Contacts of the helix formed by residues 503 - 523 (chain O) in PDB entry 5A31
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 503 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227O GLU* 4.0 17.2 + - - -
463O THR* 4.3 3.7 - - - -
464O GLU* 3.5 54.3 + - + +
467O ALA* 4.9 0.7 - - + -
497O PHE* 3.9 33.4 - + + -
502O GLN* 1.3 93.0 + - + +
504O ALA* 1.3 65.3 + - - +
505O GLN* 3.0 13.0 - - - +
506O LEU* 3.0 33.5 + - + +
507O TRP* 3.5 9.8 + - - -
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Residues in contact with ALA 504 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU 5.2 0.9 - - - +
112A ALA* 6.4 0.2 - - - -
497O PHE* 4.6 1.6 - - - +
498O PRO 3.8 3.1 - - - +
499O PRO* 3.1 41.3 - - + +
501O SER 3.2 9.0 - - - +
502O GLN 2.9 6.7 + - - -
503O HIS* 1.3 75.2 - - - +
505O GLN* 1.3 63.5 + - - +
507O TRP* 3.2 16.3 + - - +
508O MET* 2.8 40.4 + - + +
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Residues in contact with GLN 505 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA* 4.2 26.5 - - + +
113A VAL 5.8 1.7 - - - +
114A TYR* 6.0 3.2 - - - +
265O GLN* 5.2 10.1 - - - +
501O SER 6.1 0.2 - - - +
502O GLN* 5.5 1.3 - - - -
503O HIS* 4.4 11.7 - - - +
504O ALA* 1.3 76.1 - - - +
506O LEU* 1.3 61.8 + - + +
508O MET* 3.2 3.5 + - - +
509O LEU* 2.9 31.8 + - - +
538O LEU* 3.5 34.1 - - + +
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Residues in contact with LEU 506 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.7 25.3 - - + +
464O GLU* 3.7 38.6 - - + +
467O ALA* 3.2 33.0 - - + -
468O VAL* 4.4 4.7 - - + +
471O CYS* 3.6 19.4 - - - -
503O HIS* 3.0 20.1 + - + +
505O GLN* 1.3 81.1 - - + +
507O TRP* 1.3 75.3 + - + +
509O LEU* 3.4 8.7 + - + +
510O CYS* 3.1 18.5 + - - +
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Residues in contact with TRP 507 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A SER 5.8 0.4 - - - -
109A GLN* 5.2 4.5 - - + -
471O CYS* 3.6 10.1 - - - -
490O LEU* 4.6 11.6 - - + +
493O LEU* 3.7 43.7 + - + -
494O LYS* 3.6 41.7 - - + -
497O PHE* 3.1 34.6 + + + -
499O PRO* 4.5 9.2 - - + -
503O HIS 3.5 12.9 + - - -
504O ALA* 3.2 12.9 + - - +
506O LEU* 1.3 80.0 - - + +
508O MET* 1.3 89.2 + - + +
510O CYS* 3.4 2.6 + - - +
511O ASP* 2.8 47.0 + - + +
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Residues in contact with MET 508 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 5.6 1.3 - - + -
108A SER 3.6 24.5 - - - +
109A GLN 3.0 21.1 - - - +
110A ALA 4.1 3.6 - - - +
111A LEU* 3.2 29.6 - - + +
499O PRO* 3.7 28.5 - - + +
504O ALA* 2.8 36.5 + - + +
505O GLN 3.5 4.9 - - - +
507O TRP* 1.3 98.4 - - + +
509O LEU* 1.3 55.6 + - - +
511O ASP* 2.8 20.8 - - - +
512O GLN* 2.9 23.0 + - - +
538O LEU* 3.8 9.8 - - + +
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Residues in contact with LEU 509 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 5.9 6.5 - - + -
505O GLN 2.9 16.6 + - - +
506O LEU* 3.7 9.6 - - + +
507O TRP 3.2 0.2 - - - -
508O MET* 1.3 74.7 - - - +
510O CYS* 1.3 64.9 + - - +
512O GLN* 3.3 3.4 + - - +
513O LYS* 3.0 44.3 + - + +
535O ILE* 3.7 34.8 - - + +
