Contacts of the helix formed by residues 456 - 477 (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 HIS 456 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I LEU* 5.4 9.0 - - + +
173I TYR* 3.1 28.8 + - + +
242I THR* 4.5 19.6 + - - +
302I LEU* 5.5 9.9 - - + -
345I TYR* 4.0 22.0 + + - -
398I PHE* 6.0 1.1 - - + -
402I ILE* 5.3 11.6 - - + +
453I PHE 4.8 2.1 + - - +
454I ASN 3.7 0.6 - - - -
455I ARG* 1.3 78.3 - - - +
457I PRO* 1.3 82.0 - - + +
458I MET* 3.0 57.4 + - + +
459I VAL* 3.1 23.8 + - - +
500I PHE* 3.6 0.6 - - - -
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Residues in contact with PRO 457 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172I TYR* 3.2 20.2 - - - +
241I ALA 5.2 2.0 - - - +
242I THR 3.4 13.0 - - - +
243I THR 3.7 19.7 - - - +
244I THR* 4.6 3.4 - - + +
247I TYR* 3.7 27.8 - - + +
302I LEU* 6.4 1.8 - - + -
456I HIS* 1.3 95.2 - - + +
458I MET* 1.3 57.9 + - - -
459I VAL 3.3 0.7 - - - -
460I MET* 3.3 4.8 - - + +
461I GLN* 2.9 32.1 + - - +
500I PHE* 3.8 14.4 - - + -
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Residues in contact with MET 458 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345I TYR* 6.1 0.7 - - - -
398I PHE* 6.3 0.2 - - + -
401I PHE* 4.9 3.1 - - + +
402I ILE* 3.7 46.2 - - + +
405I PHE* 3.5 21.5 - - + -
406I GLN* 3.2 34.1 - - - +
453I PHE 4.5 13.9 - - - +
456I HIS* 3.0 41.3 + - + +
457I PRO* 1.3 76.3 - - - +
459I VAL* 1.3 60.2 + - + +
461I GLN* 3.5 4.0 + - - +
462I THR* 2.3 39.7 + - - +
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Residues in contact with VAL 459 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401I PHE* 5.3 3.1 - - + -
405I PHE* 3.6 33.9 - - + -
442I ILE* 5.3 9.4 - - + -
453I PHE 4.5 15.0 - - - +
454I ASN* 3.4 31.6 - - + +
456I HIS 3.1 18.5 + - - +
458I MET* 1.3 80.2 - - + +
460I MET* 1.3 61.0 + - - +
463I ILE* 3.0 41.2 + - + +
496I LEU* 5.3 10.1 - - + -
500I PHE* 3.8 9.2 - - + -
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Residues in contact with MET 460 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I TYR* 3.7 15.9 - - + +
247I TYR* 6.0 1.6 - - + -
457I PRO* 3.2 12.9 + - + +
459I VAL* 1.3 83.2 - - - +
461I GLN* 1.3 67.5 + - - +
463I ILE* 3.8 2.9 - - - +
464I THR* 2.3 35.8 + - - -
496I LEU* 4.7 12.3 - - - -
500I PHE* 3.5 48.0 - - + -
503I LYS* 3.5 39.5 - - + +
504I LEU* 3.6 9.9 - - - +
507I LEU* 3.9 16.8 - - + +
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Residues in contact with GLN 461 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I THR 3.4 9.7 - - - +
74I ASN* 4.5 5.2 - - - +
78I TYR* 3.2 46.3 + - - -
247I TYR* 3.3 50.0 - - - +
413I LYS* 4.4 8.7 + - - +
457I PRO 2.9 14.9 + - - +
458I MET* 4.2 4.0 - - - +
460I MET* 1.3 81.4 - - - +
462I THR* 1.3 61.4 + - - +
464I THR* 3.3 13.0 - - - -
465I ARG* 3.3 19.0 + - - +
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Residues in contact with THR 462 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405I PHE* 3.2 31.7 - - + -
409I THR* 3.4 29.4 - - + +
412I TRP* 5.6 4.3 - - + -
413I LYS* 4.9 3.0 + - - +
438I ILE* 4.6 14.8 - - + -
458I MET* 2.3 25.8 + - - +
459I VAL 3.7 2.2 - - - -
460I MET 3.2 0.2 - - - -
461I GLN* 1.3 75.4 - - - +
463I ILE* 1.3 64.5 + - + +
465I ARG* 3.0 9.3 + - - +
466I VAL* 3.0 39.1 + - + +
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Residues in contact with ILE 463 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405I PHE* 6.2 0.4 - - + -
438I ILE* 5.5 2.2 - - + -
