Contacts of the helix formed by residues 501 - 524 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206I LEU* 4.6 5.6 - - - -
498I THR* 3.8 13.4 + - - -
500I PHE* 1.3 74.9 - - - +
502I SER* 1.3 65.1 + - - -
503I LYS 3.5 0.4 - - - -
504I LEU* 3.3 23.8 - - - +
505I ASP* 3.3 16.5 + - - +
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Residues in contact with SER 502 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206I LEU* 5.4 0.8 - - - +
248I ASP* 3.4 20.3 + - - +
500I PHE 3.3 3.4 + - - -
501I GLY* 1.3 70.1 - - - -
503I LYS* 1.3 70.4 + - - +
505I ASP* 3.2 9.9 + - - +
506I LYS* 2.9 39.5 + - - +
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Residues in contact with LYS 503 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I LEU* 3.5 21.4 - - + +
78I TYR* 3.7 37.8 + - + +
81I LYS* 5.8 3.2 - - - +
247I TYR* 3.1 30.4 + - + -
248I ASP* 3.2 33.4 + - - +
460I MET* 3.5 10.9 - - + +
500I PHE* 4.1 5.9 + - + +
501I GLY 3.5 0.2 - - - -
502I SER* 1.3 83.5 + - - +
504I LEU* 1.3 60.4 + - - +
506I LYS* 3.6 27.2 - - + +
507I LEU* 2.8 28.9 + - - +
608I SER* 6.0 3.0 - - - -
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Residues in contact with LEU 504 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460I MET* 3.6 10.7 - - + +
493I THR 3.8 12.8 - - - +
494I ALA 5.7 1.8 - - - +
496I LEU* 3.7 43.5 - - + +
497I PRO 3.7 22.0 - - - +
498I THR* 4.5 8.7 - - + -
500I PHE* 4.3 5.6 - - + -
501I GLY* 3.3 27.9 + - - +
503I LYS* 1.3 77.9 - - - +
505I ASP* 1.3 64.3 + - - +
507I LEU* 3.1 6.1 + - + +
508I VAL* 2.9 33.9 + - + +
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Residues in contact with ASP 505 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501I GLY 3.3 12.9 + - - +
502I SER* 3.2 9.8 + - - +
504I LEU* 1.3 80.6 - - - +
506I LYS* 1.3 61.2 + - + +
508I VAL* 3.2 11.8 + - - +
509I TYR* 2.9 27.5 + - - +
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Residues in contact with LYS 506 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I LEU* 3.7 18.6 - - + +
502I SER* 2.9 25.2 + - - +
503I LYS* 3.6 40.4 - - + +
505I ASP* 1.3 76.0 - - + +
507I LEU* 1.3 56.5 + - - +
509I TYR* 3.4 3.6 + - - +
510I LEU* 2.9 27.7 + - - +
605I ASP 3.5 20.4 + - - +
606I ILE* 3.7 36.9 - - + +
607I LEU 5.4 0.2 - - - -
608I SER* 4.2 25.8 - - - +
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Residues in contact with LEU 507 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I LEU* 4.6 6.7 - - + +
78I TYR* 4.7 0.7 - - - +
460I MET* 3.9 15.7 - - + +
463I ILE* 4.4 15.0 - - + -
464I THR* 4.0 26.5 - - + +
467I VAL* 3.8 24.9 - - + -
493I THR* 4.8 8.3 - - + -
496I LEU* 3.8 29.2 - - + -
503I LYS 2.8 17.5 + - - +
504I LEU* 3.1 6.5 + - + +
506I LYS* 1.3 74.6 - - - +
508I VAL* 1.3 60.4 + - - +
510I LEU* 3.2 18.8 + - + +
511I THR* 2.9 32.7 + - - +
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Residues in contact with VAL 508 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493I THR* 3.8 35.9 - - + +
494I ALA* 5.2 2.5 - - - +
504I LEU* 2.9 24.8 + - + +
505I ASP* 3.2 15.2 + - - +
507I LEU* 1.3 77.1 - - - +
509I TYR* 1.3 56.7 + - - +
511I THR* 3.3 4.6 + - - -
512I GLU* 2.9 29.6 + - + +
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Residues in contact with TYR 509 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505I ASP 2.9 13.5 + - - +