538O LEU* 4.3 15.2 - - + +
539O ASN* 3.9 37.9 - - + +
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Residues in contact with CYS 510 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 5.3 4.0 - - + -
471O CYS* 3.8 36.3 - - + -
474O ALA* 4.1 5.2 - - - -
475O GLU* 3.9 16.3 - - - +
490O LEU* 3.9 23.3 - - - -
506O LEU 3.1 13.9 + - - +
507O TRP 3.8 1.8 - - - +
509O LEU* 1.3 79.6 - - - +
511O ASP* 1.3 65.8 + - - +
513O LYS* 3.3 14.3 + - + +
514O ILE* 3.1 28.8 + - - +
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Residues in contact with ASP 511 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLN* 4.2 9.9 - - - +
490O LEU* 3.3 35.4 - - + -
507O TRP* 2.8 29.9 + - + +
508O MET* 2.8 27.8 - - - +
510O CYS* 1.3 73.9 - - - +
512O GLN* 1.3 78.1 + - - +
514O ILE* 3.4 5.5 - - - +
515O GLN* 3.1 34.7 + - - +
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Residues in contact with GLN 512 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LYS* 3.5 39.0 - - - +
109A GLN* 3.6 21.6 - - - +
110A ALA* 4.4 3.4 - - + +
508O MET 2.9 17.3 + - - +
509O LEU* 3.7 6.5 - - - +
510O CYS 3.2 0.2 - - - -
511O ASP* 1.3 90.7 - - - +
513O LYS* 1.3 57.8 + - - +
515O GLN* 3.0 10.6 + - - +
516O PHE* 2.8 28.4 + - - +
531O LEU* 4.0 19.4 + - + +
534O GLY* 4.2 7.5 - - - -
535O ILE* 3.6 33.0 - - + +
538O LEU* 5.8 2.2 - - + -
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Residues in contact with LYS 513 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D SER 4.3 14.8 + - - +
3D THR* 5.9 0.2 - - - +
4D LEU* 4.6 13.3 - - - +
475O GLU* 3.8 29.0 + - - +
509O LEU* 3.0 44.7 + - + +
510O CYS* 3.5 10.4 - - - +
512O GLN* 1.3 75.3 - - - +
514O ILE* 1.3 62.1 + - - +
516O PHE* 3.2 9.1 + - - +
517O ASP* 3.0 27.1 + - - +
535O ILE* 4.6 4.4 - - + +
539O ASN* 5.5 1.4 - - - +
542O GLU* 2.6 44.9 + - - +
546O ARG* 3.8 16.8 + - - +
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Residues in contact with ILE 514 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474O ALA 3.9 19.5 - - - +
475O GLU* 4.3 10.8 - - + -
478O ALA* 3.7 34.1 - - + -
483O PHE* 5.1 11.2 - - + +
486O ALA* 4.4 7.9 - - + -
487O SER 6.3 0.2 - - - +
490O LEU* 4.0 24.5 - - + -
510O CYS* 3.1 19.4 + - - +
511O ASP* 3.4 9.6 - - - +
513O LYS* 1.3 80.0 - - - +
515O GLN* 1.3 63.7 + - + +
517O ASP* 3.9 3.2 - - - +
518O ARG* 2.9 32.2 + - + +
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Residues in contact with GLN 515 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLN* 5.2 4.8 - - - +
511O ASP* 3.1 29.2 + - - +
512O GLN* 3.0 19.3 + - - +
514O ILE* 1.3 78.9 - - + +
516O PHE* 1.3 66.7 + - - +
518O ARG* 3.3 7.1 + - - +
519O ALA* 2.9 25.8 + - - +
527O LEU* 5.8 2.3 - - - +
531O LEU* 3.4 25.7 - - + +
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Residues in contact with PHE 516 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512O GLN 2.8 12.9 + - - +
513O LYS* 3.5 8.3 - - - +
515O GLN* 1.3 78.5 - - - +
517O ASP* 1.3 68.7 + - - +
519O ALA* 3.3 4.2 + - - +
520O MET* 3.0 47.1 + - + +
528O ALA* 3.6 33.0 - - + +
531O LEU* 3.4 11.0 - - + +
