Contacts of the helix formed by residues 261 - 282 (chain G) in PDB entry 5EIG
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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F HIS* 3.7 23.6 + - - +
261F THR* 4.0 11.1 - - - +
265F ARG* 3.8 28.3 - - + -
344F PHE* 5.5 1.1 - - + -
380F LEU* 4.4 4.7 - - + -
217G HIS* 4.1 6.4 - - - -
258G GLY 3.2 5.2 + - - -
259G LEU 3.1 0.4 - - - -
260G LYS* 1.3 82.3 - - + +
262G LEU* 1.3 65.7 + - - +
263G HIS* 3.2 2.9 - - - -
264G VAL* 3.2 17.5 - - + +
265G ARG* 2.9 44.7 + - - +
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Residues in contact with LEU 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G PHE* 3.9 29.8 - - + -
78G LEU* 4.3 0.4 - - + -
192G SER* 4.6 5.4 - - - +
193G PRO* 4.3 8.1 - - + -
194G TYR* 4.8 0.2 - - + -
213G TYR 3.5 18.4 - - - +
214G MET* 4.2 14.1 - - - +
258G GLY 3.4 2.0 + - - -
259G LEU* 3.0 38.5 + - + +
260G LYS 3.6 0.2 - - - -
261G THR* 1.3 77.7 - - - +
263G HIS* 1.3 58.8 + - - +
265G ARG* 3.4 26.9 - - - +
266G MET* 2.9 57.1 + - + +
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Residues in contact with HIS 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F LYS* 4.5 9.6 - - - +
380F LEU* 3.0 34.4 + - + +
18G PHE* 4.3 8.8 - - + -
19G ALA* 3.5 27.3 - - + +
22G ALA* 5.1 3.2 - - - +
23G ILE* 4.4 4.7 - - + -
194G TYR* 3.5 36.5 - - + +
259G LEU 4.9 1.4 + - - -
260G LYS 3.4 26.6 + - - -
261G THR* 4.1 4.0 - - - -
262G LEU* 1.3 80.2 + - - +
264G VAL* 1.3 86.7 + - + +
266G MET* 4.2 0.3 - - - +
267G GLU* 3.2 31.2 + - - +
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Residues in contact with VAL 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F VAL* 3.8 45.8 - - + +
265F ARG* 4.9 3.6 - - + +
268F LYS* 3.9 26.9 - - + -
380F LEU* 4.9 3.4 - - + -
261G THR* 3.2 34.1 - - + +
263G HIS* 1.3 97.4 - - + +
265G ARG* 1.3 64.1 + - - +
267G GLU* 3.8 8.1 + - - +
268G LYS* 3.5 18.2 + - - +
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Residues in contact with ARG 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F THR* 3.8 20.9 - - + -
264F VAL* 4.9 1.8 - - + -
213G TYR* 3.0 18.8 + - - +
214G MET 3.2 20.4 + - - -
215G ASN 3.7 6.7 + - - -
216G GLY* 3.5 15.9 + - - -
217G HIS* 4.0 9.4 - - - -
258G GLY 2.7 24.2 + - - -
261G THR* 2.9 35.4 + - - +
262G LEU* 3.4 22.4 - - - +
264G VAL* 1.3 76.9 - - + +
266G MET* 1.3 62.4 + - - +
268G LYS 3.0 2.9 + - - -
269G HIS* 2.9 41.2 + - + -
342G GLY 4.6 3.4 + - - -
344G PHE* 5.6 0.2 - - - -
380G LEU* 3.5 30.0 - - + +
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Residues in contact with MET 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G MET 3.5 24.2 - - - +
192G SER* 3.6 10.5 - - - +
194G TYR* 3.9 15.0 - - + -
195G PHE* 3.4 36.4 - - + -
213G TYR* 3.4 38.6 - - + -
262G LEU* 2.9 45.3 + - + +
263G HIS 4.2 0.2 - - - +
265G ARG* 1.3 77.2 - - - +
267G GLU* 1.3 62.5 + - - +
269G HIS* 3.7 7.4 - - + +
270G PHE 3.0 17.5 + - - -
311G THR* 3.8 12.8 - - + -
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Residues in contact with GLU 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F LYS* 6.2 1.6 - - - +
14G HIS* 3.3 18.4 + - - -
194G TYR* 2.5 36.0 + - + +
195G PHE* 4.7 2.7 - - - -
263G HIS 3.2 19.4 + - - +
264G VAL* 4.0 7.6 - - - +
265G ARG 3.2 0.6 - - - -
