Contacts of the helix formed by residues 501 - 524 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C LEU* 4.0 17.7 - - - -
498C THR 3.6 8.9 + - - -
499C ILE 3.4 2.6 - - - -
500C PHE* 1.3 78.2 - - - +
502C SER* 1.3 57.4 + - - -
504C LEU* 2.8 34.9 + - - +
505C ASP* 3.2 11.4 + - - +
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Residues in contact with SER 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500C PHE 3.6 0.8 + - - -
501C GLY* 1.3 69.2 - - - -
503C LYS* 1.3 65.9 + - - +
505C ASP* 2.8 15.7 + - - +
506C LYS* 2.6 59.8 + - - +
608C SER* 4.5 8.2 + - - -
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Residues in contact with LYS 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 3.3 30.0 - - + +
78C TYR* 3.6 42.1 + - + +
80C THR 5.1 6.1 + - - -
247C TYR* 3.8 43.9 + - + +
460C MET* 3.4 16.9 - - + +
500C PHE* 4.1 10.5 - - + +
501C GLY 3.3 0.4 - - - -
502C SER* 1.3 81.9 + - - +
504C LEU* 1.3 67.2 + - - +
506C LYS* 4.3 15.0 - - + +
507C LEU* 3.3 14.6 + - - +
606C ILE 5.5 1.6 + - - -
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Residues in contact with LEU 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C MET* 3.6 15.4 - - + +
493C THR* 4.3 7.2 - - + +
496C LEU* 3.7 39.9 - - + +
497C PRO 3.4 25.1 - - - +
498C THR* 4.4 13.2 - - + -
500C PHE* 4.0 12.6 + - + -
501C GLY 2.8 18.2 + - - +
503C LYS* 1.3 75.9 - - - +
505C ASP* 1.3 65.4 + - - +
507C LEU* 3.0 13.7 + - + +
508C VAL* 2.9 34.1 + - + +
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Residues in contact with ASP 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C GLY 3.5 11.6 - - - +
502C SER* 2.8 24.9 + - - +
504C LEU* 1.3 84.3 - - - +
506C LYS* 1.3 51.5 + - + +
508C VAL* 2.9 16.5 - - - +
509C TYR* 2.6 32.1 + - - +
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Residues in contact with LYS 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 3.7 21.0 - - + +
502C SER* 2.6 43.1 + - - +
503C LYS* 4.3 16.8 - - + +
505C ASP* 1.3 69.8 - - + +
507C LEU* 1.3 55.2 + - - +
509C TYR* 2.9 13.5 + - - +
510C LEU* 2.5 34.9 + - - +
605C ASP 3.1 13.7 + - - +
606C ILE* 2.9 28.1 - - + +
607C LEU* 2.5 44.9 + - - +
608C SER* 4.0 4.9 + - - -
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Residues in contact with LEU 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 4.7 5.0 - - + +
78C TYR* 4.8 2.0 - - - +
460C MET* 4.1 14.8 - - + -
463C ILE* 5.4 6.3 - - + -
464C THR* 3.8 41.7 - - + +
467C VAL* 3.9 16.8 - - + -
493C THR* 5.6 7.9 - - + +
496C LEU* 5.1 13.2 - - + -
503C LYS 3.3 12.3 + - - +
504C LEU* 3.0 15.1 + - + +
506C LYS* 1.3 77.2 - - - +
508C VAL* 1.3 49.9 + - + +
510C LEU* 3.4 15.4 - - + +
511C THR* 2.5 54.5 + - - +
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Residues in contact with VAL 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493C THR* 3.8 26.5 - - + -
504C LEU* 2.9 23.0 + - + +
505C ASP* 2.9 19.7 + - - +
507C LEU* 1.3 73.9 - - - +
509C TYR* 1.3 56.4 + - - +
511C THR* 3.7 6.8 - - - -
512C GLU* 2.8 26.3 + - - +
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Residues in contact with TYR 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C ASP 2.6 12.9 + - - +
506C LYS* 2.9 19.0 + - + +
508C VAL* 1.3 74.0 - - - +
510C LEU* 1.3 52.8 + - + +
512C GLU* 2.7 34.1 - - - +
