Contacts of the helix formed by residues 467 - 488 (chain A) in PDB entry 1XBA
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 LYS 467 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A HIS 4.1 6.1 - - - +
466A VAL* 1.3 79.8 - - - +
468A ASP* 1.3 60.0 - - - +
469A LYS* 4.3 10.5 - - + +
470A ASN* 3.1 17.2 + - + +
471A ILE* 3.0 27.6 + - - +
505A GLN* 5.4 1.0 - - - +
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Residues in contact with ASP 468 (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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466A VAL 3.9 1.0 + - - -
467A LYS* 1.3 68.8 - - - +
469A LYS* 1.3 65.7 + - - +
471A ILE* 3.1 11.2 + - - +
472A ILE* 2.9 41.2 + - - +
566A PHE* 3.3 15.7 - - - -
568A TYR* 4.4 4.4 + - - +
596A GLY 3.8 10.2 - - - +
598A PRO* 3.0 42.2 - - - +
633A VAL* 5.6 1.4 - - - +
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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
----------------------------------------------------------
467A LYS* 3.5 9.7 - - + +
468A ASP* 1.3 77.3 + - - +
470A ASN* 1.3 56.5 + - - +
472A ILE* 3.4 13.4 + - - +
473A GLU* 2.9 27.5 + - - +
630A TYR* 3.7 11.2 - - + -
633A VAL* 3.9 22.9 - - + +
634A VAL* 5.9 3.1 - - + -
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Residues in contact with ASN 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A VAL* 3.6 14.6 - - + +
467A LYS* 3.1 22.3 + - + +
469A LYS* 1.3 74.0 - - - +
471A ILE* 1.3 64.4 + - - +
473A GLU* 3.3 10.1 + - - +
474A LEU* 3.0 25.0 + - - +
505A GLN* 2.7 57.5 + - - +
506A HIS* 3.1 24.0 + - + -
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Residues in contact with ILE 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LEU* 6.4 0.7 - - + -
460A LEU* 4.3 11.2 - - + -
466A VAL* 4.1 11.2 - - + +
467A LYS 3.0 16.9 + - - +
468A ASP* 3.1 9.6 + - - +
470A ASN* 1.3 73.5 - - - +
472A ILE* 1.3 64.4 + - - +
474A LEU* 3.1 9.8 + - + +
475A VAL* 3.0 22.6 + - + +
565A ALA* 3.8 40.2 - - + +
566A PHE* 3.8 29.6 - - + -
568A TYR* 3.5 42.4 - - + +
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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
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468A ASP* 2.9 38.7 + - - +
469A LYS* 3.6 9.4 - - - +
471A ILE* 1.3 75.9 - - - +
473A GLU* 1.3 56.2 + - - +
475A VAL* 3.3 8.6 - - - +
476A HIS* 2.8 30.0 + - - +
566A PHE* 3.6 18.8 - - + -
598A PRO* 4.6 1.3 - - + -
601A MET* 4.2 6.3 - - - -
626A LEU* 4.2 17.3 - - + +
629A TYR* 3.7 26.5 - - + -
630A TYR* 3.8 31.9 - - + +
633A VAL* 4.0 13.9 - - + -
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Residues in contact with GLU 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LYS 2.9 13.7 + - - +
470A ASN* 3.3 14.7 + - - +
471A ILE 3.3 0.2 - - - -
472A ILE* 1.3 77.3 - - - +
474A LEU* 1.3 62.1 + - - +
476A HIS* 3.5 5.8 + - - +
477A GLN* 3.2 41.8 + - + +
506A HIS* 2.8 53.1 + - - +
630A TYR* 3.7 35.2 + - + +
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Residues in contact with LEU 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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456A LEU* 4.1 28.0 - - + -
459A TYR* 6.1 1.1 - - + -
460A LEU* 5.5 3.8 - - + -
466A VAL* 5.4 5.8 - - + -
470A ASN* 3.0 24.1 + - - +
471A ILE* 3.1 9.1 + - + +
473A GLU* 1.3 74.5 - - + +
475A VAL* 1.3 65.6 + - + +
477A GLN* 3.1 23.2 + - - +
