Contacts of the helix formed by residues 498 - 519 (chain B) in PDB entry 5AM8
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 TYR 498 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLN* 3.5 10.4 + - - -
435B PHE* 3.4 32.8 - + - -
438B PHE* 3.4 32.8 - + - -
439B GLY* 3.8 13.4 - - - +
442B VAL* 3.7 24.2 - - + -
443B ASP* 2.9 25.6 + - - +
446B ARG* 3.4 5.3 - - - +
489B LYS* 3.8 7.6 + - - -
491B HIS* 3.5 41.5 - + + -
497B PRO* 1.3 72.7 - - - +
499B ILE* 1.3 58.1 + - - +
500B ARG* 3.0 3.4 - - - -
501B TYR* 2.8 49.9 + + - +
502B PHE 3.9 1.4 + - - -
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Residues in contact with ILE 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B TRP 6.5 0.9 - - - -
199B ARG* 6.0 0.4 - - + -
202B TYR* 4.0 24.2 - - + +
207B PHE* 4.3 7.9 - - + -
211B LEU* 3.8 33.0 - - + -
439B GLY 4.1 10.3 - - - +
440B TYR* 4.1 21.5 - - + +
443B ASP* 3.0 19.5 + - + +
444B GLN* 6.4 0.2 - - + -
447B TRP* 4.1 23.6 - - + +
497B PRO* 5.7 3.1 - - + -
498B TYR* 1.3 76.0 - - - +
500B ARG* 1.3 65.0 + - - +
501B TYR 3.1 0.2 - - - -
502B PHE* 3.1 19.8 + - + -
503B VAL* 2.9 22.7 + - + +
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Residues in contact with ARG 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B TRP* 3.5 30.7 - - - -
202B TYR* 3.3 18.6 + - - +
385B PRO* 3.8 19.0 - - + +
386B GLY* 3.5 19.7 - - - +
389B GLU* 3.7 28.2 + - + +
496B THR* 3.8 19.6 - - - +
497B PRO* 3.3 39.4 + - - +
499B ILE* 1.3 82.0 - - - +
501B TYR* 1.3 69.6 + - + +
503B VAL* 4.4 0.4 - - - -
504B SER* 2.8 33.4 + - - -
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Residues in contact with TYR 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B HIS* 5.5 0.7 + - - -
361B HIS* 4.4 10.9 + + - -
389B GLU* 3.1 41.7 + - + -
435B PHE* 3.6 26.7 - + + -
491B HIS* 3.0 37.1 + + - -
496B THR* 4.5 5.4 - - - +
497B PRO 3.9 2.5 - - - -
498B TYR* 2.8 49.0 + + + +
500B ARG* 1.3 82.3 + - + +
502B PHE* 1.3 66.5 + - - +
504B SER* 3.4 3.5 + - - -
505B PHE* 3.0 38.6 + + + +
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Residues in contact with PHE 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 3.9 36.8 - - + -
214B LEU* 4.4 13.5 - - + -
215B TYR* 4.0 32.1 - + + -
218B LEU* 4.1 18.2 - - + -
435B PHE* 4.4 2.2 - - - -
436B LEU* 3.5 45.3 - - + -
439B GLY* 3.6 22.0 + - - +
440B TYR* 3.8 13.0 - + + -
498B TYR 3.9 1.4 + - - -
499B ILE* 3.1 15.2 + - + +
501B TYR* 1.3 75.3 - - - +
503B VAL* 1.3 68.8 + - - +
505B PHE* 3.1 13.5 + - - +
506B VAL* 3.4 17.2 + - + +
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Residues in contact with VAL 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B TYR* 4.1 19.5 - - + -
207B PHE* 4.3 8.5 - - + -
211B LEU* 4.2 16.8 - - + -
384B ASN* 4.4 11.2 - - - +
386B GLY* 3.9 17.7 - - - -
499B ILE 2.9 19.2 + - - +
500B ARG* 3.7 5.2 - - - +
502B PHE* 1.3 77.9 - - - +
504B SER* 1.3 58.5 + - - +
506B VAL* 3.3 4.2 + - - +
507B LEU* 2.8 33.5 + - + +
565B LEU* 4.0 35.4 - - + +
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Residues in contact with SER 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLY 3.8 10.8 - - - -
389B GLU* 3.3 35.4 + - - +
390B ALA* 3.5 2.4 - - - +
393B ASP* 4.2 0.9 + - - -
500B ARG 2.8 18.5 + - - -
501B TYR* 3.5 8.7 - - - -
503B VAL* 1.3 78.6 - - - +
505B PHE* 1.3 61.8 + - - +
507B LEU* 4.2 4.0 - - - -