513C ARG* 2.6 62.6 + - - +
601C TYR* 3.6 15.7 - + - -
602C ASN 2.5 24.4 + - - -
603C ILE* 4.9 1.6 - - + -
605C ASP* 2.4 43.3 + - + +
606C ILE* 4.2 17.0 - - + -
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Residues in contact with LEU 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 4.7 7.6 - - + +
72C ILE* 4.8 13.9 - - + +
73C THR* 5.7 3.8 - - + -
77C LEU* 3.9 27.1 - - + -
464C THR* 4.8 1.6 - - + -
468C SER* 3.8 22.9 - - - +
506C LYS 2.5 17.2 + - - +
507C LEU* 3.4 19.5 - - + +
509C TYR* 1.3 76.8 - - + +
511C THR* 1.3 56.9 + - - +
513C ARG* 2.9 11.3 + - + +
514C LEU* 2.9 62.8 + - + +
603C ILE* 5.8 4.9 - - + -
606C ILE* 6.1 2.2 - - + -
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Residues in contact with THR 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467C VAL* 4.6 20.7 - - + +
471C SER* 5.3 5.8 + - - +
486C LEU* 5.6 5.2 - - + -
490C THR* 5.0 16.2 - - + +
493C THR* 4.4 21.1 + - + +
507C LEU* 2.5 43.7 + - - +
508C VAL* 4.0 6.7 - - - -
510C LEU* 1.3 68.9 - - - +
512C GLU* 1.3 60.5 + - - +
514C LEU* 4.8 6.7 - - - +
515C SER* 2.9 24.4 + - - -
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Residues in contact with GLU 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C VAL 2.8 16.3 + - - +
509C TYR* 2.7 35.7 + - - +
511C THR* 1.3 73.5 - - - +
513C ARG* 1.3 50.8 + - - +
515C SER* 2.3 28.6 + - - -
516C LYS* 2.7 40.1 + - + +
601C TYR* 3.0 32.2 + - - -
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Residues in contact with ARG 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 5.7 2.0 + - - -
509C TYR* 2.6 47.4 + - + +
510C LEU* 2.9 13.0 + - + +
512C GLU* 1.3 72.3 - - - +
514C LEU* 1.3 52.8 + - - +
516C LYS* 3.0 10.6 + - - +
517C LEU* 2.6 34.8 + - - +
540C ILE* 4.3 16.0 - - - +
541C LEU* 5.7 0.4 - - - +
544C ASP* 2.7 36.7 + - - -
597C PHE* 4.4 5.6 - - + -
598C GLN* 4.7 6.5 - - - +
601C TYR* 2.9 51.4 + - + +
602C ASN 3.7 1.4 + - - -
603C ILE* 3.2 30.6 - - - +
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Residues in contact with LEU 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C TRP* 6.1 1.1 - - + -
68C TYR* 3.5 29.6 - - + +
467C VAL* 5.3 1.3 - - + -
468C SER* 4.1 20.0 - - - +
471C SER* 3.7 33.7 - - - +
472C PHE* 5.7 1.8 - - + +
475C ILE* 3.3 20.4 - - + +
510C LEU* 2.9 42.6 + - + +
511C THR* 4.8 3.4 - - - +
513C ARG* 1.3 74.7 - - - +
515C SER* 1.3 56.7 + - - +
517C LEU* 2.9 16.9 + - + +
518C LYS 2.8 22.7 + - - -
541C LEU* 5.6 1.3 - - + -
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Residues in contact with SER 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C SER* 5.5 1.0 - - - -
475C ILE* 5.3 0.2 - - - -
486C LEU* 6.1 6.3 - - - -
511C THR 2.9 16.2 + - - -
512C GLU* 2.3 30.7 + - - -
514C LEU* 1.3 74.3 - - - +
516C LYS* 1.3 62.9 + - - +
518C LYS* 2.7 38.4 + - - +
519C LEU* 3.2 12.6 + - - +
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Residues in contact with LYS 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512C GLU* 2.7 41.4 + - + +
513C ARG 3.3 7.9 - - - +
515C SER* 1.3 72.6 - - - +
517C LEU* 1.3 62.1 + - - +
519C LEU* 3.0 48.4 + - + +
520C LEU 3.4 2.9 + - - -
597C PHE* 3.5 26.5 - - + -
601C TYR* 3.2 33.0 + - + +
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Residues in contact with LEU 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C ILE* 4.3 18.8 - - + -
