Contacts of the helix formed by residues 462 - 480 (chain O) in PDB entry 5G04
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 ASN 462 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496I GLN* 5.0 6.3 + - - +
225O ASN 3.5 4.5 - - - +
226O ASP* 3.8 26.9 + - - +
227O GLU 5.4 0.4 - - - +
228O THR* 4.2 2.9 + - - -
460O GLN 3.4 11.7 + - - -
461O ASN* 1.3 84.1 + - - +
463O THR* 1.3 81.9 + - - +
466O PHE* 3.3 16.5 - - - -
496O ARG* 3.1 58.7 - - - +
497O PHE* 4.1 10.6 - - + -
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Residues in contact with THR 463 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224O LYS 3.3 26.2 - - - +
225O ASN* 3.4 19.9 + - - +
226O ASP* 5.5 0.2 - - - +
419O ASP* 4.5 3.1 + - - +
420O ILE* 6.0 0.2 - - - +
461O ASN* 4.2 10.1 + - - +
462O ASN* 1.3 94.5 + - - +
464O GLU* 1.3 56.0 + - - +
465O SER* 2.7 27.9 + - - -
466O PHE 3.0 6.8 + - - -
497O PHE* 3.3 20.5 - - - -
503O HIS* 4.9 3.4 - - - -
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Residues in contact with GLU 464 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D PHE 3.7 9.6 - - - +
6D PRO* 5.1 0.4 - - + -
7D SER* 3.2 43.1 + - - +
420O ILE* 6.3 1.6 - - + -
463O THR* 1.3 73.2 - - - +
465O SER* 1.3 61.8 + - - +
467O ALA* 3.2 9.4 - - - +
468O VAL* 3.0 31.4 + - + +
503O HIS* 3.4 41.0 + - - +
506O LEU* 4.2 23.7 - - + +
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Residues in contact with SER 465 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D PRO* 5.4 1.8 - - - -
419O ASP* 3.4 20.9 - - - -
420O ILE* 3.3 35.2 + - - +
423O ALA* 3.3 28.3 - - - +
445O LEU* 4.3 2.0 - - - -
463O THR* 2.7 16.4 + - - -
464O GLU* 1.3 75.1 - - - +
466O PHE* 1.3 60.9 + - - -
468O VAL* 3.2 12.6 - - - +
469O ALA* 3.2 17.5 + - - +
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Residues in contact with PHE 466 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419O ASP* 3.1 29.4 - - - -
445O LEU* 3.2 43.7 - - + -
446O LEU* 3.7 12.6 - - + -
448O MET* 4.5 7.2 - - + -
450O SER* 6.1 1.8 - - - -
460O GLN* 3.4 20.2 - - + -
461O ASN* 3.7 20.6 - - + -
462O ASN* 3.3 25.4 - - - +
463O THR 3.0 4.0 + - - +
465O SER* 1.3 75.7 - - - +
467O ALA* 1.3 56.8 + - - +
469O ALA* 3.1 5.7 + - - +
470O LEU* 2.8 39.4 + - + +
496O ARG* 3.1 35.7 - - - +
497O PHE* 5.0 0.9 - - + -
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Residues in contact with ALA 467 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463O THR 3.6 2.8 + - - -
464O GLU* 3.2 13.5 - - - +
466O PHE* 1.3 72.9 - - - +
468O VAL* 1.3 67.7 + - - +
469O ALA 2.9 2.0 + - - -
470O LEU* 3.1 2.1 + - - -
471O CYS* 2.8 25.5 + - - +
493O LEU* 3.9 9.6 - - + +
497O PHE* 3.6 35.8 - - + -
503O HIS* 4.6 0.7 - - + +
506O LEU* 3.2 27.1 - - + -
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Residues in contact with VAL 468 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 3.6 38.6 - - + -
5D PHE* 3.8 19.5 - - - +
6D PRO* 4.3 17.0 - - + -
423O ALA* 4.1 14.4 - - + +
426O THR* 5.1 0.9 - - - -
464O GLU* 3.0 18.8 + - + +
