Contacts of the helix formed by residues 430 - 454 (chain B) in PDB entry 6NRB
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 GLY 430 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B THR 2.6 13.5 + - - -
429B PRO* 1.3 77.6 - - - +
431B LYS* 1.3 67.9 + - - -
432B GLU* 2.9 9.8 + - - +
433B ALA* 3.2 6.1 + - - +
434B VAL* 3.5 11.3 + - - +
459J ALA* 4.7 0.7 - - - +
460J ASP* 2.9 17.0 - - - -
463J ALA* 4.7 0.3 - - - +
464J GLN* 3.5 15.0 - - - -
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Residues in contact with LYS 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B THR* 3.2 40.3 - - + +
128B ALA* 5.4 4.0 - - + -
430B GLY* 1.3 72.0 - - - -
432B GLU* 1.3 63.2 + - - +
434B VAL* 3.2 26.9 - - - +
435B ALA 3.7 1.2 + - - -
467E GLY* 3.8 27.3 + - - -
468E MET* 5.0 14.1 - - - +
495E HIS* 4.9 11.4 - - - +
457J ASP* 5.2 11.5 + - - +
459J ALA* 5.2 0.7 - - + -
460J ASP* 2.8 24.3 + - - +
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Residues in contact with GLU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ALA* 4.7 4.0 - - + +
129B GLY* 3.1 32.0 - - - +
132B GLU* 4.9 9.8 - - + +
428B THR* 3.1 49.0 - - + +
430B GLY* 3.8 8.4 + - - +
431B LYS* 1.3 80.3 - - - +
433B ALA* 1.3 52.4 + - - +
435B ALA 3.0 5.2 + - - -
436B MET* 2.5 36.5 + - + +
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Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ALA* 3.2 31.0 - - + +
428B THR* 3.4 3.8 - - - +
429B PRO* 3.3 25.4 - - + -
430B GLY 3.2 1.8 + - - +
432B GLU* 1.3 78.9 - - - +
434B VAL* 1.3 62.1 + - - +
436B MET* 2.6 14.5 + - - +
437B GLU* 2.3 39.6 + - + +
463J ALA* 4.9 4.3 - - + -
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 3.5 16.4 - - + +
119B LYS* 4.0 7.2 - - - +
121B ILE* 3.5 41.5 - - + -
125B THR* 4.6 3.6 - - + -
430B GLY 3.5 8.7 - - - +
431B LYS* 3.2 19.3 - - - +
432B GLU 3.2 0.2 - - - -
433B ALA* 1.3 76.2 - - - +
435B ALA* 1.3 52.6 + - - +
437B GLU* 4.0 14.1 - - - +
438B SER* 2.7 28.8 + - - -
459J ALA* 3.5 31.2 - - + -
463J ALA* 5.5 3.5 - - + +
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Residues in contact with ALA 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 4.7 2.2 - - - -
125B THR 3.7 6.9 + - - +
126B ILE* 3.1 31.1 - - - +
129B GLY* 3.7 6.3 - - - +
130B TRP* 2.3 46.1 + - + +
431B LYS 3.7 1.4 + - - -
432B GLU 3.0 8.3 + - - +
433B ALA 3.1 2.2 - - - -
434B VAL* 1.3 77.3 - - - +
436B MET* 1.3 52.9 + - - +
437B GLU 3.4 0.2 - - - -
438B SER* 3.0 3.4 + - - -
439B TYR 2.5 20.8 + - - -
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Residues in contact with MET 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLY* 4.1 5.4 - - - +
132B GLU* 4.0 13.0 - - + -
133B ALA* 3.6 33.7 - - + +
421B VAL* 3.4 19.5 - - + +
424B LEU* 3.6 19.3 - - + -
425B ALA* 3.4 31.2 - - + +
428B THR* 3.5 27.8 - - + -
432B GLU* 2.5 25.3 + - + +
433B ALA* 2.6 11.0 + - - -
435B ALA* 1.3 69.3 - - - +
437B GLU* 1.3 62.1 + - - +
439B TYR* 3.2 6.5 - - - +
440B ALA* 3.1 20.1 + - - +
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Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 5.9 0.9 - - - +
119B LYS* 5.7 3.6 + - - -
422B THR* 4.8 8.8 + - + +
425B ALA* 3.4 16.1 - - + +
426B ASN* 6.0 1.1 - - - +
433B ALA* 2.3 43.4 + - + +
434B VAL* 4.0 17.8 - - - +
436B MET* 1.3 65.2 - - - +
438B SER* 1.3 67.7 + - - +
439B TYR 3.2 0.9 + - - -
440B ALA* 3.7 0.3 + - - -
441B LYS* 3.0 42.8 + - + +
444J ARG* 4.2 23.0 + - - -
463J ALA* 5.6 5.7 - - - +
466J ARG* 5.1 5.1 + - - +
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Residues in contact with SER 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 3.4 5.5 - - - +
