Contacts of the helix formed by residues 407 - 441 (chain D) in PDB entry 7RSC
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 ALA 407 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403D LEU* 3.3 13.8 + - + +
404D SER* 3.3 17.1 + - - +
406D LYS* 1.3 78.9 - - - +
408D LYS* 1.3 68.7 + - + +
410D ALA* 3.4 4.2 + - - +
411D LEU* 3.0 26.2 + - - +
548D 7Q9 5.5 3.4 - - - -
873E 17F 6.0 12.3 - - + -
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Residues in contact with LYS 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404D SER* 3.8 14.0 + - - +
405D GLU 5.2 0.2 - - - +
407D ALA* 1.3 80.9 - - + +
409D PRO* 1.4 70.9 - - + +
411D LEU* 3.2 4.8 + - - +
412D GLU* 3.0 24.0 + - - +
548D 7Q9 5.9 5.7 - - - +
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Residues in contact with PRO 409 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D GLU 3.4 21.3 - - - +
406D LYS* 4.1 5.8 - - + +
407D ALA 3.7 1.6 - - - -
408D LYS* 1.4 95.7 - - + +
410D ALA* 1.3 61.5 + - - +
412D GLU* 3.4 6.8 + - + +
413D ASP* 3.1 23.9 + - - +
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Residues in contact with ALA 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D LYS 3.5 19.9 + - - +
407D ALA* 3.4 4.7 + - - +
408D LYS 3.2 0.4 - - - -
409D PRO* 1.3 81.6 - - - +
411D LEU* 1.3 61.7 + - - +
413D ASP* 3.3 15.8 + - - +
414D LEU* 3.3 12.6 + - - +
873E 17F 6.2 5.4 - - + -
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Residues in contact with LEU 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407D ALA 3.0 18.1 + - - +
408D LYS* 3.8 5.2 - - - +
410D ALA* 1.3 76.6 - - - +
412D GLU* 1.3 61.8 + - - +
414D LEU* 3.4 19.6 + - + +
415D ARG* 3.3 19.6 + - - +
551D 7Q9 5.3 11.9 - - - -
873E 17F 6.3 4.0 - - + -
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Residues in contact with GLU 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408D LYS 3.0 16.0 + - - +
409D PRO* 3.7 8.1 - - + +
411D LEU* 1.3 74.8 - - - +
413D ASP* 1.3 63.8 + - - +
415D ARG* 2.7 58.2 + - - +
416D GLN* 3.2 36.9 + - - +
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Residues in contact with ASP 413 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D PRO 3.1 17.0 + - - +
410D ALA* 3.3 8.9 + - - +
412D GLU* 1.3 76.6 - - - +
414D LEU* 1.3 61.4 + - - +
416D GLN* 3.7 18.9 + - - +
417D GLY* 3.5 14.7 + - - -
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Residues in contact with LEU 414 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D ALA 3.3 9.5 + - - +
411D LEU* 3.7 21.3 - - + +
412D GLU 3.2 0.4 - - - -
413D ASP* 1.3 78.3 - - - +
415D ARG* 1.3 64.7 + - - +
417D GLY* 3.0 11.7 + - - -
418D LEU* 3.1 29.7 + - + +
739E LYS* 3.4 44.9 - - + +
740E LEU* 4.1 26.9 - - + +
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Residues in contact with ARG 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D LEU 3.3 9.8 + - - +
412D GLU* 2.7 47.6 + - - +
414D LEU* 1.3 78.5 - - - +
416D GLN* 1.3 68.3 + - - +
417D GLY 3.1 1.4 + - - -
418D LEU* 3.3 8.9 + - - +
419D LEU* 3.2 28.5 + - + +
549D 7Q9 5.1 20.8 - - - -
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Residues in contact with GLN 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412D GLU* 3.2 33.1 + - - +
413D ASP* 3.7 23.3 - - - +
414D LEU 3.3 0.2 - - - -
415D ARG* 1.3 84.4 - - - +
417D GLY* 1.3 57.1 + - - +
419D LEU* 4.6 6.2 - - - +
420D PRO* 3.3 21.5 - - - +
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Residues in contact with GLY 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D ASP 3.5 8.4 + - - -
414D LEU* 3.0 9.0 + - - -
416D GLN* 1.3 80.4 - - - +
418D LEU* 1.3 60.9 + - - +
420D PRO* 3.5 14.0 - - - +
421D VAL* 5.1 5.4 + - - +
739E LYS* 3.8 30.0 + - - -
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Residues in contact with LEU 418 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D LEU* 3.1 30.8 + - + +
415D ARG* 3.3 6.7 + - - +
417D GLY* 1.3 78.7 - - - +
419D LEU* 1.3 63.9 + - - +
420D PRO 3.4 0.5 - - - -
421D VAL* 3.5 3.1 + - - +
422D LEU* 3.2 24.7 + - + +
736E TYR* 3.7 44.2 - - + +
739E LYS* 3.7 29.8 - - + -
740E LEU* 4.7 6.7 - - + -
870E 7Q9 4.4 17.0 - - - -
876E 7Q9 5.5 7.0 - - - -
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Residues in contact with LEU 419 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415D ARG* 3.2 19.8 + - + +
