Contacts of the helix formed by residues 468 - 489 (chain A) in PDB entry 2PFV
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 468 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A LEU* 3.6 45.5 + - + +
451A MET* 3.6 35.0 - - + +
466A ASN* 2.9 6.0 + - - -
467A LYS* 1.3 94.7 + - + +
469A LYS* 1.3 63.5 + - - +
470A GLN* 3.2 4.0 + - - -
471A ARG* 3.4 9.5 + - + +
472A ILE* 3.0 28.3 + - + +
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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
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460A ASN 4.1 7.2 - - - +
461A PRO* 3.1 33.4 - - + +
462A ASN 4.7 1.1 - - - -
463A SER 3.1 22.1 + - - +
464A SER* 4.9 2.2 - - - +
466A ASN* 3.0 40.4 + - + +
467A LYS* 3.6 2.6 + - - +
468A HIS* 1.3 77.4 - - - +
470A GLN* 1.3 57.4 + - - +
472A ILE* 4.5 0.4 - - - -
473A GLY* 2.7 29.3 + - - -
514A TYR* 3.5 25.0 - - + +
517A SER* 3.1 34.2 + - - +
518A ASP* 4.2 11.8 + - - +
521A ASP* 5.1 6.4 + - - -
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Residues in contact with GLN 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A HIS 3.2 0.8 - - - -
469A LYS* 1.3 79.6 - - - +
471A ARG* 1.3 63.9 + - - +
473A GLY 3.4 0.2 + - - -
474A PHE* 3.1 22.2 + - - +
514A TYR 3.9 8.4 + - - -
515A MET* 3.8 31.1 + - + +
518A ASP* 3.7 23.9 + - - +
519A TRP* 4.1 5.7 - - - +
559A LEU* 4.2 6.5 - - - +
562A LYS* 3.4 27.7 - - - +
563A THR* 3.0 35.3 + - - +
566A TYR* 3.5 24.3 + - + +
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Residues in contact with ARG 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ILE* 3.6 23.6 + - + +
363A PRO 3.6 8.9 + - - -
364A SER* 4.5 7.0 + - - +
366A ASN* 2.7 41.2 + - - +
450A LEU* 3.5 38.7 - - + +
468A HIS* 3.4 12.5 + - + +
470A GLN* 1.3 76.3 - - - +
472A ILE* 1.3 62.1 + - - +
474A PHE* 3.3 4.0 + - - +
475A PHE* 2.9 27.1 + - + +
566A TYR* 3.5 32.2 + - + +
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Residues in contact with ILE 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ILE* 5.8 0.2 - - + -
443A GLU* 3.6 28.5 - - + -
446A ALA* 4.2 15.5 - - + -
447A GLN* 3.7 26.7 - - + -
450A LEU* 3.9 19.7 - - + -
451A MET* 4.9 1.1 - - + -
466A ASN* 3.7 21.1 - - - +
468A HIS* 3.0 26.0 + - + +
469A LYS* 3.9 3.4 - - - +
471A ARG* 1.3 73.6 - - - +
473A GLY* 1.3 69.1 + - - +
475A PHE* 3.1 8.1 + - + +
476A ILE* 2.9 28.3 + - + +
514A TYR* 4.3 8.5 - - + -
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Residues in contact with GLY 473 (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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469A LYS 2.7 23.1 + - - -
470A GLN 3.8 1.3 - - - -
472A ILE* 1.3 73.6 - - - +
474A PHE* 1.3 54.2 + - - +
476A ILE 3.4 0.5 + - - -
477A LEU* 2.8 42.0 + - - +
511A TYR* 3.7 25.6 - - - +
514A TYR* 3.7 8.3 - - - +
515A MET* 3.9 1.8 - - - -
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Residues in contact with PHE 474 (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 ASN 3.9 8.5 - - - -
366A ASN* 3.7 23.6 - - + -
470A GLN 3.1 13.5 + - - +
471A ARG 3.4 6.5 - - - +
473A GLY* 1.3 73.0 - - - +
475A PHE* 1.3 59.0 + - - +
477A LEU* 3.2 3.4 + - - +
478A MET* 2.8 50.9 + - + +
515A MET* 3.7 15.5 - - - +
565A GLN 5.2 1.1 - - - -
566A TYR* 3.5 39.0 - + + -
567A LYS 3.3 41.7 - - - -
568A LEU* 3.4 35.4 - - + -
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Residues in contact with PHE 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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362A ILE* 4.2 8.5 - - + -
