 74.0 - - - +
273B GLY* 1.3 57.6 + - - +
275B ALA* 3.3 5.9 + - - +
276B VAL* 2.9 34.4 + - - +
378B VAL* 3.5 19.5 - - + -
379B GLY 2.9 21.5 + - - +
380B LEU* 3.6 2.6 - - - +
381B GLU 3.0 29.9 + - - +
383B GLU* 3.6 22.0 + - - +
386B LEU* 4.1 8.8 - - + +
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Residues in contact with GLY 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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269B HIS 2.7 23.0 + - - -
270B PHE 3.6 1.6 - - - -
272B ASN* 1.3 74.9 - - - +
274B MET* 1.3 55.8 + - - +
277B ALA* 3.0 30.5 + - - +
291B TYR* 3.8 13.0 - - - -
312B GLY* 4.4 3.4 - - - -
314B VAL* 3.5 18.4 - - - +
378B VAL* 4.1 8.9 - - - +
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Residues in contact with MET 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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11B PHE* 5.9 0.7 - - - -
270B PHE* 2.8 27.5 + - + +
271B LYS* 3.4 9.9 - - - +
273B GLY* 1.3 72.6 - - - +
275B ALA* 1.3 67.0 + - - +
277B ALA* 3.4 1.6 + - - +
278B GLN* 2.9 49.8 + - - +
291B TYR* 3.5 20.3 + - - -
293B GLY* 3.2 34.1 - - - +
294B LEU* 3.4 26.5 - - + -
295B PRO* 5.1 2.2 - - + -
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Residues in contact with ALA 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 3.0 11.4 + - - +
272B ASN 3.6 7.2 - - - +
274B MET* 1.3 77.0 - - - +
276B VAL* 1.3 63.4 + - + +
278B GLN* 3.1 11.6 + - - +
279B PHE* 2.9 25.1 + - - +
383B GLU* 3.2 43.7 - - + +
387B LEU* 4.1 8.0 - - + +
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Residues in contact with VAL 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 ASN 2.9 24.4 + - - +
273B GLY 3.9 3.1 - - - +
275B ALA* 1.3 72.1 - - + +
277B ALA* 1.3 58.6 + - - +
279B PHE* 3.3 1.2 + - - +
280B LEU* 3.0 43.0 + - + +
314B VAL* 4.2 10.8 - - + -
335B PHE* 4.7 2.2 - - + -
376B LEU* 4.0 12.3 - - + -
378B VAL* 4.0 23.6 - - + -
386B LEU* 4.5 13.7 - - + -
387B LEU* 4.0 15.5 - - + -
390B LEU* 3.8 26.9 - - + -
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Residues in contact with ALA 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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273B GLY 3.0 19.7 + - - +
274B MET 3.8 2.7 - - - +
276B VAL* 1.3 76.8 - - - +
278B GLN* 1.3 62.8 + - - +
280B LEU* 4.8 0.9 - - - -
281B GLU* 3.1 23.9 + - - +
289B VAL* 3.9 5.8 - - + +
291B TYR* 3.4 39.0 - - + -
294B LEU* 3.7 11.9 - - + +
314B VAL* 3.9 14.6 - - + -
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Residues in contact with GLN 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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274B MET* 2.9 49.4 + - - +
275B ALA* 3.7 7.4 + - - +
277B ALA* 1.3 72.6 - - - +
279B PHE* 1.3 66.7 + - - +
281B GLU* 3.1 14.4 + - - +
282B SER* 3.1 16.4 + - - -
294B LEU* 3.4 20.0 - - + +
295B PRO* 6.2 0.6 - - - +
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Residues in contact with PHE 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 ALA 2.9 16.4 + - - +
276B VAL 3.6 3.1 - - - +
278B GLN* 1.3 77.5 - - - +
280B LEU* 1.3 73.1 + - + +
282B SER* 3.3 10.9 + - - -
283B ASN* 3.2 38.1 + - + +
387B LEU* 3.7 47.1 - - + -
390B LEU* 4.2 9.0 - - + -
391B ASP* 3.4 43.5 - - + -
394B LEU* 4.4 4.9 - - + -
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Residues in contact with LEU 280 (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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276B VAL* 3.0 36.3 + - + +
277B ALA 4.1 0.9 - - - +
279B PHE* 1.3 81.7 - - + +
281B GLU* 1.3 62.3 + - - +
283B ASN* 3.2 6.8 + - - -
286B VAL* 2.9 36.7 - - + +
289B VAL* 3.9 12.6 - - + -
314B VAL* 4.4 7.6 - - + -
316B PHE* 3.3 42.2 - - + -
376B LEU* 4.2 4.9 - - + -
390B LEU* 4.2 18.4 - - + -
394B LEU* 3.8 28.0 - - + -
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA 3.1 19.3 + - - +
278B GLN* 3.1 7.7 + - - +
280B LEU* 1.3 78.9 - - - +
282B SER* 1.3 58.1 + - - +
283B ASN 3.3 3.6 + - - +
286B VAL* 4.8 4.4 - - - +
288B LYS* 5.7 1.1 - - - +
289B VAL* 3.5 25.5 + - + +
294B LEU* 3.7 18.7 - - - +
295B PRO* 5.7 2.1 - - - +
296B SER* 3.0 28.4 + - - -
295C PRO* 3.3 38.0 - - + +
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B GLN 3.1 12.1 + - - -
279B PHE* 3.5 12.7 + - - -
280B LEU 3.2 0.2 - - - -
281B GLU* 1.3 76.6 - - - +
283B ASN* 1.3 61.1 + - - +
284B PRO* 3.9 5.5 - - - +
9C GLN 5.8 2.1 + - - -
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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) + - + + + + + -
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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