Contacts of the helix formed by residues 485 - 514 (chain A) in PDB entry 1P3M
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 GLN 485 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A PHE* 1.3 76.9 - - - +
486A SER* 1.3 67.9 + - - +
487A SER* 2.9 19.9 + - - +
488A ALA* 2.9 14.4 + - - +
489A VAL* 3.4 7.3 + - - +
80B THR* 4.0 7.7 - - + +
81B VAL 3.2 8.4 + - - +
82B THR* 3.4 35.0 - - + +
83B ALA* 3.0 20.5 + - - +
84B MET 4.8 0.2 + - - -
49I C 5.9 1.6 - - - -
50I C 3.7 26.2 + - - +
247J C 5.2 6.9 + - - -
248J A 5.0 6.3 + - - -
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Residues in contact with SER 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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468A GLN* 5.9 4.3 - - - +
484A PHE 3.4 3.3 + - - -
485A GLN* 1.3 71.9 - - - +
487A SER* 1.3 61.4 + - - +
489A VAL* 3.6 6.6 + - - +
490A MET* 3.3 27.4 + - - +
50I C 3.0 20.5 + - - +
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Residues in contact with SER 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A GLN* 3.3 21.8 + - - +
486A SER* 1.3 78.8 - - - +
488A ALA* 1.3 57.6 + - - -
489A VAL 3.2 0.7 - - - -
490A MET* 3.3 9.1 + - - +
491A ALA* 2.9 29.5 + - - +
83B ALA* 3.3 19.4 - - - +
100B PHE* 3.7 11.5 - - - -
50I C 4.7 0.5 + - - -
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Residues in contact with ALA 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A PHE* 4.2 10.1 - - + -
485A GLN 2.9 8.8 + - - +
487A SER* 1.3 80.7 + - - +
489A VAL* 1.3 59.4 + - - +
491A ALA* 3.4 3.4 + - - +
492A LEU* 3.0 32.9 + - - +
81B VAL 3.6 15.0 - - - +
82B THR 3.6 9.6 - - - +
83B ALA* 3.5 27.8 - - - +
86B VAL* 3.8 12.3 - - + +
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Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LYS* 5.5 2.9 - - + +
467A PHE* 3.8 21.3 - - + -
468A GLN* 4.1 43.5 - - + +
471A VAL* 4.7 7.4 - - + -
472A ARG* 5.2 0.4 - - + +
484A PHE* 3.7 34.5 - - + +
485A GLN 3.4 4.6 + - - +
486A SER* 3.9 7.9 - - - +
488A ALA* 1.3 74.8 - - - +
490A MET* 1.3 68.5 + - - +
492A LEU* 3.3 8.4 + - - +
493A GLN* 2.9 24.5 + - - +
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Residues in contact with MET 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 4.5 12.5 - - + +
464A LYS* 3.1 47.6 - - - +
486A SER* 3.3 21.0 + - - +
487A SER* 3.6 9.6 - - - +
489A VAL* 1.3 81.1 - - + +
491A ALA* 1.3 61.9 + - - +
493A GLN* 3.3 5.1 + - - +
494A GLU* 2.9 30.4 + - + +
100B PHE* 3.7 17.5 - - + -
1454H LYS* 6.3 0.9 - - - +
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Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A SER 2.9 18.1 + - - +
488A ALA* 3.7 4.9 - - - +
490A MET* 1.3 73.9 - - - +
492A LEU* 1.3 60.1 + - - +
494A GLU* 3.1 2.6 + - - +
495A ALA* 2.7 32.4 + - - +
83B ALA 4.8 3.6 - - - +
86B VAL* 4.2 16.4 - - + -
87B VAL* 5.3 1.1 - - + -
90B LEU* 5.0 0.2 - - + -
97B LEU* 3.7 25.6 - - + +
100B PHE* 3.6 20.6 - - + -
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Residues in contact with LEU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A PHE* 3.9 8.5 - - + -
471A VAL* 3.4 34.3 - - + -
484A PHE* 4.3 12.1 - - + -
488A ALA 3.0 17.4 + - - +
489A VAL* 3.5 10.3 - - - +
491A ALA* 1.3 76.4 - - - +
493A GLN* 1.3 52.0 + - - +
495A ALA* 3.3 4.6 + - + +
496A SER* 2.7 39.5 + - - -
61B PHE* 4.9 2.1 - - + -
62B LEU* 4.5 10.8 - - + -
65B VAL* 4.5 15.9 - - + -
66B ILE* 4.1 25.6 - - + +
86B VAL* 3.7 26.0 - - + +
90B LEU* 5.7 1.1 - - + -
