Contacts of the helix formed by residues 346 - 368 (chain B) in PDB entry 4P3N
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 LEU 346 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A MET* 3.7 31.9 - - + +
422A HIS* 4.3 20.6 - - + +
425A ARG* 4.9 8.7 - - - +
434A LEU* 6.3 0.7 - - + -
327B GLY 5.6 0.2 - - - +
331B GLU* 3.5 41.1 - - + +
332B LEU 2.7 16.5 + - - +
333B TYR 4.8 1.6 - - - +
334B PHE* 4.0 22.4 - - + -
344B PHE 3.6 1.0 + - - -
345B PHE* 1.3 71.7 - - - +
347B PRO* 1.4 70.2 - - + +
348B LYS 2.8 13.8 + - - -
349B GLY 2.9 3.6 + - - -
350B ALA 2.9 17.5 + - - -
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Residues in contact with PRO 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A GLN* 3.6 48.7 - - + +
371A GLU 3.2 16.8 - - - +
372A VAL* 3.6 16.6 - - + -
434A LEU* 4.5 7.9 - - + -
346B LEU* 1.4 93.2 - - + +
348B LYS* 1.3 60.6 + - + +
350B ALA* 3.6 2.2 - - - +
351B TYR* 2.9 26.0 + - - +
647B MET* 5.0 4.8 - - + +
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Residues in contact with LYS 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A GLN* 5.2 10.7 - - - +
330B GLN 4.0 3.8 - - - +
331B GLU* 3.9 13.4 + - + +
332B LEU* 3.8 10.3 - - + -
346B LEU* 2.8 5.7 + - - +
347B PRO* 1.3 74.4 - - + +
349B GLY* 1.3 63.7 + - - +
350B ALA 3.1 1.1 - - - -
351B TYR* 3.0 8.7 + - - +
352B ILE* 3.0 26.5 + - - +
618B PRO* 3.5 29.5 + - + +
619B ARG* 3.1 54.3 - - - +
647B MET* 4.9 9.4 - - + +
649B ASP* 4.8 11.6 + - - -
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Residues in contact with GLY 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU* 3.6 29.7 + - - +
333B TYR* 5.0 0.4 - - - -
345B PHE* 3.7 19.2 - - - -
346B LEU 2.9 6.2 + - - -
348B LYS* 1.3 78.4 - - - +
350B ALA* 1.3 56.1 + - - +
352B ILE* 3.2 12.9 + - - +
353B TYR* 2.9 26.5 + - - +
601B ILE* 4.5 0.8 - - - +
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Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A GLU* 3.3 28.0 - - + +
372A VAL* 3.7 19.5 - - - -
373A VAL* 4.0 7.2 - - + +
345B PHE* 3.8 5.4 - - - +
346B LEU 2.9 13.3 + - - +
347B PRO 3.6 0.7 - - - +
349B GLY* 1.3 75.2 - - - +
351B TYR* 1.3 58.9 + - - +
353B TYR* 3.2 9.5 + - - +
354B ASN* 2.9 40.0 + - - +
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Residues in contact with TYR 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B PRO 2.9 16.1 + - - +
348B LYS* 3.2 12.1 - - - +
350B ALA* 1.3 77.1 - - - +
352B ILE* 1.3 57.6 + - - +
354B ASN* 3.5 5.8 + - + +
355B ALA* 2.9 33.9 + - + +
615B TRP 3.3 17.2 + - - -
616B LEU 3.7 17.3 - - - -
617B SER 3.2 27.4 - - - -
618B PRO* 3.9 8.1 - - + -
620B GLN* 3.4 18.0 + - - -
645B LYS 5.4 4.7 + - - -
647B MET* 3.8 34.5 - - + -
712B LYS* 5.6 1.9 - - - +
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Residues in contact with ILE 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU* 3.9 13.9 - - + -
333B TYR* 6.1 0.2 - - + -
348B LYS 3.0 12.1 + - - +
349B GLY* 3.2 11.4 + - - +
351B TYR* 1.3 74.8 - - - +
353B TYR* 1.3 65.3 + - - +
355B ALA* 3.2 6.4 + - - +
356B LEU* 2.9 35.5 + - + +
601B ILE* 4.4 13.0 - - + -
612B TRP* 3.8 41.1 - - + -
616B LEU* 3.6 33.2 - - + +
618B PRO* 3.7 21.3 - - + -
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Residues in contact with TYR 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A VAL* 4.1 19.1 - - + -
345B PHE* 3.7 30.1 - + - -
349B GLY 2.9 11.0 + - - +
350B ALA* 3.2 13.7 - - - +
352B ILE* 1.3 77.2 - - - +
354B ASN* 1.3 68.3 + - - +
