Contacts of the helix formed by residues 498 - 519 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A GLN* 3.7 10.0 + - - -
435A PHE* 3.3 36.8 - + - -
438A PHE* 3.4 25.0 - + - -
439A GLY* 3.8 16.7 - - - +
442A VAL* 3.6 27.1 - - + -
443A ASP* 2.8 24.8 + - - +
446A ARG* 3.4 4.7 - - - +
489A LYS* 3.7 8.7 + - + -
491A HIS* 3.6 45.1 - + + -
497A PRO* 1.3 71.6 - - - +
499A ILE* 1.3 64.6 + - - +
500A ARG 3.1 3.1 - - - -
501A TYR* 2.9 39.8 + + - +
502A PHE 3.9 1.4 + - - -
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Residues in contact with ILE 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TRP* 5.9 2.0 - - + +
199A ARG* 6.1 0.7 - - + -
202A TYR* 3.9 26.5 - - + +
207A PHE* 4.0 11.7 - - + -
211A LEU* 3.9 33.9 - - + -
439A GLY 4.1 9.4 - - - +
440A TYR* 4.2 18.8 - - + +
443A ASP* 3.0 19.8 + - + +
447A TRP* 4.2 18.6 - - + +
497A PRO* 5.7 3.6 - - + -
498A TYR* 1.3 76.2 - - - +
500A ARG* 1.3 65.1 + - - +
501A TYR 3.0 1.2 + - - -
502A PHE* 3.0 30.3 + - + +
503A VAL* 3.0 12.2 + - + +
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Residues in contact with ARG 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TRP* 3.7 16.2 - - - -
202A TYR* 3.4 17.9 - - - +
385A PRO* 3.7 26.6 - - + +
386A GLY* 3.4 7.4 - - - +
389A GLU* 3.5 34.5 + - + -
496A THR* 3.7 19.6 - - - +
497A PRO* 3.3 51.4 + - - +
498A TYR 3.9 0.4 - - - +
499A ILE* 1.3 82.0 - - - +
501A TYR* 1.3 73.7 + - + +
503A VAL* 4.4 1.1 - - - -
504A SER* 2.8 29.1 + - - -
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Residues in contact with TYR 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A HIS* 5.6 0.2 + - - -
361A HIS* 4.4 11.2 + + - -
389A GLU* 3.2 41.4 + - + -
435A PHE* 3.6 25.4 - + + -
491A HIS* 2.9 36.4 + + - -
496A THR* 4.3 6.8 - - - +
497A PRO 3.9 3.4 - - - -
498A TYR* 2.9 45.5 + + + +
500A ARG* 1.3 84.2 - - + +
502A PHE* 1.3 62.7 + - - +
504A SER* 3.4 4.2 - - - -
505A PHE* 2.9 42.5 + + + +
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Residues in contact with PHE 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.9 40.4 - - + -
214A LEU* 4.3 13.0 - - + -
215A TYR* 4.0 31.0 - + + -
218A LEU* 3.9 26.5 - - + -
435A PHE* 4.3 2.5 - - - -
436A LEU* 3.5 36.8 - - + -
439A GLY* 3.6 22.0 + - - +
440A TYR* 3.9 10.8 - + + -
498A TYR 3.9 1.6 + - - -
499A ILE* 3.0 16.6 + - + +
501A TYR* 1.3 77.0 - - - +
503A VAL* 1.3 65.2 + - - +
505A PHE* 3.2 13.2 + - - +
506A VAL* 3.3 17.6 + - + +
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Residues in contact with VAL 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TYR* 4.3 20.2 - - + -
207A PHE* 4.4 3.4 - - + -
211A LEU* 4.2 24.5 - - + -
384A ASN* 4.4 10.1 - - - +
386A GLY* 4.0 16.2 - - - -
499A ILE* 3.0 16.4 + - + +
500A ARG* 3.7 7.4 - - - +
502A PHE* 1.3 76.5 - - - +
504A SER* 1.3 57.6 + - - +
506A VAL* 3.3 6.2 + - - +
507A LEU* 2.9 34.4 + - + +
565A LEU* 3.9 32.2 - - + +
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Residues in contact with SER 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLY* 3.6 12.5 - - - -
389A GLU* 3.1 38.9 + - - +
390A ALA* 3.3 7.4 - - - +
393A ASP* 4.3 0.9 + - - -
500A ARG 2.8 22.8 + - - -
501A TYR* 3.3 7.8 + - - -
503A VAL* 1.3 74.6 - - - +
505A PHE* 1.3 60.1 + - - +
507A LEU* 3.8 1.7 - - - +
508A GLN* 2.8 39.8 + - - +
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Residues in contact with PHE 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A HIS* 6.4 0.9 - + - -