439I ILE* 4.5 13.9 - - + -
442I ILE* 4.1 18.8 - - + -
459I VAL* 3.0 19.6 + - + +
460I MET 4.1 2.2 - - - +
462I THR* 1.3 77.6 - - + +
464I THR* 1.3 59.8 + - - +
466I VAL* 4.1 14.8 - - + -
467I VAL* 2.9 43.0 + - + +
489I LEU* 6.3 1.6 - - + -
492I LEU* 3.9 32.1 - - + -
493I THR* 5.1 7.0 - - - +
496I LEU* 4.5 15.5 - - + -
507I LEU* 4.4 15.9 - - + -
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Residues in contact with THR 464 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I THR* 3.3 38.0 - - + +
77I LEU* 4.4 7.4 - - + -
78I TYR* 2.8 28.8 + - + +
460I MET 2.3 29.3 + - - -
461I GLN* 3.3 13.4 - - - -
462I THR 3.1 0.2 - - - -
463I ILE* 1.3 76.9 - - - +
465I ARG* 1.3 53.3 + - - +
467I VAL* 4.3 1.6 - - - +
468I SER* 2.3 34.2 + - - +
507I LEU* 4.0 15.8 - - + +
510I LEU* 5.3 1.1 - - + -
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Residues in contact with ARG 465 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I GLU* 3.2 37.7 + - - +
70I TYR* 5.4 1.8 - - - +
73I THR* 3.2 27.9 + - - -
74I ASN* 4.6 17.4 - - - +
356I ASP* 5.5 2.8 + - - -
359I LEU* 4.4 25.0 - - - +
412I TRP* 3.9 18.7 - - + -
413I LYS* 3.7 33.4 - - - +
416I LYS* 4.2 18.1 - - - +
461I GLN* 3.4 16.6 + - - +
462I THR 3.0 6.8 + - - +
464I THR* 1.3 75.7 - - - +
466I VAL* 1.3 62.1 + - - +
468I SER 3.4 0.2 + - - -
469I PHE* 2.9 28.6 + - - +
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Residues in contact with VAL 466 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412I TRP* 3.7 32.3 - - + -
435I SER* 4.8 11.7 - - - +
438I ILE* 6.1 3.6 - - + -
439I ILE* 4.4 14.6 - - + -
462I THR* 3.0 29.0 + - + +
463I ILE* 3.2 16.1 + - + +
465I ARG* 1.3 74.7 - - - +
467I VAL* 1.3 58.5 + - - +
470I ILE* 2.9 44.3 + - + +
489I LEU* 3.8 24.5 - - + -
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Residues in contact with VAL 467 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463I ILE* 2.9 30.3 + - + +
464I THR 4.3 2.2 - - - +
466I VAL* 1.3 71.6 - - - +
468I SER* 1.3 66.1 + - - +
471I SER* 3.1 25.3 + - - +
489I LEU* 3.7 29.2 - - + -
493I THR* 4.0 10.5 - - - +
507I LEU* 3.8 26.9 - - + -
510I LEU* 5.5 3.4 - - + -
511I THR* 3.3 39.2 - - + +
514I LEU* 3.8 4.9 - - - +
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Residues in contact with SER 468 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I TRP* 3.5 22.9 - - - -
68I TYR* 5.1 0.2 - - - -
69I GLU* 4.1 6.1 - - - -
73I THR* 3.4 18.8 - - - +
464I THR 2.3 27.0 + - - -
465I ARG 3.4 5.1 + - - -
466I VAL 3.1 0.4 - - - -
467I VAL* 1.3 82.4 - - - +
469I PHE* 1.3 59.3 + - - +
472I PHE* 2.9 27.5 + - - +
510I LEU* 4.3 10.6 - - - +
514I LEU* 3.8 13.8 - - - +
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Residues in contact with PHE 469 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I LEU* 3.6 32.1 - - + -
65I TRP* 3.3 28.3 - + - +
69I GLU* 4.3 5.4 - - - +
412I TRP* 4.9 4.0 - + + -
416I LYS* 4.7 18.2 - - + -
419I LEU* 4.5 24.7 - - + -
420I ILE* 4.7 12.1 - - + -
428I LEU* 5.0 4.0 - - + -
431I VAL* 4.7 15.5 - - + -
465I ARG 2.9 18.2 + - - +
466I VAL 4.5 0.2 - - - +
468I SER* 1.3 72.0 - - - +
470I ILE* 1.3 73.4 + - + +
472I PHE* 3.9 9.4 - + - -
473I TYR* 2.8 47.7 + + + +
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Residues in contact with ILE 470 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412I TRP* 4.7 2.7 - - + -
428I LEU* 6.4 1.6 - - + -
431I VAL* 4.2 24.2 - - + -
432I ILE* 5.6 4.9 - - + -
435I SER* 4.6 2.0 - - - +
466I VAL* 2.9 31.3 + - + +
