Contacts of the helix formed by residues 511 - 538 (chain A) in PDB entry 5EPG
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 511 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLN* 4.3 13.0 + - - -
440A ILE* 3.8 28.7 - - + -
509A GLY 3.9 9.9 + - - +
510A GLY* 1.3 73.9 - - - +
512A VAL* 1.3 65.2 + - - +
513A GLU 3.3 3.1 - - - -
514A PHE* 3.0 13.9 + - + -
515A LYS* 2.9 25.9 + - + +
1219A GLU* 3.5 25.6 + - - -
1221A ASN* 4.7 12.1 + - - +
1233A PRO* 5.1 11.8 + - + -
1234A ASP* 5.4 2.2 + - - -
1307A THR* 5.6 0.2 - - - -
1309A GLU* 3.6 46.7 + - - +
1335A ASN* 5.0 5.4 - - - +
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Residues in contact with VAL 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A LEU* 4.3 9.8 - - + +
504A LEU 3.1 28.3 - - - +
505A GLY* 3.7 26.0 - - - +
507A ALA* 3.8 16.4 - - + +
510A GLY 4.0 7.6 - - - +
511A LYS* 1.3 75.5 - - - +
513A GLU* 1.3 70.8 + - + +
515A LYS* 3.4 6.6 + - - +
516A ARG* 2.8 47.3 + - - +
1326A ASP* 4.8 1.6 - - - +
1331A TYR* 5.1 7.4 - - - +
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Residues in contact with GLU 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A LYS 3.3 0.4 - - - -
512A VAL* 1.3 85.2 - - + +
514A PHE* 1.3 61.9 + - - +
516A ARG* 3.7 17.7 + - - +
517A THR* 2.9 27.9 + - - -
1309A GLU* 6.1 0.2 - - - +
1313A MET* 3.4 12.8 - - - +
1323A ILE* 4.1 11.6 - - + +
1325A ARG* 3.6 46.0 + - - +
1326A ASP* 4.6 6.1 + - - +
1331A TYR* 5.7 2.1 + - - -
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Residues in contact with PHE 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A GLN* 4.3 1.6 - - + -
440A ILE* 4.3 26.0 - - + -
511A LYS* 3.0 14.6 + - + +
513A GLU* 1.3 76.4 - - - +
515A LYS* 1.3 60.0 + - - +
517A THR* 3.1 2.6 + - - -
518A LEU* 2.9 50.8 + - + +
1177A THR 3.3 21.5 - - - -
1308A PRO* 3.6 17.0 - - + -
1309A GLU* 3.4 48.5 + - + +
1312A ARG* 3.4 38.8 - - + -
1313A MET* 3.7 9.0 - - + -
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Residues in contact with LYS 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ILE* 4.1 22.0 - - + -
441A VAL* 3.8 25.1 - - + +
465A GLY 3.4 22.9 + - - +
466A VAL* 4.8 1.8 - - + -
467A GLY 5.8 0.6 - - - +
503A LEU* 3.3 33.9 - - + +
507A ALA* 4.6 1.8 - - - +
508A PRO 3.2 26.1 + - - -
509A GLY* 3.8 9.5 - - - -
510A GLY 3.2 23.8 + - - +
511A LYS* 2.9 13.6 + - - +
512A VAL 3.7 6.5 - - - +
514A PHE* 1.3 77.2 - - - +
516A ARG* 1.3 61.9 + - - +
518A LEU* 3.4 2.3 + - - +
519A ILE* 3.1 29.6 + - - +
1233A PRO* 6.0 3.6 - - - -
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Residues in contact with ARG 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A LEU* 3.6 17.1 - - + +
502A SER* 6.0 1.6 - - - +
503A LEU* 2.6 43.8 + - + +
504A LEU* 4.4 0.8 - - - +
505A GLY 4.0 4.6 - - - +
512A VAL* 2.8 37.7 + - - +
513A GLU* 3.7 15.8 - - - +
515A LYS* 1.3 78.4 - - - +
517A THR* 1.3 61.7 + - - +
519A ILE* 3.4 21.2 - - + +
520A ILE* 3.6 4.5 + - - +
1323A ILE* 3.9 16.2 - - + -
1324A PRO* 2.8 49.1 + - + +
1325A ARG* 3.9 3.4 - - - +
1326A ASP* 2.9 35.9 + - - -
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Residues in contact with THR 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLU 2.9 14.4 + - - -