506I LYS 3.7 6.1 - - - +
508I VAL* 1.3 77.1 - - - +
510I LEU* 1.3 58.0 + - - +
512I GLU* 3.3 22.5 + - - +
513I ARG* 2.8 40.6 + - + +
600I GLU 4.9 0.5 + - - -
601I TYR* 3.3 22.1 - + - -
602I ASN 2.6 42.1 + - - -
605I ASP* 2.8 30.0 + - + -
606I ILE* 3.6 31.2 - - + -
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Residues in contact with LEU 510 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I TYR* 3.4 26.0 - - - +
72I ILE* 5.2 5.4 - - + -
73I THR* 5.0 8.3 - - + -
77I LEU* 4.3 22.2 - - + -
464I THR* 5.2 0.7 - - + +
467I VAL* 5.5 2.5 - - + -
468I SER* 4.3 17.3 - - - +
506I LYS 2.9 18.1 + - - +
507I LEU* 3.2 18.1 + - + +
509I TYR* 1.3 77.0 - - - +
511I THR* 1.3 59.4 + - - +
513I ARG* 3.3 10.7 + - + +
514I LEU* 2.9 48.7 + - + +
603I ILE* 5.3 2.9 - - + -
606I ILE* 4.1 19.5 - - + -
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Residues in contact with THR 511 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467I VAL* 3.3 37.3 - - + +
471I SER* 4.8 6.6 + - - +
486I LEU* 6.1 1.8 - - + -
489I LEU* 6.1 0.4 - - + -
490I THR* 5.0 16.4 - - + +
493I THR* 3.8 17.4 - - + +
507I LEU 2.9 14.8 + - - -
508I VAL* 3.5 11.2 - - - -
510I LEU* 1.3 76.1 - - - +
512I GLU* 1.3 56.7 + - - +
514I LEU* 3.4 7.2 + - - +
515I SER* 2.9 28.4 + - - -
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Residues in contact with GLU 512 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508I VAL* 2.9 16.1 + - + +
509I TYR* 3.5 26.5 - - + +
511I THR* 1.3 77.7 - - - +
513I ARG* 1.3 58.6 + - - +
515I SER* 2.5 24.2 + - - +
516I LYS* 2.9 30.8 + - + +
601I TYR* 4.4 15.6 + - + -
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Residues in contact with ARG 513 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I TYR* 5.1 6.7 + - - -
509I TYR* 2.8 33.3 + - + +
510I LEU* 3.9 11.6 - - + +
512I GLU* 1.3 73.3 - - - +
514I LEU* 1.3 62.1 + - - +
516I LYS* 3.4 6.2 + - - +
517I LEU* 2.8 37.4 + - - +
540I ILE* 3.4 25.9 - - - +
541I LEU* 3.8 21.2 - - - +
544I ASP* 3.5 11.3 + - - -
597I PHE* 3.3 26.4 + - + -
601I TYR* 2.6 43.5 + - + -
602I ASN 4.2 12.5 - - - -
603I ILE* 4.3 16.3 - - - +
606I ILE* 5.7 0.2 - - - -
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Residues in contact with LEU 514 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I TRP* 4.5 16.8 - - + -
68I TYR* 4.4 14.4 - - + +
467I VAL* 3.8 7.0 - - + +
468I SER* 3.8 36.3 - - - +
471I SER* 4.1 14.7 - - - +
472I PHE* 5.2 0.4 - - + -
475I ILE* 4.0 11.2 - - + +
510I LEU* 2.9 38.9 + - + +
511I THR* 3.9 4.3 - - - +
513I ARG* 1.3 81.1 - - - +
515I SER* 1.3 60.4 + - - +
517I LEU* 3.4 27.0 - - + +
518I LYS* 2.9 26.9 + - - +
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Residues in contact with SER 515 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471I SER* 5.3 2.8 - - - -
511I THR* 2.9 13.2 + - - -
512I GLU* 2.5 30.8 + - - +
514I LEU* 1.3 74.8 - - - +
516I LYS* 1.3 62.9 + - - +
518I LYS* 3.2 12.5 + - - +
519I LEU* 3.0 34.7 + - - +
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Residues in contact with LYS 516 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512I GLU* 2.9 26.8 + - + +
513I ARG 3.6 4.0 - - - +
515I SER* 1.3 78.2 - - - +
517I LEU* 1.3 59.7 + - - +
519I LEU* 3.2 37.7 + - + +
520I LEU* 2.8 26.2 + - - +
597I PHE* 3.8 6.0 - - - -
601I TYR* 3.4 55.3 + - + +
