Contacts of the helix formed by residues 433 - 457 (chain A) in PDB entry 3N00
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 433 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A VAL* 1.3 76.5 - - - +
434A GLU* 1.3 62.3 + - - +
435A ILE 3.1 2.0 - - - +
436A TRP* 3.3 23.5 + - + +
437A GLU* 3.1 40.7 + - - +
608A SER* 5.0 1.9 + - - -
610A ARG* 5.1 3.0 - - - +
2046B HIS* 3.3 40.0 + - - -
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Residues in contact with GLU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A VAL* 3.5 15.2 - - + +
433A GLN* 1.3 84.2 - - - +
435A ILE* 1.3 55.8 + - + +
437A GLU* 3.6 13.2 + - - +
438A ASP* 3.0 25.1 + - - -
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Residues in contact with ILE 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A VAL 3.4 23.1 - - - +
433A GLN 3.1 0.4 - - - -
434A GLU* 1.3 78.9 - - + +
436A TRP* 1.3 56.2 + - - +
438A ASP* 3.3 1.2 + - - +
439A PHE* 2.9 30.3 + - - +
508A LEU* 4.0 20.0 - - + +
511A MET* 3.3 17.8 - - + +
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Residues in contact with TRP 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A VAL 5.6 0.4 - - - +
433A GLN* 3.3 27.1 + - + +
435A ILE* 1.3 76.9 - - - +
437A GLU* 1.3 56.3 + - + +
439A PHE* 3.7 6.0 - + - +
440A SER* 2.6 47.1 + - - -
511A MET* 3.3 50.5 + - + +
513A MET* 6.1 0.2 - - + -
606A LEU* 3.1 42.4 + - + -
607A LEU* 3.8 7.4 - - - +
608A SER* 3.6 26.2 - - - -
2048B LEU* 3.3 25.4 - - + -
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Residues in contact with GLU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLN* 3.1 31.4 + - - +
434A GLU* 3.9 11.6 - - - +
436A TRP* 1.3 75.4 - - + +
438A ASP* 1.3 56.3 + - - +
440A SER* 3.3 2.4 + - - -
441A MET* 3.1 40.9 + - + +
608A SER* 3.9 20.5 - - - +
610A ARG* 3.2 30.2 + - - +
2046B HIS* 2.6 36.0 + - + +
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Residues in contact with ASP 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLU 3.0 16.8 + - - -
435A ILE* 3.8 2.0 - - - +
436A TRP 3.2 0.4 - - - -
437A GLU* 1.3 74.6 - - - +
439A PHE* 1.3 63.7 + - - +
441A MET* 3.6 10.2 + - - +
442A SER* 3.3 19.8 + - - -
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Residues in contact with PHE 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ILE 2.9 17.3 + - - +
436A TRP* 3.7 7.6 - + - +
438A ASP* 1.3 73.4 - - - +
440A SER* 1.3 63.5 + - - +
442A SER* 3.1 25.5 + - - -
443A PHE* 3.2 47.7 - + - -
508A LEU* 5.9 8.1 - - + -
511A MET* 4.2 20.9 - - + -
513A MET* 4.2 17.7 - - + -
516A LEU* 4.4 19.5 - - + -
517A LEU* 6.0 5.2 - - + -
520A MET* 5.3 13.0 - - + -
605A LYS* 6.3 1.6 - - + -
606A LEU 5.8 0.4 - - - -
607A LEU* 4.2 13.2 - - + -
2051B LEU* 5.4 0.4 - - + -
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Residues in contact with SER 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A TRP* 2.6 34.2 + - - -
437A GLU 3.5 3.4 - - - -
438A ASP 3.3 0.2 - - - -
439A PHE* 1.3 74.6 - - - +
441A MET* 1.3 59.5 + - - +
442A SER 3.5 0.3 + - - -
443A PHE* 3.5 21.7 + - - +
607A LEU* 3.6 13.9 - - - +
608A SER 2.9 42.2 + - - -
609A PHE* 3.4 23.4 - - - -
2054B HIS* 4.2 1.0 + - - -
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Residues in contact with MET 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A GLU* 3.1 28.7 + - + +
438A ASP* 4.0 7.2 - - - +
439A PHE 3.3 0.2 - - - -
440A SER* 1.3 73.6 - - - +
442A SER* 1.3 64.5 + - - +
443A PHE 3.2 1.6 - - - -
444A THR* 3.8 7.5 + - - +
445A PRO* 3.2 19.6 - - - +
609A PHE* 3.7 25.6 - - + -