356B LEU* 3.2 2.9 + - - +
357B ILE* 3.0 50.7 + - + +
457B ARG* 3.2 12.7 + - - -
459B GLN* 3.4 25.4 - - - +
597B VAL* 3.6 27.6 - - + +
598B GLU* 2.6 33.3 + - - -
601B ILE* 3.8 16.8 - - + +
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Residues in contact with ASN 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ARG* 3.5 28.8 + - - +
371A GLU* 3.6 32.6 + - - +
373A VAL* 5.4 4.3 - - - +
350B ALA* 2.9 20.6 + - - +
351B TYR* 4.0 5.6 - - + +
353B TYR* 1.3 89.0 - - - +
355B ALA* 1.3 56.5 + - - +
357B ILE* 3.8 10.9 - - - +
358B GLU* 2.9 30.8 + - - +
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Residues in contact with ALA 355 (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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351B TYR* 2.9 29.1 + - + +
352B ILE* 3.4 6.5 - - - +
353B TYR 3.2 0.2 - - - -
354B ASN* 1.3 74.1 - - - +
356B LEU* 1.3 59.4 + - - +
358B GLU* 3.3 6.9 + - - +
359B PHE* 2.9 28.1 + - - +
615B TRP* 4.0 23.8 - - + +
616B LEU* 4.0 15.5 - - + -
715B ARG* 4.9 1.2 + - - -
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ILE* 2.9 20.3 + - + +
353B TYR 3.6 5.8 - - - +
355B ALA* 1.3 75.8 - - - +
357B ILE* 1.3 65.3 + - - +
359B PHE* 3.1 9.1 + - + +
360B ILE* 3.0 27.0 + - - +
490B PHE* 3.7 32.5 - - + -
594B LEU* 4.3 15.2 - - + +
597B VAL* 4.4 16.4 - - + +
600B MET* 4.6 8.5 - - + -
601B ILE* 3.7 29.8 - - + -
604B LEU* 4.2 11.7 - - + -
615B TRP* 4.1 4.3 - - + -
616B LEU* 3.9 18.4 - - + -
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Residues in contact with ILE 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B TYR* 3.0 45.5 + - + +
354B ASN* 3.8 12.3 - - - +
356B LEU* 1.3 74.5 - - - +
358B GLU* 1.3 56.0 + - - +
360B ILE* 3.3 4.5 + - - +
361B ARG* 2.9 61.7 + - - +
437B PHE* 3.8 30.7 - - + -
459B GLN* 3.9 13.0 - - - +
594B LEU* 6.0 0.2 - - - -
597B VAL* 4.0 17.5 - - + -
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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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354B ASN 2.9 18.5 + - - +
355B ALA* 3.6 7.0 - - - +
357B ILE* 1.3 73.4 - - - +
359B PHE* 1.3 61.2 + - - +
361B ARG* 4.3 14.8 + - - +
362B SER* 2.9 28.2 + - - -
365B ARG* 2.9 38.6 + - - -
715B ARG* 4.2 9.2 - - - +
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Residues in contact with PHE 359 (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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355B ALA 2.9 13.0 + - - +
356B LEU* 3.2 11.9 - - + +
358B GLU* 1.3 74.0 - - - +
360B ILE* 1.3 71.0 + - + +
362B SER* 2.3 25.5 + - - -
363B GLU* 3.0 26.8 + - + +
485B THR* 5.3 0.9 - - + -
486B VAL* 3.6 44.6 - - + -
489B VAL* 3.5 33.7 - - + -
490B PHE* 4.4 11.4 - + - -
594B LEU* 5.8 0.4 - - + -
615B TRP* 4.1 14.8 - + + -
715B ARG* 3.2 46.3 - - - +
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Residues in contact with ILE 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LEU 3.0 16.1 + - - +
357B ILE* 3.6 6.5 - - - +
359B PHE* 1.3 79.0 - - + +
361B ARG* 1.3 56.6 + - - +
363B GLU* 3.2 8.6 + - - +
364B TYR* 2.9 61.6 + - + +
437B PHE* 3.6 14.6 - - + -
461B ASP* 3.9 15.9 - - + +
482B PHE* 5.0 5.4 - - + -
486B VAL* 4.6 22.2 - - + -
593B ILE* 5.0 3.4 - - + -
594B LEU* 3.6 37.0 - - + -
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Residues in contact with ARG 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ASN* 3.6 27.0 + - - +
361A ARG* 5.1 10.5 - - - +
357B ILE* 2.9 34.8 + - - +