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Residues in contact with GLN 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 3.3 20.7 - - + +
462A ILE* 3.1 27.7 + - + +
464A LYS* 3.3 24.0 - - - +
467A PHE* 3.3 47.3 - - + -
489A VAL* 2.9 15.6 + - - +
490A MET* 3.8 5.4 - - - +
492A LEU* 1.3 71.5 - - - +
494A GLU* 1.3 68.9 + - - +
495A ALA 2.9 1.3 - - - -
496A SER* 2.9 1.3 + - - -
497A GLU* 2.9 57.4 + - + +
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Residues in contact with GLU 494 (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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458A THR 5.1 0.2 - - - +
460A LEU* 3.7 22.9 - - + +
490A MET* 2.9 21.4 + - + +
491A ALA* 3.5 7.0 - - - +
493A GLN* 1.3 77.1 - - - +
495A ALA* 1.3 58.1 + - - +
497A GLU* 4.7 0.7 - - - +
498A ALA* 3.1 26.7 + - - +
97B LEU* 4.6 5.8 - - + -
100B PHE* 4.0 19.7 - - + -
1101G THR* 4.5 4.2 - - - +
1102G ILE 4.8 0.3 - - - +
1103G ALA* 3.5 11.7 - - + +
1104G GLN* 2.9 55.1 + - - +
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Residues in contact with ALA 495 (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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491A ALA 2.7 17.3 + - - +
492A LEU* 3.5 5.6 - - + +
494A GLU* 1.3 76.3 - - - +
496A SER* 1.3 59.1 + - - +
498A ALA* 3.4 4.9 + - - +
499A TYR* 3.0 29.6 + - - +
61B PHE* 4.1 8.3 - - + -
90B LEU* 3.7 38.1 - - + -
95B ARG* 5.4 2.2 - - + +
97B LEU* 4.7 9.6 - - + +
1101G THR* 5.3 2.7 - - - -
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Residues in contact with SER 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ILE* 5.7 0.7 - - - -
467A PHE* 3.7 8.7 - - - -
492A LEU 2.7 26.3 + - - -
493A GLN* 2.9 8.4 + - - -
495A ALA* 1.3 70.0 - - - +
497A GLU* 1.3 68.1 + - - -
499A TYR* 3.0 6.1 + - - +
500A LEU* 3.0 28.4 + - - +
58B LEU* 3.9 17.3 - - - -
61B PHE* 3.8 13.1 - - - -
62B LEU* 3.1 27.7 - - - +
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Residues in contact with GLU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 2.7 44.2 - - + +
461A LEU* 2.5 32.0 + - - +
462A ILE* 2.6 33.0 + - + +
493A GLN* 2.9 32.2 + - + +
494A GLU 4.7 1.6 - - - +
496A SER* 1.3 74.6 - - - +
498A ALA* 1.3 63.5 + - - +
500A LEU* 3.1 6.8 + - - +
501A VAL* 2.8 31.3 + - + +
37B LEU* 3.6 13.5 - - + +
40B ARG* 6.3 1.3 - - - +
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Residues in contact with ALA 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLU* 3.1 21.1 + - - +
495A ALA 3.4 5.4 - - - +
496A SER 3.1 0.4 - - - -
497A GLU* 1.3 81.0 - - - +
499A TYR* 1.3 62.4 + - - +
501A VAL* 3.5 7.1 + - - +
502A ALA* 3.3 21.3 + - - +
1101G THR* 3.7 28.3 - - + +
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Residues in contact with TYR 499 (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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495A ALA 3.0 13.4 + - - +
496A SER 3.3 7.6 - - - +
498A ALA* 1.3 75.6 - - - +
500A LEU* 1.3 76.9 + - + +
502A ALA* 3.4 4.8 + - - +
503A LEU* 3.0 31.6 + - + +
528A ARG* 3.8 3.1 + - - -
531A ARG* 3.3 22.2 + - - -
533A GLU* 2.6 29.4 + - - -
57B VAL* 3.5 34.9 - - + +
58B LEU* 5.8 1.1 - - + -
61B PHE* 3.9 40.2 - + + -
95B ARG* 3.4 36.3 - - - +
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Residues in contact with LEU 500 (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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462A ILE* 4.9 3.6 - - + -
