Contacts of the helix formed by residues 468 - 490 (chain A) in PDB entry 5NTI
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 PRO 468 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A LEU 4.0 4.3 - - - +
467A PRO* 1.3 85.5 - - + +
469A LYS* 1.3 55.6 + - - +
470A GLY* 3.1 4.0 - - - +
471A LYS* 2.8 47.8 + - + +
472A LEU* 4.0 1.7 + - - +
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Residues in contact with LYS 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLU* 5.3 0.9 - - - +
423A LEU* 5.1 9.0 + - - -
424A VAL* 6.5 0.2 - - - +
427A ASN* 3.9 33.6 + - - +
429A HIS* 4.2 17.1 + - + +
443A GLN* 4.6 13.7 + - - +
447A GLU* 5.5 2.2 + - - -
467A PRO 3.4 5.6 + - - +
468A PRO* 1.3 69.7 - - - +
470A GLY* 1.3 59.3 + - - +
471A LYS 3.3 1.0 + - - -
472A LEU* 3.5 18.7 + - + +
473A ARG* 3.6 25.2 + - - +
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Residues in contact with GLY 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A PRO* 2.9 4.5 + - - +
469A LYS* 1.3 75.4 - - - +
471A LYS* 1.3 58.0 + - - +
472A LEU 3.5 0.2 - - - -
473A ARG* 3.7 28.7 - - - +
474A SER* 3.1 27.0 + - - -
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Residues in contact with LYS 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A SER* 5.4 7.8 + - - +
402A ASP* 6.1 2.6 - - - +
403A PHE* 4.2 23.9 - - + +
467A PRO* 4.7 7.9 - - + -
468A PRO* 2.8 38.7 + - + +
470A GLY* 1.3 70.7 - - - +
472A LEU* 1.3 63.1 + - - +
474A SER* 3.3 12.0 + - - -
475A LEU* 3.1 39.4 + - + +
478A GLN* 6.3 0.4 - - - +
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Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLU* 3.7 51.3 - - + +
362A LEU* 4.2 10.3 - - + -
363A VAL* 4.3 5.2 - - + -
403A PHE* 3.6 34.3 - - + -
420A TYR* 4.1 19.7 - - - +
424A VAL* 4.1 18.6 - - + -
467A PRO* 5.7 2.2 - - + -
468A PRO 4.0 1.7 + - - +
469A LYS* 3.5 13.0 + - + +
470A GLY 3.5 0.2 - - - -
471A LYS* 1.3 77.4 - - - +
473A ARG* 1.3 62.6 + - - +
475A LEU* 3.5 5.8 + - + +
476A CYS* 3.2 27.5 + - - -
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Residues in contact with ARG 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLU* 4.0 15.0 + - - +
427A ASN* 5.5 5.1 - - - +
429A HIS* 6.0 4.2 - - - +
430A ARG* 4.4 13.1 - - - +
469A LYS* 3.6 22.1 + - - +
470A GLY* 3.7 24.0 - - - +
471A LYS 3.3 0.2 - - - -
472A LEU* 1.3 77.2 - - - +
474A SER* 1.3 53.1 + - - +
476A CYS* 3.3 5.9 + - - +
477A SER* 2.8 39.5 + - - +
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Residues in contact with SER 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A GLY 3.1 17.2 + - - -
471A LYS* 3.5 15.5 - - - -
472A LEU 3.3 0.2 - - - -
473A ARG* 1.3 78.1 - - - +
475A LEU* 1.3 59.0 + - - +
477A SER* 3.5 6.8 + - - -
478A GLN* 2.9 39.9 + - - +
302C ARG* 6.0 2.1 + - - -
389C ARG* 4.8 9.5 + - - +
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Residues in contact with LEU 475 (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 MET* 5.8 0.2 - - - +
362A LEU* 3.8 27.0 - - + +
396A LEU* 3.8 6.6 - - + +
399A SER* 3.7 37.7 - - - +
400A ILE* 4.3 13.8 - - + +
403A PHE* 3.6 42.4 - - + -
471A LYS* 3.1 31.5 + - + +
472A LEU* 3.8 7.6 - - + +
474A SER* 1.3 75.7 - - - +
476A CYS* 1.3 58.3 + - - +
478A GLN* 3.4 11.6 + - - +
479A HIS* 3.0 26.7 + - - +