478A VAL* 3.1 18.8 + - - +
502A LEU* 3.9 14.4 - - + -
505A GLN* 3.6 20.6 - - + +
506A HIS* 3.9 3.1 - - - -
507A TYR 3.6 27.8 - - - +
508A ALA* 3.9 16.5 - - + +
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Residues in contact with VAL 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LEU* 5.4 3.1 - - + -
471A ILE* 3.0 18.1 + - + +
472A ILE* 3.3 14.8 - - - +
474A LEU* 1.3 73.9 - - + +
476A HIS* 1.3 69.4 + - - +
478A VAL* 3.4 8.4 + - - -
479A SER 3.0 17.2 + - - -
558A PHE* 3.5 14.6 - - + -
561A LEU* 4.7 7.0 - - + -
562A MET* 4.3 22.9 - - + -
565A ALA* 3.7 28.5 - - + -
566A PHE* 4.4 11.2 - - + -
626A LEU* 3.7 21.1 - - + -
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Residues in contact with HIS 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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472A ILE 2.8 20.6 + - - +
473A GLU* 3.8 7.9 + - - +
475A VAL* 1.3 78.7 - - - +
477A GLN* 1.3 58.7 + - - +
479A SER* 2.7 27.0 + - - -
480A MET* 2.9 38.3 + - - +
623A GLU* 2.6 31.2 + - - -
626A LEU* 3.7 15.9 - - + +
627A ARG* 3.3 40.9 - - + +
630A TYR* 4.6 16.6 - + + -
631A TYR* 5.7 2.0 - + - -
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Residues in contact with GLN 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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431A TYR* 3.6 41.4 + - + +
473A GLU* 3.2 28.9 + - + +
474A LEU* 3.1 12.8 + - - +
476A HIS* 1.3 80.8 - - - +
478A VAL* 1.3 57.4 + - - +
480A MET* 3.0 12.7 + - - +
481A GLY 3.0 23.2 + - - -
506A HIS 3.0 22.2 + - - +
507A TYR* 3.3 6.1 - - - +
508A ALA* 2.8 38.6 + - + +
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Residues in contact with VAL 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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431A TYR* 5.3 0.9 - - - -
456A LEU* 5.4 2.0 - - + -
474A LEU 3.1 14.5 + - - +
475A VAL* 3.7 9.9 - - - +
477A GLN* 1.3 75.2 - - - +
479A SER* 1.3 55.6 + - - +
481A GLY 3.2 1.6 + - - -
482A MET* 2.9 33.7 + - + +
495A LEU* 4.2 5.4 - - + -
500A VAL* 3.7 33.4 - - + -
508A ALA* 4.3 6.3 - - + +
510A ILE* 3.4 26.2 - - + +
558A PHE* 3.6 24.5 - - + -
561A LEU* 4.0 21.1 - - + -
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Residues in contact with SER 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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475A VAL 3.0 8.0 + - - -
476A HIS* 2.7 26.7 + - - -
478A VAL* 1.3 74.1 - - - +
480A MET* 1.3 58.6 + - - +
482A MET* 4.0 5.9 - - - +
483A LYS* 2.9 29.5 + - - +
558A PHE* 3.8 26.2 - - - -
619A PHE* 4.6 5.5 - - - -
622A VAL* 4.5 2.5 - - - -
623A GLU* 3.5 34.2 - - - +
626A LEU* 3.7 4.8 - - - +
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Residues in contact with MET 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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429A ASN* 4.7 2.1 + - - -
431A TYR* 3.9 36.3 - - + +
476A HIS* 2.9 41.1 + - - +
477A GLN* 3.0 10.3 + - - +
479A SER* 1.3 75.4 - - - +
481A GLY* 1.3 64.0 + - - +
483A LYS* 3.3 6.1 + - - +
484A TYR* 3.1 21.0 + - - +
623A GLU* 3.6 25.8 - - + +
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Residues in contact with GLY 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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429A ASN* 3.9 9.0 - - - -
431A TYR* 3.8 20.2 - - - +
432A ILE* 3.8 9.6 - - - +
477A GLN 3.0 11.7 + - - -
