Contacts of the helix formed by residues 501 - 524 (chain B) in PDB entry 6GYS
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 501 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B GLY* 6.4 2.2 - - - -
206B LEU* 5.4 0.9 - - - -
498B THR 4.2 5.6 + - - -
499B ILE 4.0 0.2 - - - -
500B PHE* 1.3 76.7 - - - +
502B SER* 1.3 53.9 + - - -
503B LYS 3.5 0.2 - - - -
504B LEU* 3.1 15.9 + - - +
505B ASP* 2.7 44.5 + - - -
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Residues in contact with SER 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 5.6 2.5 - - - +
500B PHE 3.0 7.8 + - - -
501B GLY* 1.3 69.5 - - - -
503B LYS* 1.3 82.6 + - - +
505B ASP* 3.1 11.1 + - - +
506B LYS* 2.9 41.3 + - - +
608B SER* 6.5 0.7 - - - -
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Residues in contact with LYS 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.6 28.3 - - + +
78B TYR* 4.2 30.1 - - + +
81B LYS* 5.9 3.4 - - - +
247B TYR* 3.3 37.2 + - + +
248B ASP 5.3 0.8 + - - -
250B PRO* 6.2 0.8 - - - +
460B MET* 3.8 19.9 - - + +
500B PHE* 4.2 9.3 + - + +
502B SER* 1.3 93.5 + - - +
504B LEU* 1.3 57.7 + - - +
506B LYS* 3.7 22.9 - - + +
507B LEU* 2.9 29.1 + - - +
607B LEU 5.9 0.8 + - - -
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Residues in contact with LEU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B MET* 4.4 4.5 - - + -
493B THR 4.1 7.2 - - - +
496B LEU* 3.7 42.0 - - + +
497B PRO 3.6 23.8 - - - +
498B THR* 4.7 5.8 - - + -
500B PHE* 3.7 11.8 - - + +
501B GLY* 3.1 27.9 + - - +
503B LYS* 1.3 78.4 - - - +
505B ASP* 1.3 64.0 + - - +
507B LEU* 3.3 11.6 - - + +
508B VAL* 3.3 30.7 + - + +
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Residues in contact with ASP 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B GLY* 2.7 24.8 + - - +
502B SER* 3.1 10.6 + - - +
504B LEU* 1.3 79.2 - - - +
506B LYS* 1.3 60.4 + - + +
507B LEU 3.2 0.4 - - - -
508B VAL* 3.1 10.4 + - - +
509B TYR* 2.9 26.7 + - - +
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Residues in contact with LYS 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.8 13.4 - - + +
81B LYS* 6.0 0.2 - - - +
502B SER* 2.9 28.2 + - - +
503B LYS* 3.3 31.8 + - + +
505B ASP* 1.3 74.8 - - + +
507B LEU* 1.3 57.1 + - - +
509B TYR* 3.3 6.3 + - - +
510B LEU* 2.9 28.8 + - - +
605B ASP 3.8 8.2 + - - +
606B ILE* 2.9 62.1 - - + +
607B LEU 2.9 20.5 - - - +
608B SER* 3.5 15.0 - - - +
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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
----------------------------------------------------------
77B LEU* 5.1 7.3 - - + +
460B MET* 4.5 11.9 - - + -
463B ILE* 5.0 7.6 - - + -
464B THR* 4.5 22.2 - - + +
467B VAL* 3.7 27.4 - - + -
493B THR* 3.8 16.6 - - + +
496B LEU* 3.7 29.8 - - + -
503B LYS 2.9 14.5 + - - +
504B LEU* 3.3 15.9 - - + +
506B LYS* 1.3 76.5 - - - +
508B VAL* 1.3 53.1 + - - +
510B LEU* 3.2 9.4 + - + +
511B THR* 2.6 40.0 + - - +
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Residues in contact with VAL 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B THR* 4.3 21.3 - - + +
494B ALA* 6.5 0.4 - - - -
504B LEU* 3.3 20.8 + - + +
505B ASP* 3.1 11.7 + - - +
507B LEU* 1.3 73.5 - - - +
509B TYR* 1.3 59.7 + - - +
511B THR* 3.4 9.9 + - + -
512B GLU* 2.8 32.0 + - + +