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Residues in contact with SER 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ASP 3.3 12.0 + - - -
439A PHE* 3.1 21.5 + - - -
441A MET* 1.3 78.9 - - - +
443A PHE* 1.3 64.7 + - - +
445A PRO* 3.3 19.3 - - - +
446A ALA* 3.5 11.5 + - - +
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Residues in contact with PHE 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A PHE* 3.2 70.2 - + - -
440A SER 3.5 11.2 - - - +
441A MET 3.2 1.4 - - - -
442A SER* 1.3 77.0 - - - +
444A THR* 1.3 55.1 + - - +
446A ALA* 4.1 4.7 - - + -
447A VAL* 2.7 44.3 + - + +
477A PHE* 5.7 1.1 - + - -
480A LEU* 3.9 25.1 - - + -
481A MET* 5.7 5.2 - - + -
516A LEU* 5.3 0.9 - - + -
520A MET* 6.3 1.8 - - - -
607A LEU* 3.6 17.5 - - + -
2051B LEU* 3.4 37.2 - - + -
2054B HIS* 3.9 14.4 - - + -
2058B ILE* 4.5 0.2 - - - -
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Residues in contact with THR 444 (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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441A MET* 3.8 7.7 + - - +
443A PHE* 1.3 77.3 - - - +
445A PRO* 1.3 70.2 - - + +
447A VAL* 3.5 2.3 + - - +
448A ARG* 3.2 58.9 + - - +
609A PHE* 4.8 5.0 - - - -
2054B HIS* 2.8 29.0 + - + -
2058B ILE* 3.4 20.0 - - + +
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Residues in contact with PRO 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A MET 3.2 17.7 - - - +
442A SER* 3.3 15.0 - - - +
444A THR* 1.3 92.3 - - + +
446A ALA* 1.3 56.9 + - - +
448A ARG* 3.2 16.2 + - + +
449A GLU* 2.8 40.0 + - + +
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Residues in contact with ALA 446 (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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300A PHE* 5.2 0.2 - - - -
442A SER 3.5 14.0 + - - +
443A PHE* 3.3 11.6 + - + +
444A THR 3.3 0.6 - - - -
445A PRO* 1.3 78.7 - - - +
447A VAL* 1.3 63.2 + - - +
449A GLU* 3.1 19.0 + - - +
450A VAL* 3.0 25.3 + - - +
480A LEU* 3.7 24.0 - - + -
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Residues in contact with VAL 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A PHE* 2.7 34.4 + - + +
446A ALA* 1.3 71.4 - - - +
448A ARG* 1.3 56.6 + - - +
450A VAL* 3.2 3.7 + - - +
451A VAL* 2.9 33.3 + - + +
476A THR* 4.1 17.5 - - + -
480A LEU* 4.1 13.0 - - + -
2054B HIS* 5.6 0.2 - - + -
2055B ILE* 3.9 27.8 - - + +
2058B ILE* 3.6 35.4 - - + -
2059B ILE* 4.0 22.7 - - + -
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Residues in contact with ARG 448 (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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444A THR* 3.2 50.6 + - - +
445A PRO* 3.6 15.1 - - + +
446A ALA 3.2 0.2 - - - -
447A VAL* 1.3 73.4 - - - +
449A GLU* 1.3 65.4 + - - +
451A VAL* 3.4 4.6 + - - +
452A GLU* 3.1 23.4 + - - +
2058B ILE* 4.1 13.6 - - + +
2061B GLN* 6.4 0.6 - - - +
2062B ASP* 3.7 27.6 + - - +
2065B ARG* 5.6 5.6 - - - +
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Residues in contact with GLU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE* 3.3 37.0 - - + +
300A PHE* 3.8 27.0 - - + -
445A PRO* 2.8 24.9 + - + +
446A ALA* 3.1 17.6 + - - +
448A ARG* 1.3 75.0 - - - +
450A VAL* 1.3 59.2 + - - +
452A GLU* 3.3 1.6 + - - -
453A PHE* 3.0 26.3 + - - +
483A ARG* 5.5 0.3 + - - -
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Residues in contact with VAL 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A PHE* 4.3 15.7 - - + -
446A ALA 3.0 18.3 + - - +
447A VAL 3.5 7.4 - - - +
449A GLU* 1.3 76.2 - - - +
451A VAL* 1.3 62.4 + - - +
453A PHE* 3.4 4.2 + - + +
454A ALA* 2.9 21.8 + - - +
472A LEU* 4.0 8.7 - - + -
