Contacts of the helix formed by residues 486 - 497 (chain G) in PDB entry 4P0S
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 486 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480G MET* 3.3 10.0 - - - +
484G GLY 3.7 0.2 + - - -
485G VAL* 1.3 73.1 - - - +
487G GLY* 1.3 55.1 + - - +
488G GLU* 3.5 7.9 + - - +
489G LYS* 2.8 32.4 + - - +
490G ALA* 2.4 38.5 + - - +
30N C 3.9 7.5 + - - -
31N A 2.9 24.7 - - - -
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Residues in contact with GLY 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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480G MET* 3.1 22.5 - - - -
486G SER* 1.3 75.7 - - - +
488G GLU* 1.3 57.9 + - - +
490G ALA* 3.8 0.7 - - - +
491G ALA* 2.9 29.8 + - - +
455H THR 5.6 0.2 - - - +
456H THR* 4.8 8.7 - - - -
457H PHE* 4.7 8.8 - - - -
460H CYS* 3.7 21.4 - - - -
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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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486G SER* 3.0 8.0 + - - +
487G GLY* 1.3 74.6 - - - +
489G LYS* 1.3 67.8 + - - +
491G ALA* 3.5 5.7 + - - +
492G ALA* 3.1 22.5 + - - +
525G CYS* 4.2 1.1 - - + +
526G GLY* 4.0 32.0 + - - +
527G ARG 5.1 1.3 + - - -
452H ARG* 5.0 11.7 - - - -
455H THR* 4.2 24.0 - - + +
456H THR* 4.9 13.4 + - - +
30N C 3.5 27.6 + - - +
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Residues in contact with LYS 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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484G GLY 3.6 13.7 - - - +
485G VAL* 4.0 9.0 - - + -
486G SER* 3.1 31.4 + - - +
488G GLU* 1.3 78.6 - - - +
490G ALA* 1.3 56.0 + - - +
492G ALA* 3.4 3.8 + - - +
493G LEU* 3.0 33.9 + - + +
525G CYS* 3.9 16.3 - - + -
531G ASN 5.5 2.0 - - - -
532G LEU* 3.4 36.6 - - + +
536G LEU* 4.2 5.2 - - - -
30N C 2.1 57.2 + - - +
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Residues in contact with ALA 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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476G ALA* 3.9 18.2 - - + +
479G LEU* 4.5 5.4 - - + -
480G MET* 3.5 32.3 - - + -
485G VAL* 4.5 0.6 - - + +
486G SER 2.4 28.7 + - - +
487G GLY 3.8 2.7 - - - +
489G LYS* 1.3 67.0 - - - +
491G ALA* 1.3 57.0 + - - +
493G LEU* 2.9 10.6 + - - +
494G VAL* 2.5 40.3 + - - +
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Residues in contact with ALA 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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476G ALA* 5.8 0.4 - - - +
487G GLY 2.9 19.4 + - - +
488G GLU* 3.9 7.2 - - - +
489G LYS 3.4 0.2 - - - -
490G ALA* 1.3 76.4 - - - +
492G ALA* 1.3 56.8 + - - +
494G VAL* 4.6 4.3 - - - +
495G ASP* 2.8 28.7 + - - +
455H THR* 5.3 6.3 - - + +
457H PHE* 4.4 21.1 - - + -
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Residues in contact with ALA 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 3.1 8.5 + - - +
489G LYS 3.6 4.0 - - - +
490G ALA 3.1 0.4 - - - -
491G ALA* 1.3 77.2 - - - +
493G LEU* 1.3 62.3 + - + +
495G ASP* 3.3 16.4 - - - +
496G ARG 3.4 6.9 + - - -
523G ILE* 3.4 18.0 - - + +
524G LYS 3.3 25.8 - - - +
525G CYS* 3.5 32.3 - - - -
526G GLY 4.7 0.7 - - - +
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Residues in contact with LEU 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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475G PHE* 4.8 1.2 - - + -
479G LEU* 3.6 34.3 - - + -
485G VAL* 4.1 18.6 - - + -
489G LYS* 3.0 24.2 + - + +
490G ALA 2.9 4.9 + - - +
492G ALA* 1.3 75.1 - - + +
494G VAL* 1.3 64.6 + - - +
495G ASP 3.0 2.1 + - - -
496G ARG* 3.4 3.3 + - - +
497G TYR* 3.3 26.1 + - + +
520G LEU* 4.1 18.6 - - + +
523G ILE* 4.9 7.6 - - + -
525G CYS* 6.1 0.2 - - - -
532G LEU* 3.6 29.6 - - + -
540G LEU* 3.9 24.7 - - + -
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Residues in contact with VAL 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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472G ARG* 3.3 44.0 + - + +
475G PHE* 3.7 23.3 - - + -
476G ALA* 3.6 34.8 - - + -
479G LEU* 3.8 7.6 - - + -
490G ALA 2.5 21.8 + - - +
491G ALA* 4.8 3.1 - - - +
493G LEU* 1.3 73.0 - - - +
495G ASP* 1.3 57.6 + - - +
497G TYR 3.0 17.8 - - - +
498G SER* 3.0 16.0 - - - +
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Residues in contact with ASP 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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472G ARG* 5.3 7.2 + - - +
491G ALA 2.8 23.1 + - - +
492G ALA* 3.3 10.4 - - - +
494G VAL* 1.3 79.0 - - - +
496G ARG* 1.3 67.5 + - - +
498G SER* 4.8 4.0 + - - -
523G ILE* 5.8 0.7 - - - +
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Residues in contact with ARG 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 ALA 3.4 11.7 + - - +
493G LEU* 3.4 2.0 + - - +
495G ASP* 1.3 84.1 - - - +
497G TYR* 1.3 104.5 + - + +
498G SER 4.0 1.6 + - - -
502G SER* 4.8 1.0 + - - -
519G LEU* 6.0 0.4 - - - +
523G ILE* 3.3 37.0 - - + +
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Residues in contact with TYR 497 (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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475G PHE* 3.1 24.2 - - + -
493G LEU* 3.3 11.7 + - + +
494G VAL 3.0 8.4 - - - +
496G ARG* 1.3 127.5 + - + +
498G SER* 1.3 57.1 + - - +
499G THR 3.3 2.7 - - - -
502G SER* 3.6 27.8 - - - +
503G LEU* 3.8 28.9 - - + +
506G ALA* 3.6 22.4 - - + +
519G LEU* 3.5 28.6 + - + +
520G LEU* 3.1 33.6 - - + +
523G ILE* 5.0 1.2 - - + +
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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
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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