Contacts of the helix formed by residues 347 - 371 (chain A) in PDB entry 4L6V
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 SER 347 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A ILE* 3.1 16.1 + - - +
344A LEU* 4.8 0.9 - - - -
346A THR* 1.3 80.6 - - - +
348A TRP* 1.3 63.3 + - - +
349A HIS* 3.7 3.1 + - - +
350A ALA* 3.3 30.8 + - - +
351A GLN* 3.4 11.6 + - - +
411A PHE* 3.5 10.1 - - - -
415A ASP* 2.9 40.3 + - - +
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Residues in contact with TRP 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 5.8 0.9 - - - +
65A LEU* 3.9 21.5 - - + +
68A VAL* 4.7 3.4 - - + -
69A SER* 2.9 43.4 + - - +
72A ILE* 3.6 45.4 - - + +
73A PHE* 5.8 1.3 - - + -
76A HIS* 5.2 7.2 - + - -
190A PHE* 4.7 19.5 - + + -
346A THR 5.0 2.0 - - - -
347A SER* 1.3 70.9 + - - +
349A HIS* 1.3 66.1 + - + +
351A GLN* 3.0 14.7 + - + +
352A LEU* 2.8 29.9 + - - +
415A ASP* 4.6 2.2 + - - -
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Residues in contact with HIS 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP* 5.7 0.7 - - - -
59A ASP* 3.0 37.5 + - - -
347A SER* 3.3 6.4 + - - +
348A TRP* 1.3 81.9 - - + +
350A ALA* 1.3 58.0 + - - +
352A LEU* 4.3 7.8 - - + +
353A ALA* 3.0 30.3 + - - +
407A HIS* 3.0 48.1 + + - +
410A ILE* 3.3 33.6 - - + +
411A PHE* 4.2 10.5 - - - +
414A ARG* 3.9 7.2 + - - -
415A ASP* 4.4 9.4 - - - +
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Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ILE* 3.6 20.6 - - + +
344A LEU* 3.8 19.4 - - + +
347A SER* 3.3 22.4 + - - +
349A HIS* 1.3 79.8 - - - +
351A GLN* 1.3 62.7 + - - +
353A ALA* 3.6 4.9 + - - +
354A ILE* 3.6 16.8 + - - +
411A PHE* 3.8 23.3 - - + +
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Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A VAL* 5.4 9.1 - - - +
344A LEU* 2.7 53.5 + - + +
347A SER 3.4 8.9 + - - +
348A TRP* 3.0 19.1 + - + +
350A ALA* 1.3 77.9 - - - +
352A LEU* 1.3 60.5 + - - +
354A ILE* 3.1 6.2 + - - +
355A ASN* 2.9 55.1 + - - +
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TRP 2.8 20.6 + - - +
349A HIS* 4.0 8.5 - - + +
351A GLN* 1.3 72.6 - - - +
353A ALA* 1.3 57.9 + - - +
355A ASN* 4.4 10.1 - - + +
356A LEU* 2.9 52.6 + - + +
407A HIS* 3.2 45.8 - - + +
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Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A HIS 3.0 19.9 + - - +
350A ALA* 3.7 7.6 - - - +
352A LEU* 1.3 77.1 - - - +
354A ILE* 1.3 62.9 + - + +
357A ALA* 3.3 21.8 + - - +
404A ALA* 3.6 18.0 - - - +
407A HIS* 4.2 5.8 - - - +
408A GLY* 3.5 31.9 - - - +
411A PHE* 5.8 0.2 - - + -
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Residues in contact with ILE 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 3.8 36.8 - - + -
350A ALA 3.6 5.5 + - - +
351A GLN* 3.1 8.3 + - - +
353A ALA* 1.3 76.8 - - + +
355A ASN* 1.3 73.3 + - - +
357A ALA* 3.1 8.5 + - - +
358A LEU* 3.1 35.2 + - + +
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Residues in contact with ASN 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A GLN* 2.9 44.5 + - - +