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Residues in contact with TYR 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B ASP 2.9 14.1 + - - +
506B LYS* 3.4 11.9 - - - +
507B LEU 3.2 0.2 - - - -
508B VAL* 1.3 78.1 - - - +
510B LEU* 1.3 58.9 + - + +
512B GLU* 3.2 17.2 + - - +
513B ARG* 2.8 47.1 + - - +
601B TYR* 3.2 35.1 - + - +
602B ASN 2.3 34.7 + - - -
603B ILE* 4.3 7.4 - - + -
605B ASP* 2.7 33.7 + - + +
606B ILE* 3.5 23.8 - - + -
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Residues in contact with LEU 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TRP* 6.5 0.4 - - + -
68B TYR* 4.4 19.3 - - + +
72B ILE* 3.9 24.9 - - + -
73B THR* 4.3 13.9 - - + -
77B LEU* 5.1 10.1 - - + -
464B THR* 5.8 1.3 - - + -
468B SER* 4.7 7.4 - - - +
506B LYS 2.9 15.4 + - - +
507B LEU* 3.8 9.0 - - + +
509B TYR* 1.3 77.7 - - + +
511B THR* 1.3 61.1 + - - +
513B ARG* 3.2 16.6 + - + +
514B LEU* 2.9 51.5 + - + +
603B ILE* 4.9 6.5 - - + -
606B ILE* 5.3 7.4 - - + -
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Residues in contact with THR 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B VAL* 4.6 20.3 - - + +
471B SER* 5.1 7.0 + - - +
486B LEU* 6.4 0.7 - - + -
490B THR* 4.6 21.1 - - + +
493B THR* 4.8 8.1 - - + +
507B LEU* 2.6 33.4 + - - +
508B VAL* 3.4 11.6 - - + -
510B LEU* 1.3 78.0 - - - +
512B GLU* 1.3 56.0 + - - +
514B LEU* 3.5 8.4 + - - +
515B SER* 2.9 29.6 + - - -
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Residues in contact with GLU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B VAL* 2.8 19.1 + - + +
509B TYR* 3.2 16.6 + - - +
511B THR* 1.3 78.1 - - - +
513B ARG* 1.3 56.6 + - - +
515B SER* 2.7 21.6 + - - +
516B LYS* 2.8 31.4 + - + +
601B TYR* 2.6 42.3 + - + +
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Residues in contact with ARG 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 3.9 10.7 + - - -
509B TYR* 2.8 36.7 + - + +
510B LEU* 3.2 13.1 + - + +
512B GLU* 1.3 76.6 - - - +
514B LEU* 1.3 61.9 + - + +
516B LYS* 3.5 1.1 + - - -
517B LEU* 3.0 33.4 + - + +
540B ILE* 3.6 12.7 - - - +
541B LEU* 4.5 6.3 - - - +
544B ASP* 3.2 37.2 + - - -
597B PHE* 3.6 28.4 - - + -
598B GLN* 5.0 6.1 - - - +
601B TYR* 3.7 25.8 + - + -
603B ILE* 3.5 41.3 - - - +
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Residues in contact with LEU 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TRP* 4.9 9.4 - - + -
68B TYR* 5.5 7.0 - - + +
467B VAL 4.5 4.0 - - - +
468B SER* 4.0 17.0 - - - +
471B SER* 3.7 28.9 - - - -
472B PHE* 4.6 13.9 - - + +
475B ILE* 3.3 30.9 - - + +
510B LEU* 2.9 39.7 + - + +
511B THR* 3.8 6.1 - - - +
513B ARG* 1.3 81.5 - - + +
515B SER* 1.3 57.2 + - - +
517B LEU* 3.3 10.0 + - + -
518B LYS* 2.8 25.5 + - - +
541B LEU* 6.0 4.0 - - + -
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Residues in contact with SER 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B ILE* 5.6 0.2 - - - -
486B LEU* 6.5 1.3 - - - -
511B THR* 2.9 14.6 + - - -
512B GLU* 2.7 28.8 + - - +
514B LEU* 1.3 76.3 - - - +
516B LYS* 1.3 63.0 + - - +
518B LYS* 3.2 27.9 - - - +
519B LEU* 3.3 15.6 - - - +
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Residues in contact with LYS 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B GLU* 2.8 28.4 + - + +
513B ARG 4.0 0.7 - - - +
515B SER* 1.3 80.8 - - - +
517B LEU* 1.3 60.4 + - - +
518B LYS 3.1 1.6 - - - -