469I PHE* 1.3 84.1 - - + +
471I SER* 1.3 57.8 + - - +
473I TYR* 4.0 1.7 - - + -
474I GLN* 2.9 28.8 + - - +
482I VAL* 3.3 32.3 - - + +
485I LEU* 3.7 38.1 - - + -
486I LEU* 4.5 2.0 - - + +
489I LEU* 3.7 17.0 - - + -
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Residues in contact with SER 471 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467I VAL* 3.1 27.1 + - - +
468I SER 3.6 1.5 + - - -
469I PHE 3.3 0.2 - - - -
470I ILE* 1.3 77.8 - - - +
472I PHE* 1.3 57.5 + - - +
474I GLN* 3.2 9.3 + - - +
475I ILE* 3.0 32.0 + - - +
486I LEU* 3.4 21.4 - - - +
489I LEU* 3.9 4.3 - - - +
511I THR* 4.8 6.1 + - - +
514I LEU* 4.1 23.6 - - - +
515I SER* 5.3 1.8 - - - -
518I LYS* 5.2 1.2 - - - +
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Residues in contact with PHE 472 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I LEU* 3.6 21.1 - - + -
62I LEU* 3.6 18.2 - - + -
65I TRP* 3.4 66.6 - + + -
468I SER 2.9 20.3 + - - +
469I PHE* 3.1 14.3 + + - +
471I SER* 1.3 77.1 - - - +
473I TYR* 1.3 58.1 + - - +
475I ILE* 3.3 24.3 - - + +
476I PHE* 3.1 54.8 - + - -
514I LEU* 5.2 1.8 - - + +
517I LEU* 4.9 4.5 - - + -
537I VAL* 5.0 6.7 - - + -
541I LEU* 5.1 5.2 - - + -
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Residues in contact with TYR 473 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I LEU* 4.6 25.1 - - + +
62I LEU* 5.6 4.5 - - + -
419I LEU* 5.8 3.1 - - + -
428I LEU* 3.4 39.7 - - + +
469I PHE* 2.8 41.7 + + + +
470I ILE* 4.1 4.7 - - + +
472I PHE* 1.3 75.5 - - - +
474I GLN* 1.3 60.4 + - - +
475I ILE 3.2 1.8 - - - -
476I PHE* 4.7 2.7 - + + +
477I VAL* 2.9 74.4 + - + +
479I SER* 4.7 1.1 - - - -
482I VAL* 3.6 26.2 - - + -
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Residues in contact with GLN 474 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470I ILE 2.9 20.0 + - - +
471I SER* 3.3 11.9 - - - +
473I TYR* 1.3 75.3 - - - +
475I ILE* 1.3 54.9 + - - -
477I VAL 3.4 9.3 - - - +
478I GLU* 3.3 18.5 - - - +
479I SER 3.9 1.8 + - - -
482I VAL* 3.2 15.7 + - + +
483I LYS* 3.1 42.7 - - - +
486I LEU* 3.6 23.4 - - + +
518I LYS* 2.1 54.0 + - + -
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Residues in contact with ILE 475 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471I SER 3.0 17.2 + - - +
472I PHE* 3.3 39.9 - - + +
473I TYR 3.2 0.6 - - - -
474I GLN* 1.3 78.1 - - - +
476I PHE* 1.3 80.7 + - + +
478I GLU* 4.9 2.3 - - - +
514I LEU* 4.0 13.5 - - + +
517I LEU* 3.7 27.1 - - + +
518I LYS* 3.7 36.0 + - + +
521I TRP* 3.5 35.4 - - + -
522I ASP* 4.8 3.1 - - - +
537I VAL* 5.4 0.4 - - + -
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Residues in contact with PHE 476 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I LYS* 2.4 24.9 + - - +
57I TYR* 3.5 21.2 + + + +
58I LEU* 5.0 7.6 - - + -
61I LEU* 3.5 37.7 - - + -
472I PHE* 3.1 52.0 - + - -
473I TYR* 3.5 4.4 + + + +
475I ILE* 1.3 88.8 - - + +
477I VAL* 1.3 60.1 + - + +
478I GLU* 3.9 3.2 + - - +
521I TRP* 3.4 54.5 + + - +
537I VAL* 4.0 10.5 - - + -
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Residues in contact with VAL 477 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I LYS* 3.1 26.5 - - - +
58I LEU* 4.9 4.0 - - + -
473I TYR* 2.9 69.7 + - + +
474I GLN* 3.4 11.5 + - - -
476I PHE* 1.3 75.4 - - + +
478I GLU* 1.3 59.9 + - - +
479I SER* 2.9 24.7 + - - +
482I VAL* 4.8 0.2 - - - +
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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