352A LEU* 4.0 11.5 - - + +
354A ILE* 1.3 84.6 - - - +
356A LEU* 1.3 59.2 + - + +
358A LEU* 4.3 2.8 - - - +
359A LEU* 2.9 34.7 + - + +
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Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A LEU* 2.9 35.0 + - + +
355A ASN* 1.3 77.2 - - + +
357A ALA* 1.3 57.7 + - - +
359A LEU* 4.5 7.9 - - + -
360A GLY* 2.7 33.6 + - - -
400A LEU* 3.3 42.7 - - + +
403A GLY* 3.4 33.7 - - - +
404A ALA* 3.8 9.2 - - - -
407A HIS* 4.1 16.2 - - + +
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Residues in contact with ALA 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A ALA 3.3 12.3 + - - +
354A ILE* 3.1 11.8 + - - +
356A LEU* 1.3 78.3 - - - +
358A LEU* 1.3 67.7 + - + +
361A SER* 3.2 29.1 + - - -
401A ILE* 3.5 7.8 - - - +
404A ALA* 3.3 16.5 - - + +
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Residues in contact with LEU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A ILE* 3.1 29.3 + - + +
355A ASN* 4.3 3.1 - - - +
357A ALA* 1.3 84.2 - - + +
359A LEU* 1.3 56.4 + - - +
360A GLY 3.1 1.6 - - - -
361A SER* 3.6 6.6 - - - -
362A LEU* 2.7 37.4 + - - +
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Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A ASN* 2.9 21.9 + - + +
356A LEU* 4.1 7.4 - - + +
358A LEU* 1.3 76.1 - - - +
360A GLY* 1.3 56.8 + - - +
362A LEU* 3.4 22.3 + - + +
363A THR* 2.8 36.4 + - - +
400A LEU* 4.0 24.2 - - + -
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Residues in contact with GLY 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU 2.7 22.8 + - - -
359A LEU* 1.3 71.5 - - - +
361A SER* 1.3 63.3 + - - +
362A LEU 3.3 0.2 + - - -
363A THR 3.4 5.0 + - - -
364A ILE* 3.4 5.2 + - - +
397A GLY* 3.1 26.5 - - - +
400A LEU* 3.5 25.5 - - - +
401A ILE* 3.5 8.7 - - - -
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Residues in contact with SER 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ALA 3.2 21.1 + - - -
358A LEU* 3.8 9.2 - - - -
360A GLY* 1.3 76.0 - - - +
362A LEU* 1.3 62.0 + - - +
364A ILE* 3.4 14.3 + - - +
365A ILE* 3.2 29.0 + - - +
401A ILE* 3.4 10.7 - - - +
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A LEU 2.7 17.8 + - - +
359A LEU* 3.5 24.0 - - + +
360A GLY 3.1 0.2 - - - -
361A SER* 1.3 74.6 - - - +
363A THR* 1.3 59.4 + - - +
364A ILE 3.0 1.6 - - - -
365A ILE* 2.7 44.4 + - + +
366A VAL* 2.8 24.7 + - + +
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Residues in contact with THR 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A LEU* 2.8 23.2 + - - +
360A GLY 3.4 0.4 + - - -
362A LEU* 1.3 77.0 - - - +
364A ILE* 1.3 60.1 + - - +
366A VAL* 3.4 12.0 - - + +
367A ALA 3.4 14.4 + - - -
393A HIS* 3.3 46.2 - - + +
396A ILE* 4.1 10.7 - - + +
397A GLY* 3.7 19.3 - - - +
400A LEU* 4.0 10.6 - - - +
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Residues in contact with ILE 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A GLY 3.4 12.1 + - - +
361A SER* 3.4 13.9 + - - +
362A LEU 3.0 0.6 - - - -
363A THR* 1.3 76.7 - - - +
365A ILE* 1.3 65.3 + - + +
