Contacts of the helix formed by residues 357 - 377 (chain B) in PDB entry 5IYB
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 CYS 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351B VAL* 3.7 21.3 - - - +
352B GLY* 4.4 8.1 - - - -
354B SER* 3.0 13.6 + - - +
356B PHE* 1.3 87.0 - - - +
358B GLU* 1.3 62.6 + - - +
359B THR 3.4 2.9 - - - +
360B LYS* 3.1 43.3 + - + +
361B LYS* 3.3 27.2 + - - +
554B GLU* 5.8 1.3 - - - -
116S GLY 4.8 5.2 - - - -
117S GLY* 5.5 1.3 - - - -
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Residues in contact with GLU 358 (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 LEU* 4.1 34.6 - - + +
340B LYS* 4.4 15.0 + - - +
343B LEU 5.9 0.4 - - - +
344B GLN* 3.9 33.6 + - + +
354B SER 3.6 3.0 + - - +
355B ASP* 3.1 36.9 + - - +
356B PHE 3.7 0.2 - - - -
357B CYS* 1.3 77.6 - - - +
359B THR* 1.3 62.4 + - - +
361B LYS* 3.4 23.6 - - + +
362B ALA* 3.5 6.1 + - - +
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Residues in contact with THR 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 4.3 22.0 - - + -
287B HIS* 4.1 0.6 - - - +
355B ASP 4.6 1.4 + - - -
357B CYS* 4.4 0.2 - - - +
358B GLU* 1.3 78.3 - - - +
360B LYS* 1.3 62.2 + - - +
362B ALA* 3.3 19.2 + - - +
363B TYR* 3.5 20.5 + - + -
554B GLU* 4.0 23.7 + - + +
113S ILE* 3.8 25.2 - - + +
145S ASN* 5.7 3.3 + - - +
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Residues in contact with LYS 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B VAL* 4.2 16.0 + - + +
356B PHE 5.3 0.4 - - - -
357B CYS* 3.1 43.5 + - - +
358B GLU 3.4 0.2 - - - -
359B THR* 1.3 77.1 - - - +
361B LYS* 1.3 63.0 + - - +
363B TYR* 3.2 21.6 + - - +
364B PHE* 3.3 11.8 + - - +
552B ASN* 5.4 8.1 - - - +
553B LEU* 3.8 28.4 - - + +
554B GLU* 4.9 12.9 + - + +
572B CYS* 5.6 7.0 - - - -
573B TRP 4.6 8.7 - - - +
574B VAL* 5.9 2.5 - - - +
117S GLY* 5.7 6.7 - - - +
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Residues in contact with LYS 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 4.9 5.8 - - + -
343B LEU 3.5 12.5 + - - +
344B GLN* 2.8 30.5 + - - +
347B MET* 3.1 38.8 + - + +
348B LEU* 4.0 24.9 - - + +
351B VAL* 3.6 17.7 - - + +
352B GLY 3.2 18.7 + - - +
354B SER 5.8 1.6 + - - -
357B CYS 3.3 12.2 + - - +
358B GLU* 3.4 18.3 - - + +
360B LYS* 1.3 77.4 - - - +
362B ALA* 1.3 64.6 + - - +
364B PHE* 3.1 5.5 + - - +
365B LEU* 3.0 22.8 + - + +
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Residues in contact with ALA 362 (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 PHE* 3.7 9.8 - - + -
276B LEU* 3.8 27.0 - - + +
278B PHE* 3.7 18.8 - - + -
287B HIS* 3.0 20.9 + - + +
358B GLU 3.5 4.2 + - - +
359B THR* 3.3 15.1 + - - +
361B LYS* 1.3 79.8 - - - +
363B TYR* 1.3 60.7 + - - +
365B LEU* 3.4 3.9 + - - +
366B GLY 3.2 15.4 + - - -
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Residues in contact with TYR 363 (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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287B HIS* 3.0 47.1 + + - +
290B TYR* 4.3 3.1 + + - -
359B THR* 3.5 18.7 + - + -
360B LYS* 3.2 13.7 + - - +
362B ALA* 1.3 75.2 - - - +
364B PHE* 1.3 58.6 + - - +
366B GLY* 3.2 3.8 + - - -
367B TYR 3.1 20.6 + - - -
553B LEU* 3.7 49.0 + - + -
554B GLU* 5.5 3.6 - - + -
556B ILE* 3.8 7.1 + - + +
558B PRO* 3.2 42.1 - - + +
573B TRP* 3.8 36.7 - + + -
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Residues in contact with PHE 364 (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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203B ASN 5.2 1.1 - - - -
204B THR* 5.9 0.2 - - - -