393A ASP* 3.7 19.1 - - - -
431A GLU* 3.7 15.3 - - + -
432A LYS* 3.5 39.7 - - + -
435A PHE* 3.5 45.5 - + + -
436A LEU* 4.0 14.4 - - + -
501A TYR* 2.9 36.8 + + + +
502A PHE* 3.2 5.1 + - - +
504A SER* 1.3 77.5 - - - +
506A VAL* 1.3 58.8 + - - +
508A GLN* 3.5 12.0 - - - +
509A PHE* 3.1 31.4 - + - -
570A LEU* 3.7 4.2 - - + +
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Residues in contact with VAL 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 4.4 24.0 - - + -
218A LEU* 4.1 26.5 - - + -
436A LEU* 4.9 4.0 - - + -
502A PHE* 3.3 17.1 + - + +
503A VAL* 3.3 8.4 + - - +
504A SER 3.2 0.2 - - - -
505A PHE* 1.3 76.2 - - - +
507A LEU* 1.3 67.1 + - - +
509A PHE* 3.2 16.6 + - - +
510A GLN* 3.6 15.7 + - - +
565A LEU* 4.6 4.5 - - + -
566A ASP 3.6 31.5 - - - +
567A ALA* 4.4 5.6 - - - +
570A LEU* 4.5 10.3 - - + +
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Residues in contact with LEU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASN* 5.5 0.2 - - - +
386A GLY 3.9 7.9 - - - +
387A PHE* 3.7 45.1 - - + +
390A ALA* 4.3 0.9 - - + -
503A VAL* 2.9 24.8 + - + +
504A SER 3.8 2.5 - - - +
506A VAL* 1.3 76.7 - - - +
508A GLN* 1.3 57.8 + - - +
510A GLN* 2.9 31.5 + - - +
511A PHE* 2.9 35.0 + - + -
556A LEU* 3.7 31.9 - - + -
565A LEU* 3.8 19.7 - - + -
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Residues in contact with GLN 508 (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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390A ALA* 4.1 10.0 - - + +
393A ASP* 2.9 33.3 + - + +
394A VAL* 3.6 28.9 - - + +
397A LEU* 3.9 13.6 - - + +
432A LYS* 2.7 34.4 + - - +
504A SER* 2.8 32.6 + - - +
505A PHE* 3.5 23.9 - - - +
506A VAL 3.2 0.2 + - - -
507A LEU* 1.3 73.3 - - - +
509A PHE* 1.3 66.7 + - + +
511A PHE* 4.4 0.2 - - - -
512A HIS* 2.9 26.9 + - - +
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Residues in contact with PHE 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A LEU* 4.1 19.5 - - + -
432A LYS* 4.1 19.1 - - + -
505A PHE 3.1 28.7 - - - -
506A VAL 3.2 5.8 + - - +
507A LEU 3.1 0.6 - - - -
508A GLN* 1.3 87.9 - - + +
510A GLN* 1.3 63.4 + - - +
512A HIS* 3.7 4.7 - + - +
513A GLU* 3.0 19.1 + - - +
525A LEU* 5.0 2.6 - - + +
569A PRO* 3.5 12.1 - - - +
570A LEU* 3.6 42.2 - - + +
573A TYR* 3.5 52.7 - + + -
574A PHE* 3.6 20.6 - + - -
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Residues in contact with GLN 510 (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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506A VAL* 3.6 5.4 + - - +
507A LEU* 2.9 32.5 + - + +
509A PHE* 1.3 78.5 - - - +
511A PHE* 1.3 62.6 + - - +
513A GLU* 3.8 2.8 - - - +
514A ALA* 3.1 24.3 + - - +
556A LEU* 4.2 3.6 - - - +
560A VAL* 3.6 30.0 - - + +
562A LEU* 4.4 3.2 - - - +
564A ALA 3.1 21.2 + - - -
565A LEU* 3.4 10.0 - - - +
566A ASP* 3.0 45.8 + - - +
569A PRO* 3.9 17.0 - - + +
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Residues in contact with PHE 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PHE* 3.9 22.0 - + - -
390A ALA* 3.9 23.3 - - + -
391A ILE* 4.2 19.7 - - + -
394A VAL* 3.6 31.9 - - + -
507A LEU* 2.9 43.5 + - + -
508A GLN 3.7 1.3 - - - +
510A GLN* 1.3 78.8 - - - +
512A HIS* 1.3 57.9 + - - +
514A ALA* 3.3 1.4 + - - +
515A LEU* 2.9 36.4 + - + +
540A LEU* 5.4 2.2 - - + -
543A VAL* 5.1 1.8 - - + -
556A LEU* 3.7 11.2 - - + -
559A MET* 3.1 41.1 - - + -
560A VAL* 4.2 4.7 - - + -