416D GLN* 4.6 5.6 - - - +
418D LEU* 1.3 78.5 - - - +
420D PRO* 1.4 71.2 - - + +
422D LEU* 3.0 23.8 + - + -
423D GLU* 2.8 41.2 + - + +
549D 7Q9 3.5 32.3 - - - -
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Residues in contact with PRO 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D GLN 3.3 23.8 - - - +
417D GLY* 3.5 9.9 - - - +
418D LEU 3.4 3.6 - - - -
419D LEU* 1.4 96.0 - - + +
421D VAL* 1.3 65.7 + - + +
423D GLU* 3.7 10.2 + - + +
424D SER* 3.3 12.1 + - - -
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Residues in contact with VAL 421 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D GLY 5.1 5.2 - - - +
418D LEU 3.5 2.5 + - - +
419D LEU 3.4 0.4 - - - -
420D PRO* 1.3 79.6 - - + +
422D LEU* 1.3 65.7 + - - +
424D SER* 3.2 18.6 + - - +
425D PHE* 3.3 10.4 + - + +
731E SER 6.2 0.2 - - - -
732E ALA* 5.1 7.6 - - + -
735E GLU* 4.1 29.6 - - + +
736E TYR* 3.3 25.6 + - + +
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Residues in contact with LEU 422 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D LEU* 3.2 17.5 + - + +
419D LEU* 3.0 31.3 + - + +
421D VAL* 1.3 77.6 - - - +
423D GLU* 1.3 62.2 + - - +
425D PHE* 3.1 13.7 + - + +
426D LYS* 3.0 43.0 + - + +
539D 17F 5.7 2.9 - - + -
549D 7Q9 2.9 38.4 - - - +
736E TYR* 3.1 10.4 + - - -
876E 7Q9 3.3 25.8 - - - -
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Residues in contact with GLU 423 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419D LEU* 2.8 28.4 + - + +
420D PRO* 3.9 7.6 - - + +
421D VAL 3.3 0.4 - - - -
422D LEU* 1.3 77.7 - - - +
424D SER* 1.3 62.0 + - - +
426D LYS* 2.7 35.3 + - - +
427D VAL* 3.3 42.6 + - + +
549D 7Q9 5.6 0.7 - - - -
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Residues in contact with SER 424 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420D PRO 3.3 15.4 + - - -
421D VAL* 3.4 12.2 + - - +
422D LEU 3.2 0.6 - - - -
423D GLU* 1.3 75.6 - - - +
425D PHE* 1.3 58.5 + - - +
427D VAL* 3.5 6.5 + - - +
428D SER* 2.7 33.7 + - - -
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Residues in contact with PHE 425 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421D VAL 3.3 7.9 + - - +
422D LEU* 3.1 19.4 + - + +
424D SER* 1.3 77.5 - - - +
426D LYS* 1.3 59.4 + - - +
428D SER* 3.3 8.5 + - - -
429D PHE* 2.9 28.2 + - + +
539D 17F 3.8 28.0 - - + -
725E PHE* 3.4 35.2 - + - -
728E SER* 4.5 15.7 - - - -
729E PHE* 3.4 48.7 - + + -
732E ALA* 4.8 10.8 - - + -
736E TYR* 4.7 6.1 - + - +
876E 7Q9 5.8 5.6 - - - -
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Residues in contact with LYS 426 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419D LEU* 5.4 0.2 - - - -
422D LEU* 3.0 44.4 + - + +
423D GLU* 2.7 46.4 + - - +
424D SER 3.3 0.2 - - - -
425D PHE* 1.3 77.9 - - - +
427D VAL* 1.3 61.4 + - - +
429D PHE* 3.2 6.0 + - - +
430D LEU* 3.0 32.2 + - + +
539D 17F 3.5 36.6 - - + -
549D 7Q9 3.7 29.9 - - - +
----------------------------------------------------------
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Residues in contact with VAL 427 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D GLU* 3.3 31.7 + - + +
424D SER* 3.9 5.2 - - - +
426D LYS* 1.3 76.3 - - + +
428D SER* 1.3 63.9 + - - +
430D LEU* 3.2 22.7 + - + +
431D SER* 3.1 24.2 + - - +
----------------------------------------------------------
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Residues in contact with SER 428 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424D SER* 2.7 24.1 + - - -
425D PHE* 3.6 10.9 - - - -
427D VAL* 1.3 77.9 - - - +
429D PHE* 1.3 62.4 + - - +
431D SER* 3.6 7.0 + - - -
432D ALA* 3.3 20.8 + - - +
725E PHE* 4.9 5.6 - - - -
728E SER* 5.9 7.2 - - - -
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Residues in contact with PHE 429 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D PHE* 2.9 16.9 + - + +
426D LYS* 3.5 5.2 - - - +
427D VAL 3.2 0.2 - - - -
428D SER* 1.3 76.0 - - - +
430D LEU* 1.3 58.3 + - + +
432D ALA* 3.2 3.5 + - + +
433D LEU* 2.8 66.9 + - + +
436D TYR* 5.6 7.0 - + - -
539D 17F 3.2 71.1 - - + -
725E PHE* 3.6 36.6 - + + -
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Residues in contact with LEU 430 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426D LYS* 3.0 24.1 + - + +
427D VAL* 3.2 20.6 + - + +
429D PHE* 1.3 79.8 - - + +
431D SER* 1.3 61.9 + - - +