363A PRO* 3.6 17.7 - - + -
366A ASN* 3.6 35.4 - - + +
367A GLY 3.6 6.5 - - - -
369A THR* 3.6 33.4 - - + -
442A LEU* 3.8 36.3 - - + -
445A LYS* 4.2 13.0 - - - -
446A ALA* 4.0 20.0 - - + -
471A ARG* 2.9 14.5 + - + +
472A ILE* 3.1 9.4 + - - +
474A PHE* 1.3 77.9 - - - +
476A ILE* 1.3 73.5 + - + +
478A MET* 3.3 2.4 + - - +
479A ASN* 2.9 29.6 + - - +
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Residues in contact with ILE 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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439A ALA* 3.7 17.3 - - + +
442A LEU* 3.7 15.3 - - + -
443A GLU* 3.6 28.7 - - + +
472A ILE* 2.9 21.1 + - + +
473A GLY 3.8 0.2 - - - +
475A PHE* 1.3 88.7 - - + +
477A LEU* 1.3 58.0 + - - +
479A ASN* 3.1 6.7 + - + +
480A LEU* 2.8 36.7 + - + +
511A TYR* 3.4 53.2 - - + -
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Residues in contact with LEU 477 (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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473A GLY 2.8 28.6 + - - +
474A PHE 3.2 4.2 + - - +
476A ILE* 1.3 75.2 - - - +
478A MET* 1.3 58.7 + - - +
480A LEU* 3.0 9.0 + - + +
481A THR* 2.8 35.4 + - - -
508A LYS* 3.8 33.7 - - + +
511A TYR* 3.1 34.5 - - + +
512A ILE* 3.8 4.0 - - + +
515A MET* 3.1 25.1 - - + -
568A LEU* 4.3 8.5 - - + -
573A LEU* 4.0 25.7 - - + +
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Residues in contact with MET 478 (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 ASN 5.9 0.9 - - - +
366A ASN 3.5 19.1 - - - +
367A GLY* 4.1 15.5 - - - -
368A VAL* 3.9 16.6 - - + +
474A PHE* 2.8 57.5 + - + +
475A PHE 3.7 1.6 - - - +
477A LEU* 1.3 72.9 - - - +
479A ASN* 1.3 62.4 + - - +
481A THR* 3.5 20.5 + - + -
482A LEU 3.7 2.9 + - - -
567A LYS 4.1 8.7 - - - +
568A LEU* 4.2 5.2 - - - -
569A SER* 3.7 30.7 - - - +
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Residues in contact with ASN 479 (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 GLY 3.2 16.1 - - - +
368A VAL* 3.5 7.5 - - - +
369A THR* 2.9 32.7 + - - +
372A THR* 2.6 33.2 + - + +
438A LEU* 5.7 1.6 - - + -
442A LEU* 3.7 17.2 - - + +
475A PHE* 2.9 26.7 - - - +
476A ILE* 3.1 8.1 + - + +
478A MET* 1.3 74.5 - - - +
480A LEU* 1.3 65.9 + - + +
481A THR 3.1 1.8 - - - -
482A LEU* 3.0 15.1 + - - +
483A VAL* 3.2 16.0 + - + +
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Residues in contact with LEU 480 (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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435A ILE* 4.1 15.5 - - + +
438A LEU* 5.9 2.0 - - + -
439A ALA* 4.8 6.1 - - + -
476A ILE* 2.8 36.0 + - + +
477A LEU* 3.0 11.4 + - + +
479A ASN* 1.3 73.6 - - + +
481A THR* 1.3 65.8 + - - +
483A VAL* 3.5 13.7 - - + +
484A GLU* 3.0 24.8 + - - +
504A LEU* 4.4 8.7 - - + +
507A LEU* 3.9 46.0 - - + +
508A LYS* 4.4 21.7 - - + +
511A TYR* 4.2 8.3 - - + -
573A LEU* 6.3 0.2 - - + -
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Residues in contact with THR 481 (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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477A LEU 2.8 19.8 + - - -
478A MET* 3.5 18.5 - - + -
479A ASN 3.1 0.4 - - - -
480A LEU* 1.3 78.8 - - - +
482A LEU* 1.3 59.5 + - - +
484A GLU* 3.6 6.7 + - - +
485A GLN* 3.1 40.7 + - + +
568A LEU* 5.5 0.9 - - - +
569A SER* 5.4 7.4 + - - -
570A ASP* 4.1 28.9 + - + +
573A LEU* 3.8 19.5 - - - +