514A PHE* 3.1 9.1 + - - -
516A ARG* 1.3 75.1 - - - +
518A LEU* 1.3 54.5 + - - +
520A ILE* 3.2 6.8 + - - +
521A SER* 2.6 37.0 + - - +
1312A ARG* 3.2 54.1 - - + +
1313A MET* 3.1 19.0 - - + +
1319A PHE* 4.4 5.8 + - + +
1320A THR* 4.8 1.3 - - - +
1323A ILE* 3.3 18.8 - - - +
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Residues in contact with LEU 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A GLN* 3.6 22.9 - - + -
440A ILE* 4.8 2.5 - - + -
441A VAL* 3.7 32.8 - - + +
514A PHE* 2.9 43.2 + - + +
515A LYS 3.4 4.2 + - - +
517A THR* 1.3 75.1 - - - +
519A ILE* 1.3 55.2 + - - +
521A SER* 4.0 2.5 - - - -
522A PHE* 2.8 57.3 + - + -
1176A LEU 3.9 5.4 - - - +
1177A THR* 3.6 37.2 - - - +
1312A ARG* 5.0 0.7 - - - -
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Residues in contact with ILE 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A VAL* 4.4 3.3 - - + +
463A TYR* 2.5 50.5 + - + -
466A VAL* 3.7 29.2 - - + -
497A ILE* 3.2 30.9 - - + +
498A LEU* 4.6 4.7 - - + -
501A VAL* 3.8 28.3 - - + +
503A LEU* 4.0 10.5 - - + -
515A LYS 3.1 20.4 + - - +
516A ARG* 3.4 10.8 - - - +
518A LEU* 1.3 77.4 - - - +
520A ILE* 1.3 65.2 + - + +
522A PHE* 5.0 0.2 - - - -
523A LEU* 3.5 7.6 + - - +
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Residues in contact with ILE 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A CYS* 4.0 20.4 - - + +
497A ILE* 4.1 8.1 - - + -
498A LEU* 3.4 48.0 - - + -
516A ARG 3.9 2.2 - - - +
517A THR 3.2 11.9 + - - +
519A ILE* 1.3 81.8 - - + +
521A SER* 1.3 60.0 + - - +
523A LEU* 3.3 7.8 - - - +
524A PHE* 3.0 25.3 + - - +
1319A PHE* 3.6 48.4 - - + +
1322A MET* 4.4 7.6 - - + -
1323A ILE* 3.9 9.9 - - + -
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Residues in contact with SER 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A THR* 2.6 31.5 + - - +
518A LEU* 3.8 7.2 - - - -
520A ILE* 1.3 72.6 - - - +
522A PHE* 1.3 59.7 + - - +
524A PHE* 3.3 6.4 + - - +
525A LYS* 3.0 30.8 + - - +
1176A LEU* 3.1 36.6 + - - +
1312A ARG* 3.0 24.3 + - - -
1319A PHE* 4.3 5.0 - - - +
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Residues in contact with PHE 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A PHE* 3.4 46.5 - + + -
429A ARG* 3.6 27.1 - - - -
430A GLN* 3.7 4.3 - - + -
441A VAL* 3.5 31.0 - - + -
442A ASN* 4.0 5.8 - - - -
443A SER* 4.2 12.1 - - - -
445A MET* 3.7 9.2 - - + -
463A TYR* 4.5 6.3 - + + -
518A LEU* 2.8 40.3 + - + +
519A ILE 4.1 2.9 - - - +
521A SER* 1.3 71.3 - - - +
523A LEU* 1.3 60.7 + - - +
525A LYS* 3.4 7.6 + - + +
526A PHE* 3.0 24.8 + - - +
1177A THR* 3.9 27.8 - - + -
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Residues in contact with LEU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A MET* 3.8 15.8 - - - +
461A ILE* 3.7 28.5 - - + -
463A TYR* 4.1 3.8 - - - +
485A TRP* 6.5 0.9 - - + -
489A MET* 6.6 0.2 - - + -
490A LEU* 4.3 8.9 - - + +
493A ALA* 4.2 13.5 - - + +
494A CYS* 4.1 33.4 - - - +
497A ILE* 3.6 26.9 - - + -
519A ILE 3.5 10.6 + - - +
520A ILE* 3.3 10.9 + - - +
522A PHE* 1.3 78.4 - - - +
524A PHE* 1.3 57.3 + - - +
526A PHE* 3.4 8.0 + - + +
527A TYR* 3.0 27.2 + - - +
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Residues in contact with PHE 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A GLU* 5.8 1.8 - - - -