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Residues in contact with CYS 476 (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 ALA 4.8 5.6 - - - +
358A MET* 3.8 32.5 - - + -
359A GLU* 3.6 25.6 - - - +
362A LEU* 4.3 4.9 - - - -
472A LEU 3.2 19.4 + - - +
473A ARG* 3.3 6.7 + - - +
475A LEU* 1.3 77.3 - - - +
477A SER* 1.3 63.3 + - - +
479A HIS* 3.3 8.8 + - - +
480A VAL* 3.1 29.9 + - + +
506A PHE* 5.9 0.6 - - + -
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Residues in contact with SER 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A ARG* 2.8 25.4 + - - +
474A SER 3.7 3.4 - - - -
476A CYS* 1.3 72.3 - - - +
478A GLN* 1.3 61.7 + - - +
480A VAL* 3.3 8.5 + - - +
481A GLU* 3.1 30.5 + - - +
389C ARG* 3.5 39.4 + - - -
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Residues in contact with GLN 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLU* 3.4 22.7 + - - +
396A LEU* 3.3 37.7 + - + +
399A SER* 3.7 16.4 + - - -
471A LYS* 6.3 0.2 - - - +
474A SER* 2.9 27.7 + - - +
475A LEU* 3.5 13.0 - - - +
477A SER* 1.3 77.6 - - - +
479A HIS* 1.3 55.9 + - - +
481A GLU* 3.5 15.5 + - - +
482A ARG* 3.1 38.7 + - + +
389C ARG* 4.6 2.0 - - - +
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Residues in contact with HIS 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A TRP* 5.2 2.0 - + - -
324A LEU* 4.0 10.2 - - + +
358A MET* 4.0 19.6 - - + +
396A LEU* 3.9 17.0 - - + +
475A LEU 3.0 14.3 + - - +
476A CYS* 3.6 11.9 + - - +
477A SER 3.3 0.2 - - - -
478A GLN* 1.3 73.0 - - - +
480A VAL* 1.3 64.2 + - - +
482A ARG* 3.3 2.4 + - - +
483A LEU* 3.0 21.6 + - + +
502A TYR* 2.8 32.7 + + - -
506A PHE* 3.4 52.8 - + + -
601A C3S 3.9 23.6 - - + +
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Residues in contact with VAL 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A CYS* 3.1 16.1 + - + +
477A SER* 3.3 10.7 + - - +
479A HIS* 1.3 75.0 - - - +
481A GLU* 1.3 59.6 + - + +
483A LEU* 3.3 6.9 + - - +
484A GLN* 3.0 32.4 + - + +
505A LEU 5.3 1.8 - - - +
506A PHE* 3.7 41.5 - - + +
508A THR* 4.1 22.0 - - + -
394C SER* 5.6 0.9 - - - +
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Residues in contact with GLU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A SER* 3.1 17.5 + - - +
478A GLN* 3.7 16.4 - - - +
479A HIS 3.3 0.2 - - - -
480A VAL* 1.3 76.3 - - + +
482A ARG* 1.3 64.1 + - - +
484A GLN* 3.2 13.6 + - - +
485A ILE* 3.1 24.1 + - - +
385C MET* 3.3 28.5 - - + +
386C GLU* 3.1 40.3 + - - +
389C ARG* 3.3 27.9 + - - +
394C SER* 6.5 1.1 - - - -
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Residues in contact with ARG 482 (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 TRP* 3.4 18.2 - - + -
392A GLY 2.9 25.2 + - - -
393A CYS* 3.5 31.4 - - + +
395A GLU* 6.0 3.8 - - - +
396A LEU* 3.9 20.6 - - + +
478A GLN* 3.1 24.1 + - + +
479A HIS 3.9 4.0 - - - +
481A GLU* 1.3 77.3 - - - +
483A LEU* 1.3 61.0 + - - +
485A ILE* 3.5 29.4 + - - +
486A PHE* 3.1 20.4 + - - +
374C ARG* 3.8 26.7 - - - +
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A TRP* 3.7 21.7 - - + -
479A HIS* 3.0 13.6 + - - +
480A VAL* 3.5 8.7 - - - +
482A ARG* 1.3 74.4 - - - +
484A GLN* 1.3 55.4 + - - +
486A PHE* 3.1 4.6 + - + -
487A GLN* 2.6 55.4 + - + +
494A VAL* 4.7 2.7 - - + -
498A PHE* 4.0 12.3 - - + -
502A TYR* 3.7 37.2 - - + +
503A LYS* 5.6 0.7 - - - -