508B GLN* 3.0 45.0 + - - +
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Residues in contact with PHE 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B HIS* 6.3 1.1 - + - -
393B ASP* 3.6 20.4 - - - -
431B GLU* 3.8 15.5 - - + -
432B LYS* 3.6 36.6 - - + -
435B PHE* 3.4 47.3 - + + -
436B LEU* 3.9 17.5 - - + -
501B TYR* 3.0 33.8 + + + +
502B PHE 3.1 2.6 + - - +
504B SER* 1.3 82.1 - - - +
506B VAL* 1.3 58.9 + - - +
508B GLN* 3.7 11.6 - - - +
509B PHE* 3.1 31.6 - - + -
570B LEU* 3.6 5.1 - - + +
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Residues in contact with VAL 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 4.5 17.7 - - + -
218B LEU* 4.2 24.7 - - + -
436B LEU* 4.9 4.7 - - + -
502B PHE* 3.6 18.2 - - + +
503B VAL* 3.3 6.7 + - - +
504B SER 3.2 0.2 - - - -
505B PHE* 1.3 78.6 - - - +
507B LEU* 1.3 66.5 + - - +
509B PHE* 3.2 15.8 + - - +
510B GLN* 3.5 14.6 + - - +
565B LEU* 4.3 7.9 - - + -
566B ASP 3.4 34.3 - - - +
567B ALA* 4.1 7.4 - - - +
570B LEU* 4.5 9.6 + - + +
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Residues in contact with LEU 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLY 3.9 5.8 - - - +
387B PHE* 3.6 48.9 - - + +
390B ALA* 4.3 1.8 - - + -
503B VAL* 2.8 27.4 + - + +
504B SER* 3.9 3.8 - - - +
506B VAL* 1.3 75.3 - - - +
508B GLN* 1.3 57.5 + - - +
510B GLN* 3.0 17.9 + - - +
511B PHE* 2.9 59.8 + - + -
552B TRP* 5.8 0.7 - - + -
556B LEU* 4.1 19.1 - - + -
565B LEU* 3.6 19.0 - - + +
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Residues in contact with GLN 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ALA* 4.2 9.6 - - + +
393B ASP* 3.0 33.5 + - + +
394B VAL* 3.8 24.9 - - + +
397B LEU* 4.0 13.0 - - + +
432B LYS* 2.7 34.7 + - - +
504B SER* 3.0 32.4 + - - +
505B PHE* 3.7 19.2 - - - +
507B LEU* 1.3 77.7 - - - +
509B PHE* 1.3 67.7 + - + +
511B PHE* 3.6 2.8 + - - +
512B HIS* 2.8 28.1 + - - +
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Residues in contact with PHE 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B LEU* 4.0 18.4 - - + -
432B LYS* 4.1 22.4 - - + -
505B PHE 3.1 28.0 - - - -
506B VAL 3.2 5.2 + - - +
507B LEU 3.1 0.4 - - - -
508B GLN* 1.3 87.7 - - + +
510B GLN* 1.3 58.5 + - - +
512B HIS* 3.7 4.1 - + - +
513B GLU* 2.9 30.1 + - - +
525B LEU* 4.9 2.6 - - + +
569B PRO* 3.5 7.6 - - - +
570B LEU* 3.5 42.0 - - + +
573B TYR* 3.5 53.6 - + + -
574B PHE* 3.7 16.8 - + - -
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Residues in contact with GLN 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B VAL* 3.5 6.4 + - - +
507B LEU* 3.0 18.2 + - + +
509B PHE* 1.3 79.5 - - - +
511B PHE* 1.3 66.7 + - + +
513B GLU* 3.5 3.6 + - - +
514B ALA* 3.1 23.0 + - - +
556B LEU* 4.3 3.6 - - + +
560B VAL* 3.8 25.7 - - + +
562B LEU* 4.2 5.3 - - - +
564B ALA 3.2 21.2 + - - -
565B LEU* 3.4 20.8 - - - +
566B ASP* 3.0 43.9 + - - +
569B PRO* 3.9 17.7 - - + +
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Residues in contact with PHE 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B PHE* 3.7 26.7 - + - -
390B ALA* 3.9 21.8 - - + -
391B ILE* 4.2 20.2 - - + -
394B VAL* 3.6 30.3 - - + -
507B LEU* 2.9 35.2 + - + -
508B GLN 3.7 2.2 - - - +
510B GLN* 1.3 77.8 - - - +
512B HIS* 1.3 58.0 + - - +
514B ALA* 3.3 1.6 + - - +
515B LEU* 2.9 36.7 + - + +
540B LEU* 5.1 2.7 - - + -
543B VAL* 5.2 1.1 - - + -
556B LEU* 3.8 17.3 - - + -