490A LEU* 3.8 19.6 - - + +
520A ILE 3.0 9.6 + - - +
521A SER 3.4 8.1 - - - +
522A PHE 3.3 0.2 - - - -
523A LEU* 1.3 72.1 - - - +
525A LYS* 1.3 65.7 + - - +
527A TYR* 3.2 12.9 + + - +
528A LEU* 3.1 67.3 + - + +
549A TYR* 3.8 13.2 - + - -
1002A TRP* 3.4 40.6 - + - -
1176A LEU* 3.5 22.4 - - + -
1318A LYS* 4.5 10.3 - - - -
1319A PHE* 3.4 34.3 - + + -
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Residues in contact with LYS 525 (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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428A PHE* 3.9 26.7 - - + -
521A SER 3.0 19.6 + - - +
522A PHE* 3.4 12.3 + - + +
524A PHE* 1.3 76.9 - - - +
526A PHE* 1.3 57.7 + - - +
528A LEU* 3.4 7.7 + - - +
529A GLU* 2.9 31.5 + - - +
552A ALA* 2.9 32.1 + - + +
553A LEU* 4.1 5.4 - - + +
555A ASP* 3.3 17.3 + - - -
1174A ASP* 2.9 28.3 + - - -
1176A LEU* 3.6 26.1 - - + +
1177A THR* 3.8 22.7 - - + -
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Residues in contact with PHE 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A PHE* 4.4 3.4 - - + -
425A VAL 4.6 2.9 - - - -
426A SER* 3.3 33.9 - - - -
428A PHE* 3.6 8.6 - - + -
445A MET* 3.3 51.8 - - + -
446A ARG 4.1 3.1 - - - -
447A VAL* 4.0 26.9 - - + -
459A LEU* 4.7 4.9 - - + -
461A ILE* 5.4 1.6 - - + -
485A TRP* 4.1 22.0 - + - -
522A PHE 3.0 17.3 + - - +
523A LEU* 3.5 11.0 - - + +
525A LYS* 1.3 74.1 - - - +
527A TYR* 1.3 65.2 + - - +
529A GLU* 4.3 3.1 - - + -
530A VAL* 3.1 40.4 + - + +
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Residues in contact with TYR 527 (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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485A TRP* 3.1 56.0 + + + +
486A ASN* 3.6 31.7 + - - -
487A GLU* 3.3 37.9 + - + +
489A MET* 4.5 4.5 - - + -
490A LEU* 3.5 38.4 - - + -
523A LEU 3.0 7.9 + - - +
524A PHE* 3.2 11.0 + + - +
526A PHE* 1.3 76.4 - - - +
528A LEU* 1.3 80.7 + - + +
531A SER* 2.9 41.2 + - - -
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Residues in contact with LEU 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A PHE* 3.1 61.4 + - + +
525A LYS* 3.6 5.6 - - - +
527A TYR* 1.3 93.3 - - + +
529A GLU* 1.3 65.2 + - - +
531A SER* 3.2 25.8 - - - +
532A GLN* 3.6 5.4 - - - +
545A LEU* 3.8 20.5 - - + +
549A TYR* 4.4 17.3 - - + +
552A ALA* 4.0 14.6 - - + -
553A LEU* 3.4 27.1 - - + +
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Residues in contact with GLU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A VAL 4.4 4.3 - - - +
426A SER* 2.5 31.9 + - - +
428A PHE* 3.6 17.3 - - - -
525A LYS 2.9 16.2 + - - +
526A PHE* 3.8 6.5 - - + +
528A LEU* 1.3 77.2 - - - +
530A VAL* 1.3 62.8 + - + +
532A GLN* 3.3 17.4 + - - +
533A ILE* 3.5 7.8 + - - +
553A LEU* 3.7 29.3 - - + +
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Residues in contact with VAL 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A PHE* 3.2 50.7 - - + -
447A VAL* 3.7 9.9 - - + -
449A PHE* 4.5 3.8 - - + -
485A TRP* 3.0 47.8 - - + +
526A PHE* 3.1 21.2 + - + +
529A GLU* 1.3 76.5 - - - +
531A SER* 1.3 57.2 + - - +
532A GLN 3.0 10.2 + - - -
533A ILE* 3.4 15.3 - - + +
534A LEU* 3.4 13.3 + - + +
