Contacts of the helix formed by residues 482 - 496 (chain G) in PDB entry 6V3O
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 SER 482 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480G GLU 3.5 3.3 + - - -
481G TRP* 1.3 75.4 - - - +
483G GLU* 1.3 67.7 + - - +
484G ASP* 4.1 6.0 + - - +
485G LYS* 2.8 26.2 + - - +
486G ARG* 2.9 11.2 + - - +
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Residues in contact with GLU 483 (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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482G SER* 1.3 73.8 - - - +
484G ASP* 1.3 61.4 + - - +
486G ARG* 3.4 11.3 + - - +
487G GLN* 2.8 56.8 + - - +
539G ALA* 3.2 27.4 - - + +
540G PRO* 3.6 1.1 - - + -
541G SER* 2.9 41.4 + - - -
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Residues in contact with ASP 484 (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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482G SER* 3.2 6.3 + - - +
483G GLU* 1.3 77.3 - - - +
485G LYS* 1.3 66.2 + - - +
487G GLN* 3.4 16.3 + - - +
488G GLU* 3.1 25.2 + - - +
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Residues in contact with LYS 485 (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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481G TRP* 3.4 58.1 - - + +
482G SER* 2.8 21.1 + - - +
484G ASP* 1.3 75.4 - - - +
486G ARG* 1.3 63.0 + - - +
488G GLU* 3.5 18.1 + - - +
489G TRP* 3.1 23.7 + - + +
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Residues in contact with ARG 486 (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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460G GLU* 5.3 4.9 + - - -
463G THR* 4.0 18.0 + - - +
478G TYR* 3.3 54.0 + - + +
479G ARG* 2.8 34.6 + - - +
481G TRP* 3.1 26.7 + - + +
482G SER 2.9 16.7 + - - +
483G GLU* 3.6 14.8 + - - +
485G LYS* 1.3 76.8 - - - +
487G GLN* 1.3 57.6 + - - +
489G TRP* 3.3 2.1 + - - +
490G LEU* 2.8 36.4 + - - +
541G SER* 4.0 19.2 + - - -
542G ASP* 5.0 3.8 + - - -
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Residues in contact with GLN 487 (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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483G GLU* 2.8 50.5 + - - +
484G ASP* 3.8 15.4 + - - +
486G ARG* 1.3 75.5 - - - +
488G GLU* 1.3 58.9 + - - +
490G LEU* 3.3 7.5 + - - +
491G LEU* 2.8 39.3 + - + +
540G PRO* 3.6 24.6 - - + +
541G SER* 4.5 8.3 - - - +
544G LEU* 4.9 8.3 - - + -
580G ARG* 2.7 45.4 + - - +
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Residues in contact with GLU 488 (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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484G ASP 3.1 13.6 + - - +
485G LYS* 3.5 21.9 + - - +
487G GLN* 1.3 79.1 - - - +
489G TRP* 1.3 65.7 + - + +
491G LEU* 4.0 7.4 - - - +
492G SER* 3.2 23.7 + - - -
580G ARG* 6.2 0.4 - - - +
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Residues in contact with TRP 489 (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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466G ILE* 3.8 19.5 - - + -
469G ILE* 5.2 1.8 - - + -
470G THR* 3.9 20.6 - - + -
475G ILE* 4.5 19.8 - - + +
478G TYR* 4.2 9.9 - + - -
481G TRP* 3.6 29.6 - + + -
485G LYS* 3.1 19.3 + - + +
486G ARG 3.7 2.0 - - - +
488G GLU* 1.3 76.1 - - + +
490G LEU* 1.3 101.7 + - + +
492G SER* 3.1 7.8 + - - -
493G GLU* 3.0 59.3 + - + +
500G LEU* 3.8 28.5 - - + -
548G LEU* 4.3 4.7 - - + -
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Residues in contact with LEU 490 (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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466G ILE* 4.0 20.2 - - + -
478G TYR* 3.3 26.7 - - + +
486G ARG 2.8 23.9 + - - +
487G GLN* 3.7 5.2 - - - +
489G TRP* 1.3 96.7 - - + +
491G LEU* 1.3 58.2 + - - +
493G GLU* 3.2 4.4 + - - +
494G LEU* 2.8 41.8 + - + +
541G SER* 3.8 30.3 - - - +
544G LEU* 4.1 11.2 - - + +
545G ALA* 4.1 11.7 - - - +
548G LEU* 4.2 11.4 - - + -
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Residues in contact with LEU 491 (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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487G GLN* 2.8 26.8 + - + +
488G GLU* 4.1 7.2 - - - +
490G LEU* 1.3 73.0 - - - +
492G SER* 1.3 57.6 + - - +
494G LEU* 4.5 6.5 - - + +
495G ARG* 2.9 65.8 + - - +
544G LEU* 3.8 29.4 - - + -
580G ARG* 3.8 25.6 - - - +
584G VAL* 3.7 33.0 - - + -
586G TRP* 5.1 7.2 - - + -
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Residues in contact with SER 492 (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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488G GLU 3.2 16.9 + - - -
489G TRP* 3.1 7.8 + - - -
491G LEU* 1.3 74.4 - - - +
493G GLU* 1.3 61.5 + - - +
495G ARG* 3.8 6.3 - - - +
496G GLY* 2.9 25.6 + - - -
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Residues in contact with GLU 493 (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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498F ARG* 2.9 42.6 + - - +
475G ILE* 5.6 1.4 - - - +
489G TRP* 3.0 64.1 + - + +
490G LEU 3.7 6.1 - - - +
492G SER* 1.3 78.1 - - - +
494G LEU* 1.3 55.9 + - - +
496G GLY* 3.1 17.8 + - - +
498G ARG 4.8 4.3 - - - +
500G LEU* 3.6 12.9 - - - +
548G LEU* 4.1 17.7 - - + -
551G ARG* 3.1 16.4 + - - -
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Residues in contact with LEU 494 (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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490G LEU* 2.8 39.7 + - + +
491G LEU* 4.3 5.8 - - + +
493G GLU* 1.3 72.8 - - - +
495G ARG* 1.3 64.4 + - - +
496G GLY 3.7 1.9 - - - +
544G LEU* 4.1 16.8 - - + +
547G GLU* 3.9 4.5 - - + +
548G LEU* 3.6 50.7 - - + +
551G ARG* 2.9 29.0 + - - +
586G TRP* 3.2 57.8 + - + -
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Residues in contact with ARG 495 (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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491G LEU* 2.9 51.4 + - - +
492G SER* 4.2 5.3 - - - +
494G LEU* 1.3 75.1 - - + +
496G GLY* 1.3 65.2 + - - +
497G LYS* 4.7 5.4 - - - +
584G VAL* 3.9 16.3 - - - +
585G ASP* 3.0 37.2 + - - +
586G TRP* 4.5 17.6 - - + +
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Residues in contact with GLY 496 (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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492G SER 2.9 19.3 + - - -
493G GLU* 3.1 14.0 + - - +
494G LEU 3.7 5.2 - - - +
495G ARG* 1.3 83.5 - - - +
497G LYS* 1.3 63.3 + - - +
498G ARG* 3.5 3.4 - - - -
551G ARG* 4.2 7.8 + - - -
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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