112B GLU* 3.0 55.9 + - - +
116B LEU* 3.6 13.9 - - - +
130B TRP* 3.7 10.1 - - - -
434B VAL 2.7 20.3 + - - -
435B ALA* 3.0 11.1 + - - -
437B GLU* 1.3 82.8 - - - +
439B TYR* 1.3 63.1 + - - +
441B LYS* 3.6 2.5 + - - +
442B ALA 3.8 5.7 + - - -
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Residues in contact with TYR 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 5.5 4.0 - - + -
109B LEU* 3.7 21.6 - - + +
130B TRP* 3.3 24.7 - + + +
133B ALA* 3.0 23.8 - - + -
134B THR* 3.1 36.2 + - - +
137B ALA* 3.2 28.9 - - + +
421B VAL* 3.4 19.7 - - + -
435B ALA 2.5 15.2 + - - +
436B MET* 3.2 13.5 - - - +
437B GLU 3.0 0.8 - - - -
438B SER* 1.3 72.3 - - - +
440B ALA* 1.3 60.8 + - - +
442B ALA* 2.9 28.2 + - - +
443B LEU* 3.4 16.8 + - + +
504B LEU* 4.4 11.8 + - - +
508B ALA* 4.5 4.7 - - + -
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Residues in contact with ALA 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ALA* 3.2 23.4 - - - +
421B VAL* 3.4 16.2 - - + -
422B THR* 3.0 37.0 + - - +
436B MET 3.1 4.5 + - - +
439B TYR* 1.3 76.1 - - - +
441B LYS* 1.3 61.4 + - - +
442B ALA 3.2 0.2 - - - -
443B LEU* 3.1 14.9 + - + +
444B ARG* 2.7 22.7 + - - +
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Residues in contact with LYS 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLU* 3.0 38.3 + - - +
422B THR* 4.3 6.3 + - + +
437B GLU* 3.0 36.7 + - + +
438B SER* 3.6 7.4 + - - +
439B TYR 3.1 1.0 - - - -
440B ALA* 1.3 74.9 - - - +
442B ALA* 1.3 53.2 + - - +
444B ARG* 2.9 16.3 + - + +
445B MET* 2.3 46.6 + - + +
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Residues in contact with ALA 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 4.5 9.9 - - + +
108B GLU* 3.5 24.0 - - + -
109B LEU* 3.7 20.6 - - + -
438B SER 3.8 1.2 + - - -
439B TYR 2.9 12.1 + - - +
441B LYS* 1.3 77.5 - - - +
443B LEU* 1.3 56.3 + - + +
445B MET* 2.9 17.8 + - + +
446B LEU* 2.8 38.1 + - - +
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Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 4.5 9.9 - - + -
137B ALA* 3.5 20.4 - - + -
414B GLU* 3.2 46.0 - - - +
417B MET* 3.4 49.1 - - + +
418B ALA* 3.6 3.4 - - + -
421B VAL* 3.8 0.9 - - + -
439B TYR* 3.4 16.1 + - + +
440B ALA* 3.1 26.1 + - - +
442B ALA* 1.3 76.7 - - - +
444B ARG* 1.3 54.7 + - - +
446B LEU* 5.6 0.2 - - - -
447B PRO* 3.0 18.4 - - - +
504B LEU* 4.2 11.0 - - + -
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Residues in contact with ARG 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B MET* 3.3 27.0 - - + -
418B ALA* 3.4 9.3 + - + +
419B HIS* 4.1 30.9 + - - +
422B THR* 4.8 15.8 + - - +
440B ALA 2.7 12.6 + - - +
441B LYS* 2.9 18.1 + - - +
443B LEU* 1.3 77.5 - - - +
445B MET* 1.3 61.6 + - + +
447B PRO* 3.3 12.1 - - - +
448B THR* 3.7 12.0 - - - +
462B VAL* 3.6 10.7 - - + +
466B ARG* 3.0 45.3 - - - +
426J ASN* 3.9 6.9 + - - +
437J GLU* 2.8 30.7 + - - -
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Residues in contact with MET 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLU* 3.1 49.8 - - - +
111B ARG* 5.1 9.6 - - + -
112B GLU* 3.2 27.1 - - - +
441B LYS* 2.3 32.8 + - + +
442B ALA* 2.9 23.9 + - + +
444B ARG* 1.3 70.8 - - + +
446B LEU* 1.3 62.1 + - - +
447B PRO 3.4 0.2 - - - -
448B THR* 2.0 39.6 + - + +
449B ILE* 3.3 6.8 - - + +
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Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 4.4 8.0 - - + +
101B SER* 5.0 5.2 - - - +
104B VAL* 3.6 32.5 - - + -
105B LEU* 3.5 39.7 - - + +
108B GLU* 3.6 21.3 - - + -
414B GLU* 4.2 18.2 - - + +
442B ALA 2.8 18.0 + - - +
445B MET* 1.3 69.8 - - - +
