Contacts of the helix formed by residues 387 - 408 (chain A) in PDB entry 1ZVR
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 HIS 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A SER* 3.4 4.9 - - - -
365A LYS* 5.0 7.8 + - - -
383A LEU 3.7 1.3 + - - -
384A GLU* 3.2 20.1 + - + -
385A SER* 3.1 27.1 + - - -
386A THR* 1.3 77.4 + - - +
388A TRP* 1.3 65.1 + - - +
389A LEU 3.6 1.6 - - - -
390A GLU* 3.2 21.1 + - + +
391A HIS* 2.9 42.5 + - + +
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Residues in contact with TRP 388 (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 MET 3.9 8.3 - - - -
362A SER* 3.4 21.8 - - - +
363A LEU* 3.6 37.0 - - + -
366A LEU* 3.9 24.7 - - + -
383A LEU* 4.5 2.6 + - + -
386A THR* 3.2 17.6 + - - +
387A HIS* 1.3 77.7 - - - +
389A LEU* 1.3 69.5 + - + +
390A GLU 2.9 1.4 + - - -
391A HIS* 3.0 15.1 + + - +
392A ILE* 3.0 26.9 + - + +
478A PRO* 4.0 13.0 - - + -
481A LEU* 4.4 8.5 - - + -
482A GLN* 3.6 39.5 - - + -
485A ASP* 3.2 11.5 + - - -
575A LEU* 4.5 10.3 - - + -
580A TYR* 3.0 38.7 + + - -
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Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LEU* 3.4 41.3 + - + +
386A THR* 5.1 0.2 + - - -
388A TRP* 1.3 88.4 - - + +
390A GLU* 1.3 56.0 + - - +
392A ILE* 3.6 9.3 - - + +
393A LYS* 2.9 21.1 + - - +
485A ASP* 5.6 0.9 - - - +
489A GLN* 4.3 8.5 - - - +
570A MET* 3.3 35.0 - - + +
573A LEU* 4.1 13.8 - - + +
574A GLU* 3.4 28.9 - - - +
575A LEU* 4.1 18.6 - - + +
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Residues in contact with GLU 390 (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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387A HIS* 3.3 28.2 - - + +
388A TRP 3.0 0.2 - - - -
389A LEU* 1.3 78.0 - - - +
391A HIS* 1.3 69.2 + - + +
393A LYS* 3.2 31.8 + - - +
394A LEU* 2.9 42.2 + - + +
570A MET* 4.2 14.8 - - - +
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Residues in contact with HIS 391 (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 HIS* 4.3 16.0 + + - -
358A VAL* 3.6 30.7 - - + +
359A MET* 3.3 25.0 - - + +
362A SER* 3.3 25.7 + - - -
387A HIS* 2.9 39.6 + + + +
388A TRP* 3.0 6.9 + - - +
390A GLU* 1.3 78.8 - - + +
392A ILE* 1.3 63.4 + - - +
394A LEU* 3.2 11.9 + - + +
395A ILE* 3.0 30.2 + - - +
482A GLN* 3.7 20.2 - - - +
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Residues in contact with ILE 392 (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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388A TRP* 3.0 34.1 + - + +
389A LEU* 3.6 13.5 - - + +
391A HIS* 1.3 77.1 - - - +
393A LYS* 1.3 60.8 + - - +
395A ILE* 3.4 1.5 + - - -
396A LEU* 3.1 27.6 + - + +
482A GLN* 3.9 25.1 - - + +
485A ASP* 3.6 40.4 - - + +
486A CYS* 3.7 19.3 - - - -
489A GLN* 4.1 18.2 - - + +
573A LEU* 4.5 6.3 - - + -
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Residues in contact with LYS 393 (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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389A LEU 2.9 19.0 + - - +
390A GLU* 3.5 32.8 + - - +
391A HIS 3.1 0.4 - - - -
392A ILE* 1.3 75.8 - - - +
394A LEU* 1.3 72.1 + - + +
396A LEU* 3.3 0.8 + - - -
397A ALA* 2.8 37.4 + - + +
568A ALA* 3.4 38.0 - - + +
569A SER* 3.8 3.4 - - - +
570A MET* 4.6 13.5 - - + +
573A LEU* 3.6 15.0 - - + -
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Residues in contact with LEU 394 (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 LEU 4.3 14.2 - - - +
