Contacts of the helix formed by residues 473 - 480 (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 GLU 473 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472G ARG* 1.3 82.3 - - - +
474G VAL* 1.3 64.0 + - + +
476G ALA* 3.6 15.6 + - - +
477G ARG* 4.1 15.3 + - - +
459H PHE* 4.7 17.2 - - + -
490H ASN* 5.7 3.1 + - - -
562H PRO 3.6 5.8 + - - +
564H LEU 4.3 10.4 - - - +
565H SER* 5.4 1.2 - - - -
566H LEU* 4.0 23.4 + - - +
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Residues in contact with VAL 474 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472G ARG 2.9 5.8 + - - +
473G GLU* 1.3 81.3 - - + +
475G PHE* 1.3 56.4 + - - +
476G ALA 3.2 2.2 - - - -
477G ARG* 3.2 16.6 + - + +
478G GLN* 3.0 30.6 + - - +
488H GLN 5.3 3.4 - - - +
489H LEU* 3.7 34.1 - - + -
556H GLN* 2.7 45.3 - - + +
564H LEU 5.7 2.5 - - - +
566H LEU* 3.8 24.9 - - + -
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Residues in contact with PHE 475 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472G ARG* 2.9 18.5 + - - +
474G VAL* 1.3 72.2 - - - +
476G ALA* 1.3 65.5 + - - +
478G GLN* 3.4 21.0 + - - -
479G LEU* 3.3 41.4 + - + +
493G LEU* 4.8 2.2 - - + -
494G VAL* 3.7 22.0 - - + -
497G TYR* 3.1 27.8 - - + -
499G THR 4.1 20.9 - - - -
500G PRO* 3.8 31.9 - - + -
503G LEU* 4.4 18.2 - - + -
544G TYR* 3.7 23.8 - + - -
556H GLN* 3.8 1.3 - - - +
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Residues in contact with ALA 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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472G ARG* 3.5 5.0 + - + +
473G GLU 3.8 10.8 - - - +
474G VAL 3.2 0.8 - - - -
475G PHE* 1.3 78.6 - - - +
477G ARG* 1.3 62.6 + - - +
479G LEU* 3.3 13.0 + - - +
480G MET* 3.2 31.2 + - + +
490G ALA* 3.9 6.6 - - + +
491G ALA* 6.3 0.2 - - - -
494G VAL* 3.6 22.3 - - + +
457H PHE* 6.5 0.9 - - + -
459H PHE* 4.3 13.5 - - + -
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Residues in contact with ARG 477 (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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473G GLU* 4.1 20.0 - - - +
474G VAL* 3.2 15.5 + - - +
476G ALA* 1.3 77.4 - - - +
478G GLN* 1.3 62.3 + - - +
480G MET* 3.0 18.3 + - - +
481G GLN* 3.2 20.1 + - - +
459H PHE* 3.9 38.0 - - + +
462H GLU* 3.7 22.4 + - - -
463H SER* 6.1 2.2 - - - -
465H TRP* 6.4 0.9 - - - -
488H GLN* 3.3 58.4 + - + +
490H ASN* 5.7 3.1 + - - -
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Residues in contact with GLN 478 (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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474G VAL* 3.0 18.9 + - + +
475G PHE* 3.4 30.2 - - + +
476G ALA 3.3 0.2 - - - -
477G ARG* 1.3 78.5 - - + +
479G LEU* 1.3 60.3 + - - +
480G MET 3.4 0.5 + - - -
481G GLN* 3.5 8.0 + - - -
482G VAL* 5.2 0.3 - - - +
500G PRO* 4.1 6.9 - - - +
544G TYR* 4.6 4.6 + - - +
481H VAL* 4.7 0.2 - - - +
485H GLN* 2.9 62.8 + - + +
488H GLN* 4.7 1.5 - - + +
489H LEU* 4.6 6.5 - - + +
556H GLN* 3.4 27.9 - - - +
557H MET* 3.6 24.1 - - - +
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Residues in contact with LEU 479 (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* 3.3 36.9 + - + +
476G ALA* 3.6 7.9 - - - +
477G ARG 3.2 0.4 - - - -
478G GLN* 1.3 78.3 - - - +
480G MET* 1.3 57.9 + - - +
481G GLN 3.2 0.2 - - - -
482G VAL* 2.9 28.6 - - - +
485G VAL* 3.0 19.0 - - + +
490G ALA* 4.5 4.0 - - + +
493G LEU* 3.6 34.3 - - + -
494G VAL* 3.8 22.0 - - + -
503G LEU* 5.6 1.1 - - + -
540G LEU* 4.6 9.4 - - + -
544G TYR* 3.3 34.5 - - + +
485H GLN* 4.9 0.9 - - - +
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Residues in contact with MET 480 (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* 3.2 31.1 + - + +
477G ARG* 3.0 13.4 + - - +
479G LEU* 1.3 80.3 - - - +
481G GLN* 1.3 71.0 + - - -
482G VAL 3.3 3.4 - - - -
485G VAL* 3.4 23.8 - - + +
486G SER* 3.3 6.7 - - - +
487G GLY* 3.1 34.1 - - - -
490G ALA* 3.5 14.4 - - + -
457H PHE* 6.0 0.7 - - + -
459H PHE* 4.7 13.0 - - + -
460H CYS* 4.2 14.8 - - - -
465H TRP* 3.4 28.6 - - + -
468H GLY* 4.0 7.9 - - - -
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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