465O SER* 3.2 17.3 - - - +
467O ALA* 1.3 76.8 - - - +
469O ALA* 1.3 55.2 + - - +
471O CYS* 3.6 5.1 - - - +
472O HIS* 3.0 42.1 + - + +
506O LEU* 4.8 8.7 - - + -
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Residues in contact with ALA 469 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426O THR* 4.5 13.0 - - + +
442O ALA* 4.1 13.1 - - - +
445O LEU* 3.9 19.3 - - + -
446O LEU* 4.0 14.6 - - + -
465O SER 3.2 13.8 + - - +
466O PHE* 3.1 14.8 + - - +
467O ALA 2.9 1.6 + - - -
468O VAL* 1.3 72.4 - - - +
470O LEU* 1.3 53.7 + - - +
471O CYS 3.0 1.1 - - - -
472O HIS* 3.0 5.7 + - - +
473O LEU* 2.8 34.6 + - - +
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Residues in contact with LEU 470 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497I TRP* 3.9 17.0 - - + -
446O LEU* 4.1 20.2 - - + -
466O PHE 2.8 27.6 + - - +
467O ALA 4.6 0.4 - - - +
469O ALA* 1.3 71.0 - - - +
471O CYS* 1.3 53.4 + - - +
473O LEU* 3.6 7.0 - - + -
474O ALA* 2.6 29.1 + - - +
489O VAL* 3.1 18.8 - - + +
492O HIS* 3.5 24.7 - - + +
493O LEU* 3.6 32.5 - - + -
496O ARG* 3.8 34.5 - - + +
497O PHE* 4.9 0.2 - - + -
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Residues in contact with CYS 471 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 4.4 11.7 - - + -
467O ALA 2.8 20.9 + - - +
468O VAL* 3.6 8.5 - - - +
470O LEU* 1.3 75.4 - - - +
472O HIS* 1.3 62.8 + - + +
474O ALA* 2.8 5.6 + - - +
475O GLU* 2.7 36.2 + - - +
493O LEU* 3.8 13.2 - - - -
506O LEU* 3.7 14.1 - - - -
507O TRP* 3.7 32.8 - - - -
510O CYS* 3.8 13.3 - - + -
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Residues in contact with HIS 472 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D THR* 4.5 2.1 - - - -
4D LEU* 3.2 48.6 + - + +
426O THR* 3.6 29.9 + - - +
427O ALA* 3.8 16.8 + - + -
430O ARG* 3.5 35.8 - - + +
442O ALA* 5.4 0.4 - - + -
468O VAL* 3.0 27.3 + - + +
469O ALA 3.0 3.4 + - - +
471O CYS* 1.3 75.1 - - + +
473O LEU* 1.3 57.8 + - - +
475O GLU* 4.1 14.6 + - - -
476O LEU* 2.9 41.2 + - + +
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Residues in contact with LEU 473 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497I TRP* 3.7 24.0 - - + -
507I LEU* 4.9 0.7 - - + -
513I LEU* 3.7 24.7 - - + -
439O LEU* 4.0 21.3 - - + +
442O ALA* 4.5 15.3 - - + +
443O GLN* 4.4 9.0 - - - +
446O LEU* 3.6 20.9 - - + -
469O ALA 2.8 13.7 + - - +
470O LEU* 3.4 9.0 - - + +
472O HIS* 1.3 79.5 - - - +
474O ALA* 1.3 60.5 + - - +
476O LEU* 4.3 6.0 - - - +
477O HIS* 3.1 35.5 + - + +
489O VAL* 4.2 17.7 - - + -
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Residues in contact with ALA 474 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470O LEU 2.6 21.0 + - - +
471O CYS* 2.8 6.8 + - - +
473O LEU* 1.3 72.1 - - - +
475O GLU* 1.3 56.4 - - - +
477O HIS* 3.3 1.6 - - - +
478O ALA* 3.1 10.7 + - - +
486O ALA* 2.9 28.8 - - - +
489O VAL* 3.7 26.7 - - + +
490O LEU* 4.0 24.5 - - + -
493O LEU* 4.4 0.9 - - + -
510O CYS* 4.1 6.7 - - - -
514O ILE* 4.2 3.4 - - + -