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Residues in contact with SER 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A TRP* 3.5 22.4 - - - -
527A TYR* 2.9 34.0 + - - -
528A LEU* 3.2 9.2 + - - +
530A VAL* 1.3 73.6 - - - +
532A GLN* 1.3 57.9 + - - +
534A LEU* 4.5 10.8 - - - -
535A LYS* 4.8 4.0 - - - +
543A PRO 4.8 5.6 + - - +
545A LEU* 3.0 24.4 - - - +
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Residues in contact with GLN 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A LEU 3.6 4.9 - - - +
529A GLU* 3.3 9.9 - - - +
530A VAL 3.0 2.4 + - - -
531A SER* 1.3 77.9 - - - +
533A ILE* 1.3 59.7 + - - +
534A LEU 3.2 2.5 - - - +
535A LYS* 3.2 15.4 + - + +
536A LYS* 2.7 33.4 + - - +
545A LEU* 3.5 17.6 - - + +
550A GLU* 4.4 17.6 - - - +
553A LEU* 3.1 27.4 - - - +
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Residues in contact with ILE 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLU* 6.0 0.4 - - - -
332A GLN* 6.0 2.2 - - - +
424A PHE* 3.3 46.2 - - + -
529A GLU 3.5 5.0 + - - +
530A VAL* 3.4 21.8 - - + +
532A GLN* 1.3 76.1 - - - +
534A LEU* 1.3 59.7 + - - +
536A LYS* 3.5 16.6 - - + +
537A MET* 2.9 45.6 + - + +
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Residues in contact with LEU 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A TRP* 3.6 31.4 - - + -
424A PHE* 4.0 14.1 - - + -
449A PHE* 4.2 26.9 - - + -
485A TRP* 4.5 14.6 - - + -
530A VAL 3.4 17.4 + - - +
531A SER* 4.5 10.5 - - - -
532A GLN 4.4 2.0 - - - +
533A ILE* 1.3 80.4 - - - +
535A LYS* 1.3 56.6 + - - +
537A MET* 4.7 4.0 - - - -
538A ASP* 2.8 39.7 + - - +
542A TYR* 3.9 40.8 - - + +
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Residues in contact with LYS 535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A SER 4.8 1.1 - - - +
532A GLN* 3.2 25.7 + - + +
534A LEU* 1.3 77.5 - - - +
536A LYS* 1.3 64.8 + - - +
538A ASP 4.4 4.5 - - - -
539A PRO* 3.1 57.7 + - - +
542A TYR* 3.5 21.9 + - + +
543A PRO 3.7 16.8 - - - +
544A SER* 3.4 34.4 + - - +
545A LEU* 5.4 1.1 - - + +
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Residues in contact with LYS 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A GLN 2.7 20.2 + - - +
533A ILE* 3.5 22.9 - - + +
535A LYS* 1.3 77.8 - - - +
537A MET* 1.3 64.5 + - + +
538A ASP 3.6 0.2 + - - -
539A PRO* 4.3 8.3 - - - +
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Residues in contact with MET 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLU* 3.3 25.4 - - - +
421A LYS* 4.2 13.2 - - + +
422A TRP* 3.8 42.7 - - + -
424A PHE* 3.7 28.5 - - - -
533A ILE* 2.9 34.6 + - + +
534A LEU 4.0 1.8 - - - +
536A LYS* 1.3 78.9 - - + +
538A ASP* 1.3 57.6 + - - +
539A PRO* 4.0 4.8 - - - +
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Residues in contact with ASP 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A TRP* 3.9 20.0 - - + -
452A GLY* 4.4 10.7 - - - +
534A LEU 2.8 19.3 + - - +
535A LYS 3.5 2.4 - - - +
537A MET* 1.3 75.9 - - - +
539A PRO* 1.4 67.6 - - - +
540A VAL* 3.4 3.1 + - - +
541A HIS* 2.7 40.3 + - - +
542A TYR* 3.4 33.7 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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).
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