358B GLU* 3.7 18.3 + - - +
360B ILE* 1.3 73.6 - - - +
362B SER* 1.3 60.8 + - - +
364B TYR* 3.0 11.6 + - + +
365B ARG* 2.9 50.3 + - + +
371B GLU* 2.8 40.5 + - - +
437B PHE* 3.5 26.5 - - + +
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Residues in contact with SER 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B GLU* 2.9 16.3 + - - -
359B PHE* 2.3 35.2 + - - -
361B ARG* 1.3 75.2 - - - +
363B GLU* 1.3 64.1 + - - +
365B ARG* 3.7 25.8 + - - +
366B LYS* 3.5 27.7 + - - +
715B ARG* 3.7 17.1 + - - -
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Residues in contact with GLU 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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359B PHE* 3.0 33.0 + - + +
360B ILE* 3.6 5.8 - - - +
361B ARG 3.1 0.2 - - - -
362B SER* 1.3 84.1 + - - +
364B TYR* 1.3 59.5 + - - +
366B LYS* 3.2 30.6 + - - +
367B ARG* 2.9 63.1 + - - +
482B PHE* 3.3 27.8 - - + -
485B THR* 3.9 17.5 - - - +
486B VAL* 4.7 3.8 - - + -
715B ARG* 5.6 0.9 + - - -
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Residues in contact with TYR 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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360B ILE* 2.9 38.0 + - + +
361B ARG* 3.0 18.8 + - + +
363B GLU* 1.3 76.8 - - - +
365B ARG* 1.3 62.3 + - + +
367B ARG 3.2 0.2 + - - -
368B GLY* 3.1 6.9 + - - -
369B PHE* 3.0 61.0 + + + +
371B GLU* 5.2 5.4 - - + +
435B ALA* 3.4 27.0 - - + +
436B ASP 5.5 0.4 - - - -
437B PHE* 3.9 16.8 - + - -
461B ASP* 4.0 16.5 + - - +
462B ASP 4.1 2.3 + - - -
463B ALA* 4.2 3.1 - - + +
482B PHE* 3.7 27.8 - + - -
591B ARG* 3.8 23.4 + - - -
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Residues in contact with ARG 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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639A GLN* 5.8 0.7 + - - -
642A HIS* 3.3 42.3 + - + +
643A ASP* 5.0 2.3 - - - +
645A LYS* 4.6 27.5 - - - +
358B GLU* 2.9 30.5 + - - -
361B ARG* 2.9 30.8 + - + +
362B SER* 3.7 23.1 - - - +
363B GLU 3.3 0.4 - - - -
364B TYR* 1.3 76.7 - - + +
366B LYS* 1.3 62.2 + - + +
368B GLY* 4.3 2.6 + - - -
369B PHE 4.9 3.1 - - - +
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Residues in contact with LYS 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A GLN* 4.8 10.0 + - - +
643A ASP* 4.6 21.5 - - + +
362B SER* 3.5 16.8 - - - +
363B GLU* 3.2 35.4 + - - +
364B TYR 3.1 0.6 - - - -
365B ARG* 1.3 80.1 - - + +
367B ARG* 1.3 65.8 + - + +
368B GLY 3.5 0.6 + - - -
485B THR* 6.2 0.2 - - - +
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Residues in contact with ARG 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B GLU* 2.9 41.2 + - - +
364B TYR 3.2 0.6 + - - -
366B LYS* 1.3 84.5 - - + +
368B GLY* 1.3 60.9 + - - +
369B PHE* 3.5 24.1 - - + -
433B ARG* 4.1 11.1 + - - -
478B GLY* 4.0 5.5 + - - -
481B ASP* 2.5 33.3 + - - +
482B PHE* 3.4 47.4 - - - +
485B THR* 3.0 28.1 + - - +
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Residues in contact with GLY 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A HIS* 5.8 5.2 - - - -
364B TYR 3.1 3.5 + - - -
365B ARG 4.3 3.4 + - - -
366B LYS 3.5 3.4 + - - -
367B ARG* 1.3 78.2 - - - +
369B PHE* 1.3 61.4 + - - +
370B GLN* 4.0 6.6 + - - +
433B ARG* 3.2 33.2 + - - +
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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
------------------------------------------------------------
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