559B MET* 3.4 41.3 - - + -
560B VAL* 4.2 4.5 - - + -
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Residues in contact with HIS 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B VAL* 4.3 15.9 + - + +
397B LEU* 4.0 29.4 + - + +
398B SER* 4.0 12.7 + - - -
508B GLN 2.8 20.0 + - - +
509B PHE* 3.7 6.5 - + - +
510B GLN 3.3 0.2 - - - -
511B PHE* 1.3 76.4 - - - +
513B GLU* 1.3 57.8 + - - +
515B LEU* 3.9 1.5 - - - +
516B CYS* 2.8 56.0 + - - -
525B LEU* 3.3 45.5 + - + -
526B HIS 5.5 0.2 - - - -
528B CYS* 3.9 16.6 + - - +
530B ILE* 5.1 3.0 - - - +
573B TYR* 4.2 19.7 - + - -
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Residues in contact with GLU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B PHE 2.9 17.2 + - - +
510B GLN 3.7 4.5 - - - +
512B HIS* 1.3 77.6 - - - +
514B ALA* 1.3 60.5 + - - +
516B CYS* 3.8 1.4 - - - +
517B LYS* 3.0 28.4 + - + +
525B LEU* 3.7 22.8 - - + +
569B PRO* 3.5 28.7 - - + +
572B LYS* 2.7 34.5 + - - +
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Residues in contact with ALA 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510B GLN 3.1 15.3 + - - +
511B PHE* 3.7 4.3 - - - +
513B GLU* 1.3 79.3 - - - +
515B LEU* 1.3 59.6 + - + +
517B LYS* 3.4 7.5 + - - +
518B GLU* 2.9 28.2 + - - +
539B LYS* 4.2 9.0 - - + +
559B MET* 3.7 17.5 - - + +
560B VAL* 3.6 26.7 - - + +
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Residues in contact with LEU 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B VAL* 3.8 24.5 - - + -
511B PHE* 2.9 21.7 + - + +
512B HIS* 4.0 2.7 - - - +
514B ALA* 1.3 72.8 - - - +
516B CYS* 1.3 59.6 + - - +
518B GLU* 3.3 3.9 + - - +
519B ALA* 2.8 30.7 + - - +
530B ILE* 4.2 20.0 - - + -
536B ALA* 3.4 38.1 - - + +
539B LYS* 3.8 25.4 - - + -
540B LEU* 4.0 22.2 - - + +
559B MET* 4.2 17.3 - - + -
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Residues in contact with CYS 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B HIS* 2.8 43.4 + - - +
513B GLU 3.8 3.8 - - - +
515B LEU* 1.3 78.0 - - - +
517B LYS* 1.3 59.0 + - - +
519B ALA* 3.5 5.2 + - - +
521B TYR* 3.0 38.4 + - + +
525B LEU* 4.3 7.9 - - + -
528B CYS* 2.0 53.6 - - + -
530B ILE* 3.8 5.8 - - - -
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Residues in contact with LYS 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B GLU* 3.0 23.0 + - + +
514B ALA* 3.5 8.1 - - - +
516B CYS* 1.3 74.5 - - - +
518B GLU* 1.3 60.9 + - - +
520B GLY* 2.8 22.0 + - - -
521B TYR 4.6 6.3 - - - -
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Residues in contact with GLU 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B ALA 2.9 16.6 + - - +
515B LEU* 3.3 5.4 + - - +
517B LYS* 1.3 75.8 - - - +
519B ALA* 1.3 50.5 + - - +
520B GLY 3.1 0.7 + - - -
535B LYS* 2.8 76.3 + - + +
536B ALA* 4.2 1.3 - - - -
539B LYS* 3.7 33.2 - - + +
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Residues in contact with ALA 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B LEU 2.8 18.0 + - - +
516B CYS* 3.6 11.0 - - - +
517B LYS 3.1 0.4 - - - -
518B GLU* 1.3 77.6 - - - +
520B GLY* 1.3 58.0 + - - +
521B TYR* 3.5 6.9 + - + +
529B ASP 5.6 1.1 - - - +
530B ILE* 4.7 9.6 - - + -
533B SER* 3.5 33.2 + - - +
535B LYS* 4.1 7.7 + - - +
536B ALA* 4.5 2.0 - - + +
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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