266G MET* 1.3 77.0 - - - +
268G LYS* 1.3 58.1 + - - +
270G PHE* 3.4 16.1 - - - +
271G LYS* 3.2 44.7 + - - +
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Residues in contact with LYS 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F HIS* 4.6 8.7 - - - -
264F VAL* 3.9 23.3 - - + -
267F GLU* 6.4 0.2 - - - +
264G VAL 3.5 11.0 + - - +
265G ARG 3.0 8.1 + - - +
267G GLU* 1.3 76.0 - - - +
269G HIS* 1.3 65.3 + - - +
270G PHE 3.1 1.6 - - - -
271G LYS* 4.5 16.2 - - + +
272G ASN* 3.0 48.3 + - - +
380G LEU* 3.7 26.9 - - + +
381G GLU 5.2 0.7 - - - +
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Residues in contact with HIS 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G TYR* 3.5 34.6 + + + -
216G GLY 5.8 0.2 + - - -
265G ARG* 2.9 36.6 + - + +
266G MET* 3.4 15.0 + - + +
268G LYS* 1.3 76.5 - - - +
270G PHE* 1.3 57.3 + - - +
272G ASN* 4.8 0.2 - - - -
273G GLY* 2.8 28.8 + - - -
311G THR 4.1 3.1 - - - -
312G GLY* 3.5 19.2 - - - +
342G GLY* 4.3 4.0 + - - -
343G GLY 3.2 27.4 + - - -
377G SER* 5.8 0.4 - - - -
378G VAL 2.8 27.8 + - - +
379G GLY* 3.8 5.6 - - - -
380G LEU* 3.5 24.2 - - + +
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Residues in contact with PHE 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G PHE* 4.3 20.2 - + - -
14G HIS* 6.2 1.1 - + - -
195G PHE* 4.0 11.0 - + + -
266G MET 3.0 12.3 + - - +
267G GLU* 3.4 19.3 - - - +
268G LYS 3.1 0.2 - - - -
269G HIS* 1.3 75.0 - - - +
271G LYS* 1.3 63.0 + - + +
274G MET* 2.9 43.7 + - + +
291G TYR* 3.6 8.9 + - - -
293G GLY* 5.2 0.4 - - - -
308G THR 4.8 2.7 - - - -
309G GLY* 3.8 15.9 - - - -
310G CYS* 3.1 50.2 + - + +
311G THR 4.2 1.1 - - - -
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Residues in contact with LYS 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267G GLU* 3.2 35.7 + - - +
268G LYS* 3.5 18.8 + - + +
270G PHE* 1.3 82.2 - - + +
272G ASN* 1.3 61.9 + - - +
274G MET* 3.8 4.8 - - - +
275G ALA* 3.1 28.4 + - - +
383G GLU* 4.4 5.8 - - - +
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Residues in contact with ASN 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268G LYS* 3.0 31.0 + - - +
269G HIS 4.2 0.4 - - - +
271G LYS* 1.3 78.6 - - - +
273G GLY* 1.3 59.9 + - - +
275G ALA* 3.3 5.5 + - - +
276G VAL* 2.9 34.1 + - - +
378G VAL* 3.7 16.2 - - + -
379G GLY 3.1 18.1 + - - +
380G LEU* 3.9 4.4 - - - +
381G GLU 2.7 29.2 + - - -
383G GLU* 3.7 24.3 + - - +
386G LEU* 3.8 8.7 - - + +
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Residues in contact with GLY 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269G HIS 2.8 23.1 + - - -
270G PHE 3.8 0.4 - - - -
272G ASN* 1.3 73.7 - - - +
274G MET* 1.3 56.9 + - - +
276G VAL* 3.4 0.5 + - - +
277G ALA* 2.8 30.8 + - - +
291G TYR* 3.9 8.7 - - - -
311G THR 4.2 0.2 - - - -
312G GLY* 4.1 8.1 - - - -
314G VAL* 3.5 7.5 - - - +
378G VAL* 3.9 20.3 - - - +
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Residues in contact with MET 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G PHE* 2.9 29.7 + - + +
271G LYS* 3.8 5.8 - - - +
273G GLY* 1.3 77.0 - - - +
275G ALA* 1.3 57.3 + - - +
277G ALA* 3.3 1.6 + - - +
278G GLN* 2.9 60.4 + - - +
291G TYR* 3.6 26.1 + - + +
293G GLY* 3.3 28.0 - - - +
294G LEU* 4.3 10.3 - - + -
295G PRO* 5.2 3.4 - - + -