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Residues in contact with LEU 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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368A VAL* 3.5 41.3 - - + -
372A THR* 3.6 16.6 - - + +
373A VAL* 4.3 16.8 - - + -
376A MET* 4.9 1.3 - - + -
478A MET 3.7 1.6 + - - -
479A ASN 3.0 9.6 + - - +
481A THR* 1.3 79.7 - - - +
483A VAL* 1.3 65.7 + - - +
485A GLN* 3.2 21.3 + - - +
486A ILE* 3.0 44.0 + - + +
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Residues in contact with VAL 483 (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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372A THR* 4.1 5.2 - - + -
376A MET* 3.8 31.2 - - - -
435A ILE* 4.0 34.8 - - + -
438A LEU* 4.0 23.1 - - + -
479A ASN 3.2 14.1 + - - +
480A LEU* 3.5 21.3 - - + +
482A LEU* 1.3 78.7 - - - +
484A GLU* 1.3 62.3 + - - +
486A ILE* 3.3 2.6 + - - +
487A VAL* 3.0 30.6 + - + +
504A LEU* 5.1 5.8 - - + -
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Residues in contact with GLU 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 LEU 3.0 16.2 + - - +
481A THR* 3.7 8.5 - - - +
483A VAL* 1.3 79.3 - - - +
485A GLN* 1.3 59.8 + - + +
487A VAL* 3.3 7.4 + - - +
488A GLU* 2.9 31.1 + - + +
501A HIS* 5.2 6.4 + - - -
504A LEU* 4.2 20.0 - - + +
505A GLU* 4.0 11.4 - - - +
508A LYS* 3.1 34.8 + - - +
570A ASP* 5.2 8.5 - - - +
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Residues in contact with GLN 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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481A THR* 3.1 28.7 - - + +
482A LEU* 3.2 29.5 + - + +
484A GLU* 1.3 78.0 - - + +
486A ILE* 1.3 63.4 + - + +
488A GLU* 3.4 5.2 + - - +
489A LYS* 3.1 32.3 + - + +
570A ASP* 6.2 0.4 - - - +
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Residues in contact with ILE 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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376A MET* 3.8 43.7 - - + +
380A ARG* 4.7 16.2 - - - -
482A LEU* 3.0 37.8 + - + +
483A VAL 3.7 4.3 - - - +
485A GLN* 1.3 78.2 - - + +
487A VAL* 1.3 59.8 + - - +
489A LYS* 3.6 6.1 - - - +
490A SER* 2.8 26.9 - - - -
492A LEU* 4.4 13.2 - - + -
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Residues in contact with VAL 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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376A MET* 5.4 2.5 - - - -
431A ILE* 5.9 0.7 - - + -
435A ILE* 4.7 5.6 - - + -
483A VAL* 3.0 31.1 + - + +
484A GLU* 3.6 9.4 - - - +
486A ILE* 1.3 75.7 - - + +
488A GLU* 1.3 70.6 + - - +
490A SER* 3.1 10.0 + - - +
492A LEU* 3.8 17.5 - - + -
493A ASN* 3.1 39.9 + - - +
496A LEU* 3.7 28.9 - - + -
501A HIS* 4.0 14.4 - - + +
504A LEU* 5.1 6.7 - - + -
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Residues in contact with GLU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A GLU* 2.9 19.7 + - + +
485A GLN* 3.7 5.8 - - - +
487A VAL* 1.3 77.7 - - - +
489A LYS* 1.3 59.2 + - + +
490A SER 2.7 13.5 + - - +
493A ASN* 3.5 27.6 + - - +
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Residues in contact with LYS 489 (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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380A ARG* 3.4 17.3 + - - -
485A GLN* 3.1 17.1 + - + +
486A ILE* 3.6 4.6 - - + +
488A GLU* 1.3 75.1 - - + +
490A SER* 1.3 61.6 + - - +
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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