532O VAL* 4.3 4.7 - - + -
535O ILE* 3.6 23.1 - - + -
546O ARG* 3.2 55.2 - - + -
549O VAL* 4.0 13.9 - - + -
550O VAL* 4.1 11.9 - - + -
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Residues in contact with ASP 517 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513O LYS 3.0 14.5 + - - +
514O ILE* 4.1 3.6 - - - +
516O PHE* 1.3 92.7 - - - +
518O ARG* 1.3 65.6 + - - +
520O MET* 3.1 19.0 + - - +
521O ASN* 3.1 25.1 + - - +
546O ARG* 4.4 15.4 + - - -
658O LEU* 5.5 5.5 - - - +
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Residues in contact with ARG 518 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483O PHE* 3.6 61.3 - - + +
484O ALA 5.3 1.4 - - - +
514O ILE* 2.9 21.2 + - + +
515O GLN* 3.8 6.7 - - - +
517O ASP* 1.3 75.5 - - - +
519O ALA* 1.3 58.4 + - - +
521O ASN* 3.3 11.3 + - + +
522O ASP* 3.0 27.4 + - + +
704O VAL 6.0 0.2 - - - +
705O ASP* 5.3 4.4 + - - -
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Residues in contact with ALA 519 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515O GLN 2.9 18.1 + - - +
516O PHE 3.4 6.3 - - - +
517O ASP 3.2 0.2 - - - -
518O ARG* 1.3 74.3 - - - +
520O MET* 1.3 58.3 + - - +
522O ASP* 3.4 8.9 - - - +
523O GLY 2.8 24.1 + - - -
524O LYS 3.4 11.8 + - - +
527O LEU* 4.0 26.5 - - + -
528O ALA* 4.0 18.2 - - + +
531O LEU* 4.4 3.6 - - + -
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Residues in contact with MET 520 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516O PHE* 3.0 44.2 + - + +
517O ASP* 3.1 13.2 + - - +
519O ALA* 1.3 74.9 - - - +
521O ASN* 1.3 65.5 + - - +
523O GLY* 3.3 13.1 + - - -
525O TYR* 3.4 40.6 - - + -
528O ALA* 4.2 15.5 - - + -
549O VAL* 4.9 11.2 - - + +
550O VAL* 4.3 14.6 - - - -
553O ALA* 3.7 13.7 - - + -
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Residues in contact with ASN 521 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483O PHE* 4.8 7.5 - - - -
517O ASP* 3.1 21.3 + - - +
518O ARG* 3.6 13.2 - - + +
519O ALA 3.3 0.2 - - - -
520O MET* 1.3 77.4 - - - +
522O ASP* 1.3 66.2 + - - +
523O GLY* 3.1 2.3 + - - -
658O LEU* 3.7 24.2 - - - +
704O VAL* 3.5 24.5 - - + +
705O ASP 5.1 1.5 - - - +
706O CYS* 3.6 47.4 - - - +
708O GLU* 5.5 3.3 - - - +
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Residues in contact with ASP 522 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518O ARG* 3.0 14.6 + - + +
519O ALA* 3.4 12.9 - - - +
521O ASN* 1.3 74.7 - - - +
523O GLY* 1.3 58.6 + - - +
524O LYS* 3.4 40.6 - - - +
527O LEU* 4.4 9.9 - - - +
705O ASP 5.9 1.8 - - - -
708O GLU* 4.4 13.0 - - - +
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Residues in contact with GLY 523 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519O ALA 2.8 9.2 + - - -
520O MET 3.3 13.7 + - - -
521O ASN 3.1 3.1 - - - -
522O ASP* 1.3 75.5 - - - +
524O LYS* 1.3 62.6 - - - +
525O TYR* 3.1 34.8 + - - -
708O GLU* 4.8 10.3 - - - +
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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
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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