519B LEU* 3.0 35.9 + - + +
520B LEU* 3.2 10.2 + - - +
597B PHE* 3.8 22.2 - - + -
600B GLU* 5.4 5.7 + - - +
601B TYR* 3.3 36.6 - - + +
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Residues in contact with LEU 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B PHE* 6.4 0.4 - - + -
475B ILE* 4.3 12.2 - - + +
513B ARG* 3.0 21.5 + - + +
514B LEU* 3.8 12.1 - - + +
516B LYS* 1.3 73.6 - - - +
518B LYS* 1.3 59.7 + - - +
520B LEU* 3.5 13.9 - - + -
521B TRP* 2.9 31.2 + - - +
537B VAL* 3.7 42.2 - - + -
540B ILE* 3.7 30.3 - - + -
541B LEU* 4.2 24.7 - - + -
597B PHE* 4.2 10.9 - - + -
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Residues in contact with LYS 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B GLN* 4.0 30.5 + - + +
475B ILE* 3.7 27.8 - - + +
478B GLU* 4.0 18.8 + - - +
483B LYS* 5.1 17.5 - - - +
486B LEU* 5.7 7.0 - - + -
514B LEU 2.8 13.6 + - - +
515B SER* 3.2 23.8 - - - +
517B LEU* 1.3 75.8 - - - +
519B LEU* 1.3 63.8 + - + +
521B TRP* 4.2 1.0 - - - +
522B ASP* 2.7 38.7 + - - +
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Residues in contact with LEU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B SER 3.3 25.6 - - - +
516B LYS* 3.0 26.2 + - + +
518B LYS* 1.3 86.0 - - + +
520B LEU* 1.3 63.8 + - + +
522B ASP* 3.1 14.8 + - - +
523B LYS* 3.1 25.5 + - + +
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Residues in contact with LEU 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B LYS 3.2 6.6 + - - +
517B LEU* 3.0 32.5 + - + +
519B LEU* 1.3 76.6 - - - +
521B TRP* 1.3 65.9 + - - +
523B LYS* 4.2 11.9 - - + +
524B VAL* 3.3 36.9 + - + +
535B HIS* 3.4 1.4 - - - -
536B PRO* 4.7 5.4 - - + -
537B VAL* 4.1 4.7 - - + -
540B ILE* 3.9 15.0 - - + -
593B ILE* 3.7 33.9 - - + -
597B PHE* 4.3 15.7 - - + -
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Residues in contact with TRP 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LYS* 5.5 1.6 - - - +
57B TYR* 3.1 38.4 + + - -
475B ILE* 4.1 17.3 - - + -
476B PHE* 3.5 31.4 + + + +
517B LEU 2.9 15.1 + - - +
518B LYS 4.2 0.2 - - - +
520B LEU* 1.3 77.7 - - - +
522B ASP* 1.3 83.4 + - - +
524B VAL 3.0 25.9 - - - +
526B LEU* 3.6 28.9 - - + -
535B HIS* 3.3 49.0 + + + -
537B VAL* 3.7 14.1 - - + +
538B PHE* 4.2 12.3 - + - -
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Residues in contact with ASP 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B ILE 3.6 10.1 - - - +
478B GLU* 3.1 24.3 - - - +
518B LYS* 2.7 30.6 + - - +
519B LEU* 3.1 6.4 + - - +
521B TRP* 1.3 96.3 - - - +
523B LYS* 1.3 59.1 + - - +
524B VAL 4.8 0.2 - - - -
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Residues in contact with LYS 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B LEU* 3.1 23.3 + - + +
520B LEU* 4.0 13.8 - - + +
522B ASP* 1.3 78.1 - - - +
524B VAL* 1.3 79.6 + - + +
525B GLN 3.9 1.6 + - - -
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Residues in contact with VAL 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B LEU* 3.3 34.1 + - + +
521B TRP* 3.0 9.9 + - - +
522B ASP 4.8 0.3 - - - -
523B LYS* 1.3 94.4 - - + +
525B GLN* 1.3 67.2 + - - +
526B LEU 3.7 0.7 + - - -
535B HIS* 2.7 34.6 + - + +
536B PRO* 3.8 18.6 - - + -
593B ILE* 4.9 13.2 - - + -
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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