478A VAL 3.2 3.8 + - - -
480A MET* 1.3 77.5 - - - +
482A MET* 1.3 56.5 + - - +
484A TYR* 3.3 5.9 - - - +
485A LEU* 2.9 25.6 + - - +
510A ILE* 3.9 13.2 - - - -
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Residues in contact with MET 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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478A VAL* 2.9 23.2 + - + +
479A SER* 4.0 1.1 - - - +
481A GLY* 1.3 73.2 - - - +
483A LYS* 1.3 61.4 + - - +
485A LEU* 3.6 28.4 - - + +
486A GLU* 2.8 30.2 + - + +
490A PHE 5.6 0.7 - - - +
492A HIS* 4.3 4.7 - - + -
495A LEU* 3.8 24.0 - - + -
510A ILE* 3.8 20.6 - - + -
551A SER* 6.1 0.7 - - - +
554A ASP* 3.8 26.0 - - + +
619A PHE* 3.4 51.0 - - + -
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Residues in contact with LYS 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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479A SER 2.9 18.5 + - - +
480A MET* 3.3 6.5 + - - +
482A MET* 1.3 76.3 - - - +
484A TYR* 1.3 64.0 + - - +
486A GLU* 3.1 5.7 + - - +
487A GLU* 2.9 46.5 + - + +
619A PHE* 3.7 15.6 - - + +
620A ALA* 3.5 40.2 + - + +
623A GLU* 4.0 26.4 + - + +
627A ARG* 4.2 9.9 - - - +
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Residues in contact with TYR 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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426A GLN 3.8 5.7 + - - -
427A LEU* 3.4 24.5 - - + +
428A ASP* 2.8 45.0 + - - +
429A ASN* 3.3 38.8 - - + +
432A ILE* 4.4 2.9 - - + -
480A MET 3.1 7.3 + - - +
481A GLY 3.3 10.3 - - - +
483A LYS* 1.3 80.0 - - - +
485A LEU* 1.3 60.9 + - + +
487A GLU* 3.4 16.6 + - + +
488A SER* 2.8 56.6 + - - -
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Residues in contact with LEU 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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427A LEU* 3.3 42.0 - - + -
432A ILE* 5.0 4.7 - - + -
481A GLY 2.9 13.5 + - - +
482A MET* 3.6 27.6 - - + +
483A LYS 3.2 0.4 - - - -
484A TYR* 1.3 81.8 - - + +
486A GLU* 1.3 62.1 + - - +
488A SER* 3.2 3.3 + - - -
489A ASN 3.0 17.7 + - - -
490A PHE* 3.0 34.5 + - + +
492A HIS* 3.9 26.0 - - + +
513A PHE* 3.7 24.9 - - + -
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Residues in contact with GLU 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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482A MET* 2.8 14.5 + - - +
483A LYS* 3.3 10.5 - - - +
485A LEU* 1.3 76.2 - - - +
487A GLU* 1.3 60.3 + - + +
489A ASN* 2.9 29.3 + - - -
490A PHE 4.6 0.4 - - - -
551A SER* 3.5 40.4 + - - +
552A LYS* 5.4 0.9 - - - +
618A GLY* 3.7 9.3 - - - -
619A PHE* 3.1 37.5 + - + +
620A ALA* 3.5 16.6 + - - +
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Residues in contact with GLU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LYS* 2.9 47.3 + - + +
484A TYR* 3.7 20.4 + - + +
486A GLU* 1.3 76.7 - - + +
488A SER* 1.3 59.5 + - - +
489A ASN* 3.2 11.0 + - - +
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Residues in contact with SER 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLN 6.0 0.4 - - - -
427A LEU* 4.8 0.7 - - - -
484A TYR* 2.8 49.5 + - - -
485A LEU* 3.2 6.7 + - - -
486A GLU 3.1 0.6 - - - -
487A GLU* 1.3 74.5 - - - +
489A ASN* 1.3 70.9 + - - +
490A PHE* 3.4 29.2 - - - -
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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