496A SER 3.0 20.0 + - - +
497A GLU* 3.5 6.5 - - - +
499A TYR* 1.3 92.0 - - + +
501A VAL* 1.3 59.8 + - - +
502A ALA 2.9 1.8 - - - -
503A LEU* 2.6 30.8 + - + +
504A PHE* 2.7 26.4 + - + -
37B LEU* 3.9 28.7 - - + -
54B THR* 4.3 21.3 - - + -
57B VAL* 4.6 10.5 - - + -
58B LEU* 4.1 34.3 - - + +
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Residues in contact with VAL 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A GLU* 2.8 27.7 + - + +
498A ALA* 3.8 7.0 - - - +
500A LEU* 1.3 73.0 - - - +
502A ALA* 1.3 60.4 + - - +
504A PHE* 3.6 3.8 + - - -
505A GLU* 3.3 19.7 + - - +
37B LEU* 4.2 24.4 - - + +
40B ARG* 3.6 54.3 - - + +
41B GLY* 3.5 9.7 - - - -
1107G VAL* 3.7 20.4 - - + -
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Residues in contact with ALA 502 (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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498A ALA 3.3 14.2 + - - +
499A TYR* 3.6 6.3 - - - +
500A LEU 2.9 0.4 - - - -
501A VAL* 1.3 77.3 - - - +
503A LEU* 1.3 65.8 + - - +
504A PHE 3.2 0.2 - - - -
505A GLU* 3.1 31.0 + - - +
506A ASP* 3.2 13.0 + - - +
531A ARG* 3.8 11.2 - - - +
95B ARG* 5.7 2.7 - - - +
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Residues in contact with LEU 503 (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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499A TYR* 3.0 23.9 + - + +
500A LEU* 2.6 21.5 + - + +
502A ALA* 1.3 72.0 - - - +
504A PHE* 1.3 60.3 + - + +
506A ASP* 3.5 2.1 + - + +
507A THR* 2.8 36.5 + - - +
524A ILE* 4.1 20.4 - - + +
527A ALA* 4.1 15.0 - - + -
528A ARG* 3.9 18.2 - - + -
531A ARG* 3.8 32.1 - - - +
57B VAL* 3.9 28.9 - - + -
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Residues in contact with PHE 504 (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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500A LEU* 2.7 30.7 + - + +
501A VAL 3.8 6.5 - - - +
503A LEU* 1.3 75.2 - - + +
505A GLU* 1.3 65.9 + - - +
507A THR* 3.8 7.5 - - - -
508A ASN* 3.0 26.9 + - - +
519A ILE* 3.9 31.0 - - + -
524A ILE* 4.6 9.9 - - + -
34B ILE* 4.0 15.5 - - + -
37B LEU* 4.0 14.1 - - + -
38B ALA* 3.4 38.4 - - + -
41B GLY* 4.3 4.7 - - - +
43B VAL* 3.9 13.5 - - + +
50B ILE* 4.1 11.2 - - + -
54B THR* 3.6 28.0 - - + -
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Residues in contact with GLU 505 (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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501A VAL* 3.3 28.0 + - - +
502A ALA* 3.1 18.7 + - - +
504A PHE* 1.3 80.6 - - - +
506A ASP* 1.3 64.3 + - - +
508A ASN* 3.9 3.4 - - - +
509A LEU* 3.3 24.6 + - - +
40B ARG 4.4 1.4 - - - +
41B GLY* 3.5 24.6 + - - +
1107G VAL* 4.1 14.9 - - - +
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Residues in contact with ASP 506 (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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502A ALA 3.2 5.7 + - - +
503A LEU 3.5 4.5 + - - +
505A GLU* 1.3 79.7 - - - +
507A THR* 1.3 58.4 + - - +
509A LEU* 3.3 15.8 + - - +
510A CYS* 2.9 30.1 + - - -
527A ALA* 3.9 20.0 - - + -
531A ARG* 3.1 34.1 + - - +
729E ARG* 4.6 4.0 - - - +
730E ILE* 4.0 32.6 - - + +
735E ALA* 6.0 0.9 - - - +
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Residues in contact with THR 507 (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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503A LEU* 2.8 23.3 + - - +
504A PHE* 3.8 9.3 - - + -
505A GLU 3.2 0.4 - - - -
506A ASP* 1.3 73.2 - - - +