506A PHE* 3.6 35.7 - - + +
507A SER* 3.7 12.8 - - - +
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Residues in contact with GLN 484 (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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480A VAL* 3.0 21.4 + - + +
481A GLU* 3.4 16.5 - - - +
483A LEU* 1.3 76.6 - - + +
485A ILE* 1.3 61.9 + - - +
487A GLN* 4.2 6.0 - - - +
488A HIS* 2.9 35.8 + - - +
506A PHE 5.9 0.2 - - - +
508A THR* 2.8 37.3 + - + +
385C MET* 3.5 13.0 - - + +
394C SER* 3.2 36.3 + - - +
395C GLU* 4.5 2.0 - - - +
398C SER* 3.4 29.3 + - - +
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Residues in contact with ILE 485 (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 GLY 5.9 0.7 - - - +
481A GLU* 3.1 14.3 + - + +
482A ARG* 3.5 46.7 - - - +
484A GLN* 1.3 74.6 - - - +
486A PHE* 1.3 63.0 + - - +
488A HIS* 3.8 5.6 + - - +
489A LEU* 3.4 22.5 + - + +
374C ARG* 3.5 48.2 - - - +
385C MET* 3.8 21.8 - - + -
398C SER* 6.3 0.2 - - - -
402C ASP* 5.0 3.0 - - - +
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Residues in contact with PHE 486 (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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313A MET* 3.8 15.0 - - + -
314A TRP* 3.7 22.0 - - - -
317A TRP* 3.4 58.1 - + + +
482A ARG 3.1 16.0 + - - +
483A LEU* 3.1 5.9 + - + +
485A ILE* 1.3 76.9 - - - +
487A GLN* 1.3 57.1 + - - +
489A LEU* 3.2 5.3 + - - +
490A HIS* 2.8 67.0 + - + +
493A VAL* 4.0 9.4 - - + -
494A VAL* 3.6 20.2 - - + -
498A PHE* 3.6 21.5 - + - -
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Residues in contact with GLN 487 (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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483A LEU* 2.6 33.2 + - + +
484A GLN* 4.2 4.9 - - - +
486A PHE* 1.3 72.4 - - - +
488A HIS* 1.3 59.5 + - + +
490A HIS 4.3 0.4 - - - -
491A PRO* 3.1 39.8 - - + +
494A VAL* 3.8 43.0 - - + +
503A LYS* 4.8 7.4 - - - +
507A SER* 2.9 37.0 + - - +
508A THR 4.8 2.4 - - - +
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Residues in contact with HIS 488 (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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484A GLN* 2.9 26.8 + - + +
485A ILE* 4.1 3.7 - - - +
487A GLN* 1.3 80.3 - - + +
489A LEU* 1.3 61.5 + - - +
491A PRO* 3.6 10.3 - - - +
395C GLU* 2.9 27.7 + - - -
398C SER* 3.1 38.0 + - - -
399C SER* 3.1 23.0 + - - -
402C ASP* 3.6 33.0 - - + +
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Residues in contact with LEU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A MET* 4.5 15.0 - - + -
485A ILE* 3.4 15.6 + - + +
486A PHE* 3.2 5.8 + - - +
488A HIS* 1.3 79.0 - - - +
490A HIS* 1.3 89.9 + - + +
491A PRO* 3.6 4.8 - - - +
374C ARG* 6.1 3.1 - - - +
402C ASP* 4.3 9.2 + - - +
405C HIS* 6.4 2.0 - - + -
406C SER* 6.0 2.2 - - - +
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Residues in contact with HIS 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A MET* 4.0 21.8 - - + -
314A TRP* 4.7 19.0 - + + +
486A PHE* 2.8 47.4 + + + +
487A GLN 3.4 3.4 - - - -
489A LEU* 1.3 107.9 + - + +
491A PRO* 1.4 64.0 - - - +
492A ILE 3.3 3.6 + - - -
493A VAL* 3.6 18.8 + - + -
494A VAL* 3.6 16.3 + - - +
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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