205B VAL* 5.2 6.7 - - + -
221B CYS* 4.2 12.1 - - - -
348B LEU* 3.5 38.6 - - + -
350B HIS* 4.1 15.3 - + - -
351B VAL* 4.3 16.2 - - + -
360B LYS 3.3 7.6 + - - +
361B LYS 3.1 11.2 + - - +
363B TYR* 1.3 77.5 - - - +
365B LEU* 1.3 63.4 + - - +
367B TYR* 3.3 21.9 + + + +
368B MET* 3.0 38.6 + - + +
568B PHE* 4.9 4.9 - + - -
571B GLY 3.7 20.0 - - - -
572B CYS* 5.5 0.2 - - - -
573B TRP* 4.5 24.6 - - + -
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Residues in contact with LEU 365 (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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235B ILE* 5.2 7.4 - - + -
237B VAL* 5.3 2.0 - - + -
260B LEU* 6.2 1.1 - - + -
269B ILE* 4.3 15.3 - - + -
272B VAL* 4.0 20.0 - - + -
273B PHE* 3.6 25.1 - - + -
276B LEU* 3.8 29.2 - - + -
347B MET* 4.2 16.4 - - + -
348B LEU* 4.1 18.8 - - + -
361B LYS 3.0 15.0 + - - +
362B ALA 3.7 3.4 - - - +
363B TYR 3.4 0.4 - - - -
364B PHE* 1.3 72.6 - - - +
366B GLY* 1.3 61.2 + - - +
368B MET* 3.0 18.8 + - + +
369B VAL* 2.9 31.0 + - - +
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Residues in contact with GLY 366 (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 PHE* 3.5 12.9 - - - -
287B HIS 3.8 18.2 - - - -
288B ILE* 4.3 9.6 - - - +
290B TYR* 4.0 6.3 - - - -
362B ALA 3.2 10.8 + - - -
363B TYR 3.2 5.1 + - - -
365B LEU* 1.3 76.5 - - - +
367B TYR* 1.3 57.5 + - - +
369B VAL* 3.4 2.4 + - - +
370B HIS* 2.8 30.5 + - - +
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Residues in contact with TYR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL* 3.5 19.5 - - + -
290B TYR* 3.7 16.7 + + - +
363B TYR 3.1 12.2 + - - +
364B PHE* 3.5 23.6 - + + +
365B LEU 3.2 0.4 - - - -
366B GLY* 1.3 77.1 - - - +
368B MET* 1.3 57.6 + - - +
370B HIS* 4.1 9.9 - + + -
371B ARG* 2.4 72.0 + - + +
566B LYS* 4.5 16.2 - - + -
568B PHE* 3.6 34.8 - + - -
573B TRP* 4.3 8.3 - + + -
611B GLU* 3.0 24.7 + - - -
613B ARG* 4.0 1.8 + - - -
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Residues in contact with MET 368 (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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205B VAL* 4.2 22.3 - - + +
207B VAL* 5.5 0.3 - - - +
219B GLY* 4.1 15.2 - - - +
221B CYS* 3.6 26.0 - - + -
235B ILE* 3.9 21.3 - - + -
237B VAL* 3.5 34.8 - - + +
348B LEU* 4.8 2.7 - - - -
364B PHE* 3.0 41.3 + - + +
365B LEU* 3.0 17.7 + - - +
367B TYR* 1.3 76.6 - - + +
369B VAL* 1.3 62.9 + - - +
371B ARG* 4.2 4.0 - - - +
372B LEU* 3.2 23.2 + - - +
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Residues in contact with VAL 369 (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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237B VAL* 4.7 6.7 - - + -
256B ILE* 4.0 23.6 - - + -
269B ILE* 3.9 29.6 - - + -
273B PHE* 4.5 6.1 - - + -
288B ILE* 4.3 27.4 - - + -
301B VAL* 5.8 4.0 - - + -
365B LEU 2.9 19.2 + - - +
366B GLY* 3.7 7.4 - - - +
368B MET* 1.3 73.3 - - + +
370B HIS* 1.3 62.0 + - - +
372B LEU* 3.2 5.8 + - - +
373B LEU* 2.8 38.2 + - + +
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Residues in contact with HIS 370 (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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288B ILE* 3.0 23.5 + - - +
289B ILE* 4.2 10.5 - - + -
290B TYR* 3.4 30.1 - + + -
297B MET* 3.9 15.0 - - + +
366B GLY 2.8 21.8 + - - +
367B TYR* 3.7 13.5 - + - +
369B VAL* 1.3 73.6 - - - +
371B ARG* 1.3 62.7 + - + +
373B LEU* 3.2 5.7 + - - +
374B LEU* 2.8 68.1 + - + +
566B LYS* 5.4 4.0 + - - -