447B PRO* 1.3 62.8 - - + +
449B ILE* 2.7 35.6 + - + +
450B ILE* 3.4 10.2 + - - +
503B VAL* 6.5 0.2 - - + -
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Residues in contact with PRO 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B GLY* 3.5 29.6 - - - +
414B GLU* 3.6 7.2 - - + -
415B MET* 4.3 3.1 - - + -
443B LEU 3.0 28.0 - - - +
444B ARG* 3.3 9.4 - - - +
446B LEU* 1.3 89.3 - - + +
448B THR* 1.3 60.5 + - - +
450B ILE* 3.7 9.0 - - + +
451B ALA* 3.5 14.9 + - - +
462B VAL* 3.6 18.6 - - + -
465B LEU* 3.9 6.5 - - + -
478B LEU* 3.4 25.9 - - + +
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Residues in contact with THR 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ARG 3.7 8.3 - - - +
445B MET* 2.0 37.7 + - + +
447B PRO* 1.3 78.2 - - - +
449B ILE* 1.3 66.2 + - - +
451B ALA* 3.5 0.3 + - - -
452B ASP* 2.8 42.7 + - - -
458B SER* 3.4 23.3 - - - +
462B VAL* 3.5 22.2 - - + -
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Residues in contact with ILE 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 3.5 50.3 - - + +
43B LEU* 3.6 13.5 - - + -
108B GLU* 3.8 15.5 - - - +
445B MET* 3.3 12.8 - - + +
446B LEU* 2.7 33.3 + - + +
448B THR* 1.3 82.7 - - - +
450B ILE* 1.3 50.2 + - - +
452B ASP* 3.6 4.1 - - - +
453B ASN* 2.4 58.5 + - - +
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Residues in contact with ILE 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.6 36.8 - - + +
44B GLY 4.5 0.4 - - - +
46B LYS* 5.4 0.2 - - - +
410B GLY* 4.2 7.4 - - - +
411B GLY 5.2 0.7 - - - +
446B LEU 3.4 7.4 + - - +
447B PRO* 3.7 13.0 - - + +
449B ILE* 1.3 75.9 - - - +
451B ALA* 1.3 66.9 + - + +
453B ASN* 3.3 9.5 - - - +
454B ALA* 2.5 34.2 + - - +
478B LEU* 3.8 34.5 - - + +
480B MET* 3.7 50.0 - - + +
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Residues in contact with ALA 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B PRO 3.5 15.7 + - - +
448B THR 3.5 2.1 + - - +
449B ILE 3.3 0.6 - - - -
450B ILE* 1.3 88.5 - - + +
452B ASP* 1.3 58.2 + - - +
454B ALA* 3.1 10.9 + - - +
455B GLY 2.8 8.0 + - - -
456B TYR* 2.8 35.7 + - - +
458B SER* 4.5 7.4 - - - -
461B LEU* 4.5 14.1 - - + -
478B LEU* 4.2 13.7 - - + -
480B MET* 5.7 0.2 - - - +
483B GLY 4.9 2.9 - - - +
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Residues in contact with ASP 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B THR* 2.8 31.1 + - - +
449B ILE* 3.9 4.4 - - - +
451B ALA* 1.3 72.8 - - - +
453B ASN* 1.3 62.4 + - - +
455B GLY* 3.0 17.6 + - - +
456B TYR 2.9 20.8 - - - +
457B ASP* 4.3 0.7 - - - -
458B SER* 3.4 23.9 + - - -
27D ARG* 4.0 9.6 + - - +
129D HIS* 3.8 7.1 + - - -
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Residues in contact with ASN 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS 2.9 27.5 + - - +
41B SER* 3.1 12.1 - - - +
43B LEU 3.1 22.5 + - - +
44B GLY* 5.5 0.2 - - - -
46B LYS* 2.8 25.6 - - - +
47B GLY* 3.2 2.3 - - - +
449B ILE* 2.4 50.9 + - - +
450B ILE 3.3 5.6 - - - +
452B ASP* 1.3 68.1 - - - +
454B ALA* 1.3 60.6 + - - +
455B GLY 2.9 6.1 + - - -
27D ARG* 2.6 26.5 + - - +
129D HIS* 3.1 16.8 + - - -
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Residues in contact with ALA 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS* 3.3 28.5 + - - +
450B ILE 2.5 18.2 + - - +
451B ALA* 3.1 15.0 + - - +
453B ASN* 1.3 72.5 - - - +
455B GLY* 1.3 60.9 + - - +
456B TYR* 3.2 16.1 - - + -
480B MET* 4.1 12.1 - - + +
483B GLY* 3.9 9.9 - - - -
129D HIS* 4.4 0.7 - - - -
132D ILE* 3.2 23.1 - - - +
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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