366A VAL 3.1 0.2 - - - -
367A ALA* 3.1 14.1 + - - +
368A GLN* 3.1 17.9 + - + +
393A HIS 4.4 2.0 - - - -
394A MET* 3.6 39.7 - - + +
397A GLY* 4.0 12.6 - - - +
398A GLY* 4.5 1.8 - - - +
401A ILE* 3.7 30.1 - - + -
602A LEU* 5.7 4.7 - - + -
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Residues in contact with ILE 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A SER* 3.2 19.3 + - - +
362A LEU* 2.7 33.0 + - + +
364A ILE* 1.3 75.0 - - + +
366A VAL* 1.3 58.5 + - - -
368A GLN* 4.9 2.5 - - - -
369A HIS* 3.1 54.7 + - + +
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A LEU* 2.8 28.9 + - + +
363A THR* 3.4 15.7 - - + +
364A ILE 3.1 0.2 - - - -
365A ILE* 1.3 76.7 - - + +
367A ALA* 1.3 57.5 + - - +
369A HIS* 3.4 3.1 + - - +
370A MET* 2.8 49.5 + - + +
393A HIS* 3.6 29.2 - - + +
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Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A THR 3.4 2.9 + - - +
364A ILE 3.1 9.9 + - - +
366A VAL* 1.3 82.8 - - - +
368A GLN* 1.3 62.6 + - - +
369A HIS 3.1 1.6 + - - -
370A MET* 3.4 10.2 + - - +
371A TYR* 3.5 8.7 + - - +
390A PHE* 3.3 54.2 - - + +
393A HIS* 4.0 15.2 - - + +
394A MET* 4.2 10.3 - - + +
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Residues in contact with GLN 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A ILE* 3.1 19.2 + - + +
365A ILE* 4.3 4.5 - - - +
367A ALA* 1.3 77.9 - - - +
369A HIS* 1.3 68.8 + - + +
371A TYR* 3.1 45.1 + - - -
372A ALA* 4.1 6.6 - - - +
390A PHE* 4.1 10.1 - - + -
394A MET* 4.0 24.6 - - + +
605A VAL* 5.4 2.1 - - - +
609A PHE* 5.7 0.4 - - - -
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Residues in contact with HIS 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A ILE* 3.1 40.9 + - + +
366A VAL* 4.0 2.9 - - - +
367A ALA 3.1 0.6 - - - -
368A GLN* 1.3 91.6 - - + +
370A MET* 1.3 64.4 + - + +
371A TYR 3.2 1.8 - - - -
372A ALA* 4.1 0.4 - - - -
373A MET* 3.2 51.4 + - + +
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Residues in contact with MET 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A VAL* 2.8 42.4 + - + +
367A ALA* 3.4 5.1 + - - +
369A HIS* 1.3 79.2 - - + +
371A TYR* 1.3 57.6 + - - +
373A MET 4.2 4.7 - - - -
374A PRO* 3.5 21.5 - - - +
375A PRO* 3.8 29.5 - - + +
376A TYR* 3.9 21.8 - - + -
379A GLN* 3.7 20.3 + - - +
386A GLN* 4.4 1.8 - - - +
389A LEU* 4.3 19.1 - - + -
390A PHE* 6.6 0.2 - - - -
393A HIS* 4.5 13.7 - - - -
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Residues in contact with TYR 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A ALA 3.5 10.7 + - - +
368A GLN* 3.1 57.9 + - - -
369A HIS 3.2 0.8 - - - -
370A MET* 1.3 78.1 - - - +
372A ALA* 1.3 77.2 + - + +
373A MET 3.3 0.6 + - - -
374A PRO* 3.6 4.2 - - - +
386A GLN* 3.1 33.7 + - - +
390A PHE* 4.2 4.5 - + + -
508A ALA* 5.4 1.4 - - - +
522A MET* 3.3 14.6 - - + +
525A ILE* 4.0 28.5 - - + +
609A PHE* 3.6 37.0 - + + -
613A MET* 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
------------------------------------------------------------
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