433D LEU* 3.4 11.5 + - + +
434D GLU* 3.3 26.7 + - - +
539D 17F 3.6 58.3 - - + -
----------------------------------------------------------
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Residues in contact with SER 431 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427D VAL* 3.1 18.4 + - - +
428D SER* 3.9 8.1 - - - -
430D LEU* 1.3 78.8 - - - +
432D ALA* 1.3 62.5 + - - +
434D GLU* 3.5 6.9 + - - +
435D GLU* 3.4 23.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 432 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428D SER 3.3 10.6 + - - +
429D PHE* 3.2 7.9 + - + +
431D SER* 1.3 76.7 - - - +
433D LEU* 1.3 66.4 + - - +
435D GLU* 3.2 10.2 + - - +
436D TYR* 3.0 46.5 + - + +
721E VAL* 4.5 12.8 - - + -
725E PHE* 4.5 15.3 - - + -
----------------------------------------------------------
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Residues in contact with LEU 433 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429D PHE* 2.8 55.5 + - + +
430D LEU* 3.7 13.0 - - + +
432D ALA* 1.3 72.7 - - - +
434D GLU* 1.3 67.7 + - - +
436D TYR* 3.2 27.9 + - + +
437D THR* 3.0 23.8 + - - +
539D 17F 4.6 28.3 - - + -
----------------------------------------------------------
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Residues in contact with GLU 434 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D LEU 3.3 12.4 + - - +
431D SER* 3.8 10.3 - - - +
432D ALA 3.2 0.8 - - - -
433D LEU* 1.3 85.7 - - - +
435D GLU* 1.3 62.7 + - - +
437D THR* 3.3 13.6 + - - -
438D LYS* 3.2 37.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 435 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431D SER 3.4 12.1 + - - +
432D ALA* 3.2 12.2 + - - +
434D GLU* 1.3 79.3 - - - +
436D TYR* 1.3 66.1 + - + +
438D LYS* 2.7 52.5 + - - +
439D LYS* 3.4 13.2 + - - +
721E VAL* 5.3 16.4 - - + -
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Residues in contact with TYR 436 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429D PHE* 5.6 7.6 - + - -
432D ALA* 3.0 29.7 + - + +
433D LEU* 3.4 24.5 - - + +
434D GLU 3.2 0.2 - - - -
435D GLU* 1.3 78.5 - - + +
437D THR* 1.3 62.3 + - - +
439D LYS* 3.3 7.6 + - - +
440D LEU* 3.1 33.0 + - + +
718E LEU* 3.7 30.5 - - + -
721E VAL* 3.9 30.1 - - + +
722E LEU* 4.0 23.3 - - + +
725E PHE* 4.1 16.5 - + - +
----------------------------------------------------------
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Residues in contact with THR 437 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D LEU* 3.0 20.0 + - - +
434D GLU* 3.3 15.2 + - - -
436D TYR* 1.3 77.8 - - - +
438D LYS* 1.3 58.8 + - - +
440D LEU* 4.3 8.1 - - + -
441D ASN* 2.8 33.5 + - + +
543D 7Q9 3.2 39.5 - - + +
----------------------------------------------------------
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Residues in contact with LYS 438 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434D GLU* 3.2 27.9 + - - +
435D GLU* 2.7 47.4 + - - +
437D THR* 1.3 79.2 - - - +
439D LYS* 1.3 60.8 + - - +
441D ASN* 3.9 14.0 + - - +
----------------------------------------------------------
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Residues in contact with LYS 439 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435D GLU 3.4 7.2 + - - +
436D TYR* 3.3 9.3 + - - +
437D THR 3.2 0.4 - - - -
438D LYS* 1.3 76.9 - - - +
440D LEU* 1.3 68.6 + - + +
441D ASN 4.4 2.3 - - - -
713E ASP* 2.7 47.7 + - - -
714E LEU* 3.6 34.6 - - + +
717E GLY* 3.8 26.8 - - - +
718E LEU* 5.6 1.3 - - + -
----------------------------------------------------------
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Residues in contact with LEU 440 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D TYR* 3.1 26.6 + - + +
437D THR* 3.7 7.0 - - + +
439D LYS* 1.3 80.2 - - + +
441D ASN* 1.3 62.0 + - - +
543D 7Q9 3.8 29.4 - - + -
552D 17F 4.2 34.5 - - + +
714E LEU* 4.5 24.9 - - + +
----------------------------------------------------------
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Residues in contact with ASN 441 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437D THR* 2.8 22.1 + - + +
438D LYS* 4.0 13.5 - - - +
439D LYS 4.4 2.5 - - - -
440D LEU* 1.3 78.9 - - - +
543D 7Q9 4.1 25.1 + - - +
552D 17F 3.5 55.4 - - - +
----------------------------------------------------------
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il