Contacts of the helix formed by residues 462 - 476 (chain G) in PDB entry 5LS6
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 THR 462 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323G GLN* 3.1 47.2 + - + +
455G ALA* 3.5 8.1 - - - -
461G LYS* 1.3 76.1 - - - +
463G CYS* 1.3 58.8 + - - +
464G ARG* 3.9 7.1 - - - +
465G GLN* 2.5 57.6 + - - +
466G VAL* 3.0 12.3 + - - +
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Residues in contact with CYS 463 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320G CYS* 3.4 18.7 - - - -
323G GLN 4.0 6.0 + - - +
325G TYR* 3.4 23.5 - - - +
451G PHE* 4.0 7.8 - - - +
452G CYS* 3.6 17.9 - - - -
455G ALA* 3.2 14.5 - - + +
462G THR* 1.3 72.6 - - - +
464G ARG* 1.3 62.9 + - - +
466G VAL* 3.8 1.3 + - - -
467G TYR* 3.3 19.9 + - - +
802G ZN 1.9 39.0 - - - -
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Residues in contact with ARG 464 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323G GLN* 3.6 13.9 + - + +
324G CYS 3.4 23.4 + - - +
325G TYR* 4.2 6.3 - - - +
326G GLN 5.3 7.0 + - - -
425G GLU* 4.4 17.6 + - - +
426G PRO 4.0 17.0 + - - -
427G PRO* 4.5 2.2 - - - +
428G GLU* 4.1 23.5 + - - +
462G THR* 3.9 7.9 - - - +
463G CYS* 1.3 77.2 - - - +
465G GLN* 1.3 58.7 + - + +
467G TYR* 3.1 12.8 + - - +
468G GLU* 2.9 68.6 + - - +
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Residues in contact with GLN 465 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428G GLU* 4.8 7.6 + - - +
430G VAL* 4.3 17.8 - - + +
432G TRP* 3.4 12.5 - - + -
461G LYS* 3.3 27.9 - - + +
462G THR* 2.5 54.3 + - - +
464G ARG* 1.3 70.3 - - + +
466G VAL* 1.3 63.6 + - - +
468G GLU* 3.2 28.1 + - - +
469G PHE 3.1 18.0 + - - -
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Residues in contact with VAL 466 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432G TRP* 4.1 9.2 - - + -
440G PHE* 3.9 12.3 - - + -
451G PHE* 3.6 27.1 - - + -
454G ILE* 3.4 22.7 - - + -
455G ALA* 3.8 27.1 - - + +
458G ILE* 3.9 16.2 - - + -
461G LYS* 4.1 9.0 - - + -
462G THR 3.0 17.7 + - - +
463G CYS 4.1 4.9 - - - +
465G GLN* 1.3 74.7 - - - +
467G TYR* 1.3 57.0 + - - +
469G PHE* 3.3 4.0 + - - +
470G ARG* 3.0 26.0 + - - +
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Residues in contact with TYR 467 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325G TYR* 3.6 25.1 - + + -
330G GLY* 2.7 30.1 + - - -
331G ALA* 4.1 12.6 - - - -
334G PHE* 3.6 19.2 - + - +
335G ALA* 4.1 14.8 - - + -
338G LEU* 5.9 1.1 - - + -
423G ASN* 3.8 14.0 + - - -
451G PHE* 3.6 28.0 - + + -
463G CYS 3.3 11.4 + - - +
464G ARG* 3.1 14.8 + - - +
466G VAL* 1.3 77.1 - - - +
468G GLU* 1.3 68.0 - - + +
470G ARG* 4.3 6.5 - - + -
471G VAL* 3.0 45.4 + - + +
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Residues in contact with GLU 468 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427G PRO* 4.5 16.4 - - + +
428G GLU* 3.1 39.3 - - - +
430G VAL* 3.0 30.6 - - + +
432G TRP* 5.9 1.3 - - - +
464G ARG* 2.9 49.1 + - - +
465G GLN* 3.3 19.5 - - - +
467G TYR* 1.3 79.4 - - + +
469G PHE* 1.3 57.6 + - - +
471G VAL* 3.5 8.4 - - - +
472G LYS* 2.9 31.2 + - - +
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Residues in contact with PHE 469 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LYS* 5.0 9.4 - - - -
