Contacts of the helix formed by residues 470 - 480 (chain G) in PDB entry 5WUA
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 LEU 470 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466G VAL 3.0 6.9 + - - +
467G ILE* 4.1 13.0 - - - +
468G ILE 3.0 1.6 + - - -
469G LEU* 1.3 76.2 - - - +
471G ALA* 1.3 65.0 + - - +
472G PRO 3.6 0.2 - - - -
473G VAL* 3.3 12.6 - - + +
474G GLN* 3.2 20.3 + - - +
550G ILE* 5.1 15.3 - - + -
590G LEU* 5.8 6.3 - - + -
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Residues in contact with ALA 471 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467G ILE 5.0 0.4 + - - -
468G ILE 3.0 16.1 + - - +
469G LEU 3.2 0.2 - - - -
470G LEU* 1.3 78.7 - - - +
472G PRO* 1.3 64.0 - - - +
473G VAL 3.1 0.7 + - - -
474G GLN* 3.2 3.0 + - - +
475G TYR* 3.0 25.2 + - - +
590G LEU* 5.9 7.9 - - + +
594G SER* 5.0 4.4 - - - -
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Residues in contact with PRO 472 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469G LEU 4.4 5.4 - - - +
471G ALA* 1.3 77.2 - - - +
473G VAL* 1.3 53.2 + - - +
475G TYR* 4.6 3.8 - - + -
476G PHE* 2.7 42.7 + - + +
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Residues in contact with VAL 473 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469G LEU 4.4 4.9 + - - +
470G LEU* 3.3 23.6 + - + +
471G ALA 3.1 0.8 - - - -
472G PRO* 1.3 77.5 - - - +
474G GLN* 1.3 57.7 + - - +
476G PHE* 3.8 2.5 - - - +
477G VAL* 2.9 27.8 + - - +
546G MET* 5.8 8.7 - - + -
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Residues in contact with GLN 474 (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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470G LEU 3.2 9.0 + - - +
471G ALA* 3.8 3.6 - - - +
473G VAL* 1.3 77.4 - - - +
475G TYR* 1.3 57.5 + - - +
477G VAL* 2.4 34.3 + - - +
478G ALA* 2.9 8.9 + - - +
591G PHE* 5.5 4.0 - - + -
594G SER* 3.4 28.0 - - - -
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Residues in contact with TYR 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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471G ALA 3.0 16.6 + - - +
472G PRO* 4.6 4.9 - - + -
474G GLN* 1.3 74.8 - - - +
476G PHE* 1.3 57.9 + - - +
478G ALA* 3.1 14.0 - - - +
479G THR* 3.0 20.8 + - - -
594G SER* 4.4 16.2 - - - +
597G VAL* 6.1 5.6 - - + -
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Residues in contact with PHE 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 PRO* 2.7 24.5 + - + +
473G VAL* 3.9 2.0 - - - +
475G TYR* 1.3 72.2 - - - +
477G VAL* 1.3 59.9 + - - +
478G ALA 3.0 2.2 - - - -
479G THR* 2.6 31.6 + - - -
480G LYS* 2.9 12.6 + - - +
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Residues in contact with VAL 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 VAL 2.9 14.4 + - - +
474G GLN* 2.4 30.5 + - - +
476G PHE* 1.3 69.2 - - - +
478G ALA* 1.3 53.9 + - - -
480G LYS* 3.6 5.9 + - - +
481G LEU* 2.9 25.9 + - - +
539G TYR 5.6 3.0 - - - +
543G SER* 3.8 28.9 - - - -
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Residues in contact with ALA 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 GLN 2.9 6.7 + - - +
475G TYR* 3.1 18.6 - - - +
476G PHE 3.0 0.2 - - - -
477G VAL* 1.3 73.9 - - - +
479G THR* 1.3 57.1 + - - +
480G LYS 3.0 2.0 - - - -
481G LEU* 2.4 30.2 + - + -
482G SER* 3.0 16.6 + - - -
594G SER 5.6 4.7 - - - +
598G ARG* 6.1 5.6 - - + -
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Residues in contact with THR 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 TYR 3.0 8.0 + - - -
476G PHE* 2.6 29.4 + - - -
478G ALA* 1.3 70.5 - - - +
480G LYS* 1.3 54.1 + - - -
482G SER* 4.8 4.0 + - - -
483G GLN* 5.1 5.7 + - - +
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Residues in contact with LYS 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 PHE 2.9 11.2 + - - +
477G VAL* 3.7 6.1 - - - +
479G THR* 1.3 75.4 - - - +
481G LEU* 1.3 63.5 + - - +
482G SER 3.6 0.2 - - - -
483G GLN* 4.7 4.5 - - - +
484G ALA* 3.7 16.5 + - - +
539G TYR* 4.9 20.1 - - + +
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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