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Residues in contact with HIS 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A VAL* 4.2 15.5 + - + +
397A LEU* 4.0 30.1 + - + +
398A SER* 4.0 14.7 + - - -
508A GLN 2.9 19.5 + - - +
509A PHE* 3.7 7.6 - + - +
510A GLN 3.3 0.2 - - - -
511A PHE* 1.3 75.9 - - - +
513A GLU* 1.3 58.1 + - - +
515A LEU* 3.9 2.1 - - - +
516A CYS* 2.9 52.7 + - - -
525A LEU* 3.3 44.0 + - + -
526A HIS* 5.1 0.4 - - - -
528A CYS* 3.9 16.0 + - - +
530A ILE* 5.0 2.8 - - - +
573A TYR* 4.2 19.6 - + - -
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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
----------------------------------------------------------
509A PHE 3.0 17.4 + - - +
510A GLN 3.8 4.1 - - - +
512A HIS* 1.3 75.0 - - - +
514A ALA* 1.3 60.3 + - - +
516A CYS* 3.8 1.4 - - - +
517A LYS* 3.0 34.3 + - + +
525A LEU* 3.8 22.6 - - + +
569A PRO* 3.4 25.9 - - + +
572A LYS* 2.7 43.2 + - - +
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Residues in contact with ALA 514 (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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510A GLN 3.1 7.6 + - - +
511A PHE* 3.7 3.4 - - - +
513A GLU* 1.3 77.8 - - - +
515A LEU* 1.3 58.1 + - + +
517A LYS* 3.3 8.5 + - - +
518A GLU* 2.9 28.7 + - - +
539A LYS* 4.3 8.3 - - + +
559A MET* 3.6 17.5 - - + +
560A VAL* 3.5 38.1 - - + +
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Residues in contact with LEU 515 (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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394A VAL* 3.7 25.8 - - + -
511A PHE* 2.9 21.2 + - + +
512A HIS* 4.0 2.9 - - - +
514A ALA* 1.3 74.2 - - - +
516A CYS* 1.3 59.9 + - - +
518A GLU* 3.3 4.8 + - - +
519A ALA* 2.9 30.7 + - - +
530A ILE* 4.1 24.7 - - + -
536A ALA* 3.2 36.0 - - + +
539A LYS* 4.0 12.1 - - + -
540A LEU* 4.0 26.5 - - + +
559A MET* 4.0 20.9 - - + -
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Residues in contact with CYS 516 (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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512A HIS* 2.9 44.0 + - - +
513A GLU 3.8 3.6 - - - +
515A LEU* 1.3 72.4 - - - +
517A LYS* 1.3 66.7 + - - +
519A ALA* 3.4 2.3 + - - +
520A GLY 3.3 3.1 + - - -
521A TYR* 3.1 35.7 + - + +
525A LEU* 4.2 9.6 - - + -
528A CYS* 2.0 53.4 - - + -
530A ILE* 3.9 5.2 - - - -
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Residues in contact with LYS 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLU* 3.0 22.1 + - + +
514A ALA* 3.5 7.6 - - - +
516A CYS* 1.3 77.2 - - - +
518A GLU* 1.3 61.0 + - - +
520A GLY* 3.1 14.4 + - - -
521A TYR 4.6 5.8 - - - -
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Residues in contact with GLU 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ALA 2.9 17.4 + - - +
515A LEU* 3.3 6.3 + - - +
517A LYS* 1.3 76.0 - - - +
519A ALA* 1.3 60.1 + - - +
520A GLY* 3.1 1.1 + - - -
535A LYS* 3.5 58.5 + - + +
536A ALA* 4.6 1.6 - - - -
539A LYS* 3.7 35.3 + - + +
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Residues in contact with ALA 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A LEU 2.9 17.3 + - - +
516A CYS* 3.4 7.2 + - - +
517A LYS 3.3 0.2 - - - -
518A GLU* 1.3 76.2 - - - +
520A GLY* 1.3 61.3 + - - +
521A TYR* 3.5 5.5 + - + +
529A ASP 5.7 1.1 - - - +
530A ILE* 4.9 8.3 - - + -
533A SER* 3.0 36.8 + - - +
535A LYS* 4.8 9.2 + - - +
536A ALA* 4.2 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