432G TRP* 3.2 70.4 - + + +
437G ALA* 4.5 17.3 - - + -
440G PHE* 3.6 36.6 - + + -
441G ARG* 4.9 3.8 - - - -
465G GLN 3.1 2.0 + - - -
466G VAL 3.8 4.3 - - - +
468G GLU* 1.3 78.2 - - - +
470G ARG* 1.3 55.5 + - - +
472G LYS* 3.8 24.0 - - + +
473G GLU* 2.6 69.1 + - + +
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Residues in contact with ARG 470 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335G ALA* 4.7 2.5 + - - +
338G LEU* 3.5 23.0 + - + +
339G THR* 2.9 43.6 + - - +
342G ARG* 5.0 14.8 - - - +
440G PHE* 3.7 19.1 - - + -
444G ILE* 5.5 11.7 - - - +
449G ASP* 3.8 13.6 + - - -
451G PHE* 3.7 30.9 - - + -
466G VAL 3.0 16.8 + - - +
467G TYR* 3.8 8.5 - - + +
469G PHE* 1.3 74.3 - - - +
471G VAL* 1.3 53.9 + - - +
473G GLU* 3.1 2.7 + - - +
474G SER* 2.6 63.2 + - - +
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Residues in contact with VAL 471 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334G PHE* 4.5 14.4 - - + -
338G LEU* 4.6 4.5 - - + -
423G ASN* 3.4 28.5 - - - +
427G PRO* 5.2 11.0 - - + -
467G TYR* 3.0 57.9 + - + +
468G GLU* 3.5 7.6 - - - +
470G ARG* 1.3 75.1 - - + +
472G LYS* 1.3 61.5 + - - +
474G SER* 2.6 18.8 + - - -
475G SER* 3.2 14.0 + - - -
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Residues in contact with LYS 472 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LYS* 3.8 38.5 - - + +
427G PRO* 6.3 4.0 - - - -
428G GLU 5.0 5.8 + - - -
429G ASN* 6.1 0.4 - - - +
430G VAL* 3.9 25.7 + - - +
432G TRP* 4.4 13.7 - - - +
468G GLU* 2.9 20.2 + - - +
469G PHE* 3.3 28.2 - - + +
471G VAL* 1.3 77.2 - - - +
473G GLU* 1.3 59.1 + - - +
475G SER* 2.6 21.9 + - - -
476G ILE* 3.2 19.7 - - + +
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Residues in contact with GLU 473 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LYS* 5.7 3.1 - - - -
440G PHE* 4.1 10.8 - - + -
441G ARG* 3.4 40.8 + - - +
444G ILE* 6.3 0.7 - - + -
469G PHE* 2.6 53.1 + - + +
470G ARG* 3.7 5.4 - - - +
472G LYS* 1.3 70.6 - - - +
474G SER* 1.3 67.4 + - - +
476G ILE* 3.2 33.1 + - - +
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Residues in contact with SER 474 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338G LEU* 3.4 28.1 - - - +
470G ARG* 2.6 48.1 + - - +
471G VAL* 2.6 22.2 + - - -
473G GLU* 1.3 73.4 - - - +
475G SER* 1.3 58.5 + - - -
476G ILE 3.5 5.9 - - - +
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Residues in contact with SER 475 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B LYS 4.9 5.2 + - - -
286B ASN* 4.6 6.8 + - - -
471G VAL 3.2 10.5 + - - -
472G LYS* 2.6 24.4 + - - -
474G SER* 1.3 79.2 + - - +
476G ILE* 1.3 66.6 + - - +
477G ILE* 3.3 10.6 + - - +
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Residues in contact with ILE 476 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B ASN* 3.2 29.2 - - + +
284B LYS* 3.6 37.0 - - + +
286B ASN* 5.6 1.3 - - - +
472G LYS* 3.2 24.0 + - + +
473G GLU* 3.2 30.8 + - - +
474G SER 3.5 8.7 - - - +
475G SER* 1.3 77.6 + - - +
477G ILE* 1.3 74.0 + - - +
478G ALA* 3.6 2.9 + - - +
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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
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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