476A THR* 4.0 29.4 - - + +
479A VAL* 3.8 34.3 - - + -
480A LEU* 3.8 19.7 - - + -
483A ARG* 5.2 0.2 - - + -
545A LEU* 4.6 8.7 - - + -
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Residues in contact with VAL 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A VAL* 2.9 25.6 + - + +
448A ARG* 3.8 4.9 - - - +
449A GLU 3.3 0.2 - - - -
450A VAL* 1.3 76.9 - - + +
452A GLU* 1.3 61.3 + - - +
454A ALA* 3.4 3.6 + - - +
455A LYS* 3.3 32.4 + - + +
472A LEU* 4.2 19.2 - - + +
476A THR* 5.5 0.2 - - - +
2058B ILE* 5.8 0.2 - - + -
2059B ILE* 4.3 27.4 - - + -
2062B ASP* 4.0 29.2 - - + +
2063B PHE* 3.8 26.0 - - + -
2065B ARG* 5.7 0.2 - - - +
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Residues in contact with GLU 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE* 3.6 23.1 - - + -
448A ARG 3.1 17.4 + - - +
449A GLU* 3.8 4.0 - - - +
451A VAL* 1.3 74.6 - - - +
453A PHE* 1.3 65.9 + - - +
455A LYS* 3.1 33.1 + - - +
456A HIS* 2.9 39.7 + - + -
2065B ARG* 4.6 8.3 + - - -
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Residues in contact with PHE 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A VAL* 3.8 11.7 - - + -
295A ALA* 4.0 9.4 - - + -
296A HIS* 3.7 35.7 - - + -
299A ILE* 3.4 11.1 - - + +
300A PHE* 3.6 27.1 - + + -
449A GLU 3.0 17.7 + - - +
450A VAL* 3.5 6.5 - - + +
452A GLU* 1.3 75.1 - - - +
454A ALA* 1.3 55.4 + - - +
456A HIS* 2.7 31.7 + - - +
457A ILE* 3.4 16.2 + - + +
479A VAL* 5.5 2.2 - - + -
538A GLY 3.4 22.9 - - - -
541A THR* 3.8 24.0 - - + -
542A ALA* 3.8 23.6 - - + -
545A LEU* 5.1 5.4 - - + -
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Residues in contact with ALA 454 (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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450A VAL 2.9 10.6 + - - +
451A VAL 3.6 9.4 - - - +
453A PHE* 1.3 75.8 - - - +
455A LYS* 1.3 63.1 + - - +
457A ILE* 3.0 25.1 + - - +
460A PHE* 3.2 42.8 - - + +
472A LEU* 4.0 7.0 - - + -
545A LEU* 3.4 26.7 - - + -
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Residues in contact with LYS 455 (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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451A VAL* 3.3 30.0 - - + +
452A GLU* 3.1 27.5 + - - +
453A PHE 3.0 0.8 + - - -
454A ALA* 1.3 77.2 - - + +
456A HIS* 1.3 64.0 + - + +
457A ILE 3.7 2.8 + - - +
460A PHE* 4.5 3.1 - - + -
461A ARG* 3.6 65.7 - - - +
2062B ASP* 4.3 4.4 + - - -
2063B PHE* 5.0 6.7 - - + -
2065B ARG* 4.0 26.1 - - - +
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Residues in contact with HIS 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLN* 3.2 33.1 + - + +
292A VAL* 5.1 0.8 + - - -
295A ALA* 3.4 33.6 - - + +
298A GLU* 5.0 8.9 + - - -
299A ILE* 3.7 13.1 - - + +
452A GLU* 2.9 44.3 + - + -
453A PHE 2.7 12.9 + - - +
455A LYS* 1.3 75.0 - - + +
457A ILE* 1.3 61.3 + - - -
458A PRO* 3.3 3.6 - - - +
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Residues in contact with ILE 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLN* 4.8 0.2 - - - -
292A VAL* 4.7 4.0 - - + -
453A PHE* 3.6 22.0 - - + +
454A ALA* 3.0 28.5 + - + +
455A LYS 4.4 3.3 - - - +
456A HIS* 1.3 77.8 - - - +
458A PRO* 1.4 81.6 - - + +
459A GLY 3.0 0.7 + - - -
460A PHE* 2.9 27.9 + - + +
461A ARG 4.5 1.0 + - - -
542A ALA* 3.8 28.5 - - + +
545A LEU* 4.1 16.8 - - + -
546A VAL* 4.7 7.0 - - + -
562A LEU* 4.7 3.6 - - + -
566A LEU* 4.0 30.3 - - + -
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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
------------------------------------------------------------
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