476C PHE* 4.9 1.1 - - + -
513C ARG 2.6 15.7 + - - +
514C LEU* 3.1 17.0 - - + +
516C LYS* 1.3 71.1 - - - +
518C LYS* 1.3 57.6 + - - +
520C LEU* 2.9 19.2 + - + +
521C TRP* 3.1 14.2 + - - +
537C VAL* 3.7 46.4 - - + -
540C ILE* 4.3 23.8 - - + -
541C LEU* 3.7 33.0 - - + -
597C PHE* 3.8 10.9 - - + -
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Residues in contact with LYS 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474C GLN* 2.2 61.0 + - + +
475C ILE* 3.7 27.1 - - + +
478C GLU* 4.0 9.9 + - - +
483C LYS* 4.9 11.9 - - - +
486C LEU* 4.3 15.9 - - + -
514C LEU 2.8 5.7 + - - -
515C SER* 2.7 28.7 - - - +
517C LEU* 1.3 77.3 - - - +
519C LEU* 1.3 60.8 + - + +
521C TRP* 4.9 0.2 - - - +
522C ASP* 3.4 24.6 + - - +
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Residues in contact with LEU 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C SER 3.2 25.6 + - - +
516C LYS* 3.0 41.9 + - + +
518C LYS* 1.3 79.6 - - + +
520C LEU* 1.3 62.0 + - + +
521C TRP 3.4 0.3 + - - -
522C ASP* 4.5 1.6 - - - +
523C LYS* 3.3 27.6 + - + +
597C PHE* 5.6 3.4 - - + -
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Residues in contact with LEU 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C LYS 3.4 5.6 + - - +
517C LEU* 2.9 8.4 + - + +
519C LEU* 1.3 79.0 - - + +
521C TRP* 1.3 65.4 + - - +
523C LYS* 3.3 35.6 - - + +
524C VAL* 3.6 11.9 + - + +
535C HIS* 3.7 8.9 - - + -
537C VAL* 3.9 14.6 - - + +
540C ILE* 3.8 28.0 - - + -
593C ILE* 3.7 33.7 - - + -
597C PHE* 4.0 24.0 - - + -
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Residues in contact with TRP 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C TYR* 4.2 20.1 + + - -
475C ILE* 3.6 18.4 + - + -
476C PHE* 3.3 40.8 + + + +
517C LEU 3.1 13.9 + - - +
518C LYS 4.9 0.2 - - - +
519C LEU 3.4 0.2 - - - -
520C LEU* 1.3 78.4 - - - +
522C ASP* 1.3 83.0 + - - +
524C VAL 2.9 24.8 - - - +
526C LEU* 3.7 29.2 - - + -
535C HIS* 3.3 43.7 - + + -
537C VAL* 3.7 17.9 - - + +
538C PHE* 3.5 29.4 - + - -
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Residues in contact with ASP 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C ILE 3.5 9.5 - - - +
476C PHE 5.2 2.1 - - - +
478C GLU* 2.5 29.1 - - - +
518C LYS* 3.4 20.2 + - - +
519C LEU 3.8 2.5 + - - +
520C LEU 3.5 0.4 - - - -
521C TRP* 1.3 96.2 + - - +
523C LYS* 1.3 62.0 + - - +
524C VAL 3.5 2.8 + - - +
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Residues in contact with LYS 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C LEU* 3.3 20.3 + - + +
520C LEU* 3.3 36.6 - - + +
522C ASP* 1.3 79.1 - - - +
524C VAL* 1.3 68.4 + - + +
525C GLN 4.2 0.5 + - - -
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Residues in contact with VAL 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C LEU* 3.6 16.4 + - + +
521C TRP* 2.9 10.4 - - - +
522C ASP 4.4 2.6 - - - +
523C LYS* 1.3 102.8 - - + +
525C GLN* 1.3 68.8 + - - +
526C LEU 3.6 0.7 + - - -
527C LEU* 5.5 7.2 - - + -
535C HIS* 2.7 39.4 + - + +
536C PRO* 4.8 6.7 - - + -
593C ILE* 4.6 22.4 - - + -
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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) + - + + + + + -
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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