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Residues in contact with ALA 275 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271G LYS 3.1 18.5 + - - +
272G ASN 3.7 4.9 - - - +
274G MET* 1.3 76.2 - - - +
276G VAL* 1.3 57.9 + - - +
278G GLN* 3.4 11.5 + - - +
279G PHE* 3.0 30.1 + - - +
383G GLU* 3.5 37.5 - - + +
387G LEU* 3.7 9.4 - - + +
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Residues in contact with VAL 276 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G ASN 2.9 20.5 + - - +
273G GLY 3.7 3.6 - - - +
275G ALA* 1.3 76.2 - - - +
277G ALA* 1.3 62.2 + - - +
279G PHE* 3.3 2.1 + - - +
280G LEU* 3.0 38.1 + - + +
314G VAL* 4.2 4.5 - - + -
335G PHE* 4.6 4.9 - - + -
376G LEU* 4.0 8.1 - - + -
378G VAL* 3.8 34.1 - - + -
386G LEU* 4.6 8.5 - - + -
387G LEU* 3.9 14.1 - - + -
390G LEU* 3.7 28.9 - - + -
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Residues in contact with ALA 277 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273G GLY 2.8 19.0 + - - +
274G MET 3.6 3.4 - - - +
276G VAL* 1.3 78.6 - - - +
278G GLN* 1.3 61.1 + - - +
280G LEU* 3.5 2.0 + - - +
281G GLU* 3.2 24.8 + - - +
289G VAL* 4.1 3.0 - - + +
291G TYR* 3.6 38.6 - - + -
294G LEU* 3.9 13.7 - - + +
314G VAL* 4.1 13.9 - - + -
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Residues in contact with GLN 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G MET* 2.9 45.7 + - + +
275G ALA* 3.9 10.2 - - - +
277G ALA* 1.3 74.4 - - - +
279G PHE* 1.3 66.5 + - - +
281G GLU* 3.6 5.2 + - - +
282G SER* 3.4 24.4 + - - -
294G LEU* 3.9 18.8 - - + +
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Residues in contact with PHE 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275G ALA 3.0 18.6 + - - +
276G VAL 3.6 2.9 - - - +
278G GLN* 1.3 74.5 - - - +
280G LEU* 1.3 82.3 + - + +
282G SER* 3.2 14.1 + - - -
283G ASN* 3.3 27.8 + - - +
387G LEU* 3.7 30.5 - - + -
390G LEU* 3.8 29.8 - - + -
391G ASP* 3.6 40.6 - - + -
394G LEU* 4.4 0.7 - - + -
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Residues in contact with LEU 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276G VAL* 3.0 27.8 + - + +
277G ALA 3.9 2.0 - - - +
279G PHE* 1.3 91.7 - - + +
281G GLU* 1.3 60.9 + - - +
283G ASN* 3.1 11.2 + - - -
286G VAL* 3.2 30.6 - - + +
289G VAL* 3.8 15.0 - - + -
314G VAL* 3.9 11.9 - - + -
316G PHE* 3.6 36.3 - - + -
376G LEU* 3.8 16.6 - - + -
390G LEU* 4.3 10.5 - - + -
394G LEU* 4.1 22.2 - - + -
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Residues in contact with GLU 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G ALA 3.2 15.0 + - - +
278G GLN* 4.0 5.7 - - - +
279G PHE 3.2 0.6 - - - -
280G LEU* 1.3 79.6 - - - +
282G SER* 1.3 61.1 + - - +
283G ASN 3.2 3.7 + - - +
286G VAL* 5.1 3.2 - - - +
288G LYS* 6.4 0.2 - - - -
289G VAL* 3.7 24.1 + - + +
294G LEU* 3.6 21.3 - - - +
295G PRO* 5.9 1.6 - - - +
296G SER* 2.8 34.6 + - - -
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Residues in contact with SER 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G GLN 3.4 14.4 + - - -
279G PHE* 3.2 8.3 + - - -
280G LEU 3.2 0.6 - - - -
281G GLU* 1.3 77.0 - - - +
283G ASN* 1.3 59.5 + - - +
284G PRO* 3.8 5.4 - - - +
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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