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Residues in contact with GLU 475 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 5.8 2.8 - - - +
430O ARG* 3.7 24.3 + - - +
471O CYS* 2.7 22.1 + - - +
472O HIS* 3.6 18.1 - - - +
474O ALA* 1.3 69.9 - - - +
476O LEU* 1.3 67.0 + - - +
478O ALA* 3.0 4.3 + - - +
479O GLU* 2.9 31.5 + - + +
510O CYS* 4.3 14.2 - - - +
513O LYS* 4.2 27.3 + - + +
514O ILE* 4.2 19.9 - - + +
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Residues in contact with LEU 476 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512I LEU* 3.5 13.0 - - + +
430O ARG* 3.5 38.1 - - - +
435O SER* 3.3 28.3 - - - +
438O ALA* 4.0 22.4 - - + +
439O LEU* 3.8 38.1 - - + +
442O ALA* 5.9 0.4 - - + -
472O HIS* 2.9 32.7 + - + +
473O LEU* 4.3 1.3 - - - +
475O GLU* 1.3 71.5 - - - +
477O HIS* 1.3 56.5 + - - +
479O GLU* 3.4 11.9 - - - +
480O GLN* 2.9 28.2 + - - +
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Residues in contact with HIS 477 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507I LEU* 4.4 11.0 - - + -
510I SER* 3.1 24.5 + - - -
512I LEU* 3.2 34.9 - - + +
513I LEU* 4.1 18.2 - - + -
439O LEU* 5.2 0.4 - - + +
473O LEU* 3.1 30.5 + - + +
474O ALA 3.3 10.5 - - - +
475O GLU 3.1 0.2 - - - -
476O LEU* 1.3 74.5 - - - +
478O ALA* 1.3 67.9 + - - +
480O GLN 3.0 12.5 + - - -
481O GLY 3.1 9.5 + - - -
482O CYS* 3.2 20.0 + - + +
485O ALA* 3.7 20.3 - - + +
486O ALA* 3.3 16.8 - - + +
489O VAL* 4.5 4.0 - - - +
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Residues in contact with ALA 478 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474O ALA 3.1 5.8 + - - +
475O GLU 3.0 10.4 + - - +
477O HIS* 1.3 73.5 - - - +
479O GLU* 1.3 66.2 + - + +
481O GLY 3.1 9.5 + - - -
483O PHE* 3.2 34.9 - - + +
486O ALA* 3.4 9.1 - - + +
514O ILE* 3.8 41.3 - - + +
517O ASP* 5.5 3.6 - - + +
704O VAL* 5.4 0.2 - - - +
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Residues in contact with GLU 479 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430O ARG* 3.6 26.6 + - - +
475O GLU* 2.9 16.2 + - + +
476O LEU* 3.4 16.7 - - - +
478O ALA* 1.3 79.8 - - + +
480O GLN* 1.3 58.0 + - + +
481O GLY 3.1 3.1 + - - -
517O ASP* 5.6 5.6 - - - +
618O TYR* 2.7 39.7 + - - +
656O ALA* 2.7 41.3 - - + +
657O ILE* 3.9 3.1 - - - +
704O VAL* 4.5 3.8 - - - +
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Residues in contact with GLN 480 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367I LYS* 5.5 4.3 + - - -
512I LEU* 3.7 34.8 - - + +
435O SER* 3.8 20.4 + - - -
436O THR* 5.6 2.0 + - - -
439O LEU* 4.4 6.9 - - - +
476O LEU* 2.9 17.0 + - - +
477O HIS 3.0 6.0 + - - -
479O GLU* 1.3 75.7 + - + +
481O GLY* 1.3 54.2 + - - +
482O CYS* 3.4 14.1 + - - -
618O TYR* 5.4 1.2 + - - +
653O ALA 5.5 0.9 - - - +
654O ASP* 5.3 4.7 - - - +
655O GLY 3.4 25.5 + - - +
657O ILE* 3.7 22.2 - - + +
660O LYS* 4.2 11.9 + - - -
703O LYS* 5.8 0.7 - - - +
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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
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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