508A ASN* 1.3 54.6 + - - +
509A LEU 3.0 1.6 - - - -
510A CYS* 2.8 3.5 + - - +
511A ALA* 2.7 33.8 + - - +
519A ILE* 3.8 23.6 - - + -
520A MET 4.3 0.4 - - - +
523A ASP* 3.2 36.9 + - + -
524A ILE* 3.5 34.2 - - + +
527A ALA* 4.3 2.6 - - - +
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Residues in contact with ASN 508 (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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504A PHE 3.0 16.8 + - - +
505A GLU* 3.9 6.1 - - - +
507A THR* 1.3 75.7 - - - +
509A LEU* 1.3 53.8 + - + +
511A ALA* 3.5 2.2 - - - +
512A ILE* 2.7 56.3 + - - +
517A VAL* 4.6 6.6 - - - +
519A ILE* 3.6 22.7 - - + +
41B GLY 4.9 3.3 + - - +
42B GLY 3.5 14.5 + - - +
43B VAL* 4.0 11.2 - - + -
44B LYS 4.3 2.1 + - - -
1112G GLN* 3.7 11.5 - - + +
1115G LEU* 3.1 33.9 - - - +
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Residues in contact with LEU 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A GLU 3.3 13.6 + - - +
506A ASP* 3.3 18.1 + - - +
508A ASN* 1.3 81.9 - - + +
510A CYS* 1.3 57.2 + - - +
512A ILE* 3.2 9.1 + - + +
513A HIS* 2.8 29.5 + - - +
726E LEU* 4.1 20.4 - - + +
729E ARG* 3.3 49.4 - - + +
730E ILE* 5.4 0.9 - - + -
1112G GLN* 3.7 33.4 - - + +
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Residues in contact with CYS 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ASP 2.9 12.3 + - - +
507A THR 2.8 7.7 + - - +
509A LEU* 1.3 72.1 - - - +
511A ALA* 1.3 66.3 + - - +
513A HIS* 3.4 7.2 + - - +
514A ALA 3.3 9.7 + - - -
523A ASP* 3.5 27.1 - - - +
526A LEU* 3.7 25.4 - - + -
527A ALA* 4.2 5.2 - - - -
713E HIS* 3.0 27.6 + - - +
726E LEU* 4.3 2.9 - - - -
730E ILE* 3.5 32.3 - - - -
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Residues in contact with ALA 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A THR 2.7 18.4 + - - +
508A ASN* 3.5 7.4 - - - +
510A CYS* 1.3 72.0 - - - +
512A ILE* 1.3 61.6 + - + +
514A ALA* 3.3 7.4 + - - +
516A ARG* 2.9 36.6 + - + +
517A VAL 5.0 0.9 - - - -
518A ILE 4.0 17.3 - - - +
519A ILE* 4.0 13.7 - - + -
523A ASP* 3.4 23.5 + - - +
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Residues in contact with ILE 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A ASN* 2.7 39.3 + - - +
509A LEU* 3.6 9.4 - - + +
511A ALA* 1.3 74.7 - - + +
513A HIS* 1.3 56.3 - - - +
514A ALA 3.0 2.0 - - - -
515A LYS* 2.7 26.6 + - - +
516A ARG 3.7 14.6 - - - +
517A VAL* 5.6 0.7 - - - -
1112G GLN* 3.6 29.8 - - + +
1114G VAL* 3.4 38.1 - - + -
1115G LEU* 4.3 7.4 - - + -
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Residues in contact with HIS 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A LEU 2.8 11.1 + - - +
510A CYS 3.6 5.4 - - - +
511A ALA 3.3 0.2 - - - -
512A ILE* 1.3 77.5 - - - +
514A ALA* 1.3 57.0 + - - +
515A LYS* 3.1 9.9 + - - +
710E CYS* 3.3 23.2 + - + +
713E HIS* 4.6 5.6 - + - -
714E ALA* 4.0 12.0 - - + +
716E ARG* 3.5 13.8 + - - -
722E LYS* 3.9 40.5 + - + +
723E ASP* 2.7 32.5 + - - -
726E LEU* 3.3 36.6 - - + +
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Residues in contact with ALA 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A CYS 3.3 9.1 + - - +
511A ALA 3.3 5.8 + - - +
512A ILE 3.0 1.2 - - - -
513A HIS* 1.3 76.2 - - - +
515A LYS* 1.3 71.6 - - - +
516A ARG* 3.3 35.3 - - - +
713E HIS* 3.9 23.1 - - + +
714E ALA* 4.3 11.4 - - - +
71I G 5.6 0.2 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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