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Residues in contact with LEU 517 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472I PHE* 4.9 3.4 - - + -
475I ILE* 3.7 20.7 - - + +
513I ARG* 2.8 26.0 + - - +
514I LEU* 3.2 24.9 + - + +
516I LYS* 1.3 75.6 - - - +
518I LYS* 1.3 58.0 + - - +
520I LEU* 3.2 8.8 + - + +
521I TRP* 2.9 27.0 + - - +
537I VAL* 3.7 33.6 - - + +
540I ILE* 6.0 1.1 - - + -
541I LEU* 4.0 25.4 - - + -
597I PHE* 3.6 26.5 - - + -
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Residues in contact with LYS 518 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471I SER 5.2 0.9 - - - +
474I GLN* 2.1 60.1 + - + +
475I ILE* 3.7 32.0 + - + +
478I GLU* 3.2 33.8 + - - +
486I LEU* 5.6 3.6 - - + -
514I LEU 2.9 9.3 + - - +
515I SER* 3.2 13.2 - - - +
517I LEU* 1.3 76.3 - - - +
519I LEU* 1.3 62.4 + - + +
521I TRP* 3.2 4.7 + - - +
522I ASP* 2.9 38.6 + - - +
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Residues in contact with LEU 519 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515I SER* 3.0 29.9 + - - +
516I LYS* 3.2 44.0 - - + +
518I LYS* 1.3 81.7 - - + +
520I LEU* 1.3 56.7 + - - +
522I ASP* 3.2 16.2 + - + +
523I LYS* 2.9 32.6 + - + +
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Residues in contact with LEU 520 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516I LYS 2.8 15.8 + - - +
517I LEU* 3.2 24.2 + - + +
519I LEU* 1.3 73.2 - - - +
521I TRP* 1.3 64.5 + - - +
523I LYS* 3.2 38.5 - - + +
524I VAL* 3.3 4.7 + - + +
535I HIS* 3.2 19.1 - - + -
536I PRO* 3.8 26.5 - - + -
537I VAL* 3.9 8.3 - - + +
593I ILE* 4.5 11.2 - - + -
597I PHE* 3.6 47.8 - - + -
600I GLU* 5.3 1.6 - - - +
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Residues in contact with TRP 521 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I TYR* 3.3 42.8 + + - -
475I ILE* 3.5 37.6 + - + -
476I PHE* 3.4 29.0 + + - +
517I LEU 2.9 7.1 + - - +
518I LYS 3.5 7.9 - - - +
520I LEU* 1.3 74.8 - - - +
522I ASP* 1.3 67.2 + - - +
524I VAL 3.0 20.5 - - - +
526I LEU* 3.6 35.9 - - + -
535I HIS* 3.4 48.2 - + + -
537I VAL* 4.3 6.1 - - + -
538I PHE* 5.1 4.0 - + - -
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Residues in contact with ASP 522 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475I ILE 4.8 1.7 - - - +
478I GLU* 3.5 20.8 - - - +
518I LYS* 2.9 32.6 + - - +
519I LEU* 3.2 24.0 + - + +
521I TRP* 1.3 85.3 - - - +
523I LYS* 1.3 57.2 + - - +
524I VAL 5.1 0.7 - - - -
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Residues in contact with LYS 523 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519I LEU* 2.9 12.2 + - + +
520I LEU* 3.2 37.9 - - + +
522I ASP* 1.3 77.0 - - - +
524I VAL* 1.3 70.0 + - + +
525I GLN 4.2 0.7 + - - -
593I ILE* 4.7 15.1 - - - +
600I GLU* 5.0 13.1 + - - -
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Residues in contact with VAL 524 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520I LEU* 3.3 5.5 + - + +
521I TRP* 3.0 13.4 - - - +
522I ASP 3.5 1.1 - - - -
523I LYS* 1.3 97.6 - - + +
525I GLN* 1.3 71.0 + - - +
526I LEU 3.8 0.3 + - - -
535I HIS* 2.8 43.2 + - + +
536I PRO* 3.8 18.2 - - + -
589I ASP* 6.0 2.2 - - - +
590I PHE* 4.3 11.0 - - + -
593I ILE* 4.3 30.5 - - + -
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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