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Residues in contact with ARG 371 (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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205B VAL* 3.2 27.9 + - + +
206B TYR* 4.6 0.8 - - - +
207B VAL* 3.4 20.2 - - + +
367B TYR* 2.4 80.2 + - + +
368B MET* 4.2 4.3 - - - +
370B HIS* 1.3 77.2 - - + +
372B LEU* 1.3 60.7 + - - +
374B LEU* 3.7 10.7 + - - +
375B ALA* 3.4 15.2 + - - +
380B ARG* 2.9 60.8 - - - +
383B ASP* 3.2 15.0 + - - -
609B GLU* 4.4 4.5 - - - -
611B GLU* 4.4 1.0 + - - -
613B ARG* 4.0 11.9 - - - +
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Residues in contact with LEU 372 (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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207B VAL* 3.8 25.5 - - + +
217B TYR* 3.8 21.9 - - + -
218B THR 3.9 16.4 - - - +
219B GLY* 3.9 2.7 - - - +
237B VAL* 3.5 33.0 - - + +
238B SER 4.2 1.3 - - - -
239B MET* 3.9 27.4 - - + +
256B ILE* 4.4 11.0 - - + -
368B MET 3.2 19.0 + - - +
369B VAL 3.2 4.2 + - - +
371B ARG* 1.3 75.1 - - - +
373B LEU* 1.3 64.2 + - - +
375B ALA* 3.3 4.5 + - - +
376B ALA* 3.2 19.8 + - - +
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Residues in contact with LEU 373 (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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239B MET* 5.9 3.4 - - + -
288B ILE* 5.7 0.4 - - + -
297B MET* 3.3 51.6 - - + +
300B MET* 3.5 33.7 - - + -
301B VAL* 5.0 8.1 - - + +
369B VAL* 2.8 27.3 + - + +
370B HIS 3.7 2.9 - - - +
372B LEU* 1.3 73.7 - - - +
374B LEU* 1.3 66.2 + - + +
376B ALA* 3.1 7.1 + - - +
377B LEU* 3.0 44.4 + - + +
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Residues in contact with LEU 374 (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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297B MET* 4.9 3.6 - - - -
370B HIS* 2.8 59.5 + - + +
371B ARG* 3.8 10.5 - - - +
372B LEU 3.2 0.2 - - - -
373B LEU* 1.3 89.7 - - + +
375B ALA* 1.3 60.5 + - - +
377B LEU* 3.7 2.5 + - + +
378B GLY 3.3 2.1 + - - -
379B ARG* 3.2 46.6 + - + +
380B ARG* 3.3 20.6 + - + +
609B GLU* 4.8 13.7 - - - +
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Residues in contact with ALA 375 (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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207B VAL* 3.5 33.0 - - + -
217B TYR* 4.4 12.4 + - + -
371B ARG 3.4 5.6 + - - +
372B LEU 3.3 4.7 + - - +
374B LEU* 1.3 78.9 - - - +
376B ALA* 1.3 58.3 + - - +
378B GLY* 3.0 17.8 + - - -
380B ARG* 3.7 17.8 - - + +
381B GLU 5.3 1.8 - - - +
382B LEU* 3.6 20.5 - - + +
102I ALA* 5.8 0.3 - - - +
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Residues in contact with ALA 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TYR* 3.5 36.8 + - + -
239B MET* 5.0 7.0 - - + -
300B MET* 3.7 24.0 - - + +
372B LEU* 3.2 11.8 + - + +
373B LEU* 3.1 11.7 + - - +
375B ALA* 1.3 74.9 - - - +
377B LEU* 1.3 66.8 + - - +
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Residues in contact with LEU 377 (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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294B ASP* 4.3 3.1 - - - +
296B GLU* 5.2 10.5 - - + +
297B MET* 5.0 6.1 - - + +
300B MET* 4.1 17.5 - - + -
373B LEU* 3.0 36.2 + - + +
374B LEU* 4.3 2.5 - - + +
375B ALA 3.4 0.2 - - - -
376B ALA* 1.3 78.4 - - - +
378B GLY* 1.3 59.8 + - - +
379B ARG* 3.5 52.5 + - + +
103I ARG* 4.0 20.4 - - - +
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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
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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