352A ASP* 3.5 26.2 - - + +
353A ILE* 3.8 21.3 - - + +
354A HIS* 5.5 3.8 - - + -
390A GLU* 2.9 42.0 + - + +
391A HIS* 3.8 12.8 - - - +
393A LYS* 1.3 87.8 - - + +
395A ILE* 1.3 56.9 + - - +
397A ALA* 3.8 6.1 - - + +
398A GLY* 2.9 25.6 + - - -
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Residues in contact with ILE 395 (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 ILE* 3.9 28.0 - - + -
359A MET* 4.6 1.3 - - + -
391A HIS 3.0 22.3 + - - +
392A ILE* 3.8 6.3 - - - +
394A LEU* 1.3 76.8 - - - +
396A LEU* 1.3 57.7 + - - +
398A GLY* 3.3 2.1 + - - -
399A ALA* 3.0 25.1 + - - +
426A GLN* 3.3 40.2 - - + +
427A LEU* 3.7 6.7 - - + +
430A LEU* 3.6 25.6 - - + -
482A GLN* 3.3 33.9 - - + +
483A PHE* 5.9 0.4 - - - -
486A CYS* 3.8 7.6 - - - -
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Residues in contact with LEU 396 (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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392A ILE* 3.1 17.6 + - + +
393A LYS 3.9 2.5 - - - +
395A ILE* 1.3 73.9 - - - +
397A ALA* 1.3 61.5 + - - +
399A ALA* 3.2 4.2 + - - +
400A LEU* 2.8 33.0 + - - +
430A LEU* 4.5 6.5 - - + -
434A MET* 3.9 24.4 - - + +
486A CYS* 3.8 32.1 - - + +
489A GLN* 4.0 21.3 - - + -
490A MET* 4.2 13.0 - - + -
493A GLN* 6.0 0.2 - - - +
566A PRO* 4.4 11.4 - - + -
567A VAL 5.6 0.2 - - - +
568A ALA* 4.2 11.9 - - + -
573A LEU* 3.9 28.3 - - + -
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Residues in contact with ALA 397 (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 LEU* 5.6 0.2 - - - -
393A LYS* 2.8 24.9 + - + +
394A LEU* 3.8 11.7 - - + +
396A LEU* 1.3 76.5 - - - +
398A GLY* 1.3 57.3 + - - +
400A LEU* 3.3 6.7 + - - +
401A ARG* 3.0 36.1 + - + +
568A ALA* 3.7 17.4 - - + +
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Residues in contact with GLY 398 (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 LEU* 3.9 30.9 - - - +
394A LEU 2.9 17.1 + - - -
395A ILE 3.7 2.0 - - - -
397A ALA* 1.3 75.1 - - - +
399A ALA* 1.3 63.8 + - - +
401A ARG* 3.2 4.3 + - - +
402A ILE* 3.2 26.2 + - - +
427A LEU* 3.7 9.0 - - - -
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Residues in contact with ALA 399 (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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395A ILE 3.0 14.4 + - - +
396A LEU 3.6 7.4 - - - +
398A GLY* 1.3 74.2 - - - +
400A LEU* 1.3 57.5 + - - +
402A ILE* 3.2 6.4 + - - +
403A ALA* 2.9 29.3 + - - +
427A LEU* 3.5 16.4 - - + +
430A LEU* 3.5 33.9 - - + -
431A ALA* 3.7 9.3 - - - +
434A MET* 3.7 10.3 - - + -
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Residues in contact with LEU 400 (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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396A LEU 2.8 17.9 + - - +
397A ALA* 3.4 6.3 - - - +
399A ALA* 1.3 74.0 - - - +
401A ARG* 1.3 66.9 + - + +
403A ALA* 3.1 1.9 + - - +
404A ASP* 2.8 27.6 + - + +
434A MET* 3.8 14.1 - - + +
565A TYR* 3.7 30.5 - - + -
566A PRO* 3.1 44.6 - - + +
567A VAL* 4.7 0.4 - - - -
568A ALA* 4.2 20.6 - - + +
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Residues in contact with ARG 401 (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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317A PHE* 4.9 7.1 - - - -
319A PHE* 3.9 19.2 - - + -
349A VAL* 3.4 39.8 - - - +
351A LEU* 4.3 12.9 - - - +
397A ALA* 3.0 22.2 + - + +
398A GLY* 3.2 7.4 + - - +
400A LEU* 1.3 75.2 - - + +
402A ILE* 1.3 63.2 + - - +
404A ASP* 4.0 4.6 - - - +
405A LYS* 3.1 28.5 + - - +
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Residues in contact with ILE 402 (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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281A ILE* 4.3 10.5 - - + -
319A PHE* 3.7 33.9 - - + -
351A LEU* 4.5 0.7 - - + -
398A GLY 3.2 15.7 + - - +
399A ALA* 3.5 7.4 - - - +
400A LEU 3.1 0.6 - - - -
401A ARG* 1.3 73.3 - - - +
403A ALA* 1.3 66.9 + - - +
405A LYS* 3.2 4.0 + - - +
406A VAL* 3.1 21.7 + - - +
413A VAL* 3.6 23.6 - - + -
415A VAL* 3.7 27.4 - - + -
427A LEU* 3.8 30.5 - - + +
431A ALA* 3.9 14.6 - - + -
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Residues in contact with ALA 403 (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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399A ALA 2.9 16.3 + - - +
400A LEU* 3.6 4.0 - - - +
402A ILE* 1.3 77.0 - - - +
404A ASP* 1.3 57.3 + - - +
406A VAL* 3.2 1.6 + - - +
407A GLU* 2.8 32.9 + - - +
431A ALA* 4.2 3.8 - - - +
434A MET* 3.9 23.8 - - + -
435A LEU* 3.6 32.6 - - + +
565A TYR* 4.4 8.7 - - + -
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Residues in contact with ASP 404 (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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400A LEU* 2.8 17.3 + - + +
401A ARG* 4.0 5.4 - - - +
403A ALA* 1.3 77.4 - - - +
405A LYS* 1.3 60.9 + - - +
408A SER* 2.8 41.0 + - - -
409A GLY 3.0 5.7 + - - -
565A TYR* 3.9 27.0 + - + -
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Residues in contact with LYS 405 (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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317A PHE* 3.3 54.2 - - + -
319A PHE* 4.4 5.8 - - + -
401A ARG* 3.1 22.3 + - - +
402A ILE 3.2 4.5 + - - +
404A ASP* 1.3 79.7 + - - +
406A VAL* 1.3 57.2 + - - +
409A GLY* 3.1 18.7 - - - +
411A THR* 2.9 38.7 + - - +
413A VAL* 3.6 24.7 - - + -
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Residues in contact with VAL 406 (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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272A TRP* 4.0 27.4 - - + -
274A HIS* 4.6 4.9 + - + +
277A SER* 4.4 3.8 + - - -
279A ALA* 4.0 23.8 - - + +
280A THR 4.6 2.9 - - - +
281A ILE* 3.9 14.8 - - + -
402A ILE 3.1 14.4 + - - +
403A ALA 3.6 6.1 - - - +
405A LYS* 1.3 76.1 - - - +
407A GLU* 1.3 67.4 + - - +
410A LYS* 3.1 20.8 + - - -
411A THR 3.4 15.3 - - - +
413A VAL* 3.9 22.0 - - + -
435A LEU* 4.1 7.0 - - + -
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Residues in contact with GLU 407 (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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272A TRP* 5.5 0.2 - - - -
274A HIS* 3.0 35.2 + - - -
403A ALA 2.8 20.7 + - - +
406A VAL* 1.3 79.3 - - - +
408A SER* 1.3 63.5 + - - +
410A LYS* 3.4 21.8 - - - +
435A LEU* 3.7 13.1 - - + +
563A VAL* 3.6 31.0 - - + +
565A TYR* 3.4 20.9 - - + +
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Residues in contact with SER 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ASP* 2.8 29.6 + - - -
407A GLU* 1.3 77.3 - - - +
409A GLY* 1.3 62.3 + - - +
410A LYS* 3.3 10.4 + - - +
565A TYR* 4.0 11.2 + - - -
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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
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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