Contacts of the helix formed by residues 457 - 470 (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 GLY 457 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454G TYR* 3.3 13.4 + - - +
455G ILE 3.2 11.5 - - - +
456G LEU* 1.3 81.7 - - - +
458G VAL* 1.3 64.8 + - - +
459G SER* 3.3 3.1 - - - -
460G ALA* 3.3 11.6 + - - +
461G LEU* 3.9 3.3 + - - +
566G PHE* 6.5 1.1 - - - -
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Residues in contact with VAL 458 (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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456G LEU 3.7 1.2 + - - -
457G GLY* 1.3 72.6 - - - +
459G SER* 1.3 63.2 + - - +
461G LEU* 3.8 2.1 + - - +
462G ILE* 3.1 26.4 + - + +
565G PHE* 5.6 9.6 - - + -
566G PHE* 6.2 4.2 - - + +
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Residues in contact with SER 459 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457G GLY 3.3 1.0 - - - -
458G VAL* 1.3 76.7 - - - +
460G ALA* 1.3 67.1 + - - +
462G ILE* 3.7 4.1 - - - +
463G GLY* 3.1 18.4 + - - -
558G THR* 3.9 31.1 - - - +
561G GLY* 4.9 1.8 - - - -
562G HIS* 4.0 25.8 - - - -
565G PHE* 6.0 2.5 - - - +
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Residues in contact with ALA 460 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449G VAL 6.1 0.4 - - - +
452G LEU* 5.3 8.1 - - + -
453G TYR 5.0 3.1 - - - +
454G TYR 3.4 25.1 + - - +
455G ILE* 3.5 20.2 - - - +
457G GLY 3.3 2.9 + - - +
458G VAL 3.3 0.6 - - - -
459G SER* 1.3 80.4 - - - +
461G LEU* 1.3 61.7 + - - +
462G ILE 2.8 7.5 + - - -
464G ALA* 2.9 25.4 + - + +
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Residues in contact with LEU 461 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449G VAL* 6.5 0.7 - - - -
455G ILE 4.7 8.1 - - - +
457G GLY 3.9 2.7 + - - +
458G VAL* 3.8 3.6 + - - +
459G SER 3.7 0.2 - - - -
460G ALA* 1.3 78.5 - - - +
462G ILE* 1.3 49.1 - - - +
464G ALA* 4.4 4.3 - - - -
465G ALA* 2.4 41.9 + - - +
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Residues in contact with ILE 462 (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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458G VAL* 3.1 21.2 + - + +
459G SER* 3.7 5.2 - - - +
460G ALA 2.8 2.6 + - - -
461G LEU* 1.3 76.0 - - - +
463G GLY* 1.3 60.5 + - - +
465G ALA* 2.9 6.9 + - - +
466G VAL* 2.9 24.9 + - - +
558G THR* 6.3 0.9 - - - -
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Residues in contact with GLY 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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459G SER 3.1 7.5 + - - -
460G ALA 4.0 0.2 - - - -
462G ILE* 1.3 78.7 - - - +
464G ALA* 1.3 57.4 + - - +
466G VAL* 2.9 25.7 + - - +
467G ILE* 2.9 11.1 + - - +
554G ALA* 4.5 12.7 - - - +
558G THR* 3.8 25.2 - - - -
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Residues in contact with ALA 464 (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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449G VAL* 4.7 22.5 - - + +
460G ALA 2.9 20.1 + - - +
461G LEU* 4.4 3.8 - - - -
463G GLY* 1.3 75.2 - - - +
465G ALA* 1.3 56.1 + - - +
467G ILE* 3.0 13.9 + - + +
468G ILE* 2.9 26.3 + - - +
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Residues in contact with ALA 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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461G LEU 2.4 32.1 + - - +
462G ILE* 2.9 9.1 + - - +
464G ALA* 1.3 72.3 - - - +
466G VAL* 1.3 61.0 + - - +
468G ILE* 3.8 7.6 - - - +
469G LEU* 2.9 25.5 + - - +
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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
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462G ILE 2.9 7.8 + - - +
463G GLY* 2.9 17.5 + - - +
465G ALA* 1.3 74.2 - - - +
467G ILE* 1.3 55.9 + - - +
469G LEU* 2.6 29.3 + - + +
470G LEU* 3.0 13.2 + - - +
554G ALA* 4.9 12.1 - - + -
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Residues in contact with ILE 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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463G GLY 2.9 7.9 + - - +
464G ALA* 3.0 23.3 + - + +
466G VAL* 1.3 74.9 - - - +
468G ILE* 1.3 58.4 + - - +
470G LEU* 3.9 13.6 + - - +
471G ALA 5.0 0.2 + - - -
554G ALA* 5.3 7.6 - - + +
586G LEU* 6.1 4.7 - - + -
587G VAL* 6.4 2.0 - - - -
590G LEU* 4.5 14.6 - - - +
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Residues in contact with ILE 468 (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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464G ALA 2.9 13.3 + - - +
465G ALA* 4.0 7.9 - - - +
467G ILE* 1.3 71.8 - - - +
469G LEU* 1.3 59.8 + - - +
470G LEU 3.0 10.2 + - - -
471G ALA* 3.0 22.9 + - - +
590G LEU* 6.2 0.4 - - - -
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Residues in contact with LEU 469 (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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465G ALA 2.9 19.6 + - - +
466G VAL* 2.6 21.7 + - + +
468G ILE* 1.3 71.4 - - - +
470G LEU* 1.3 56.8 + - - -
471G ALA 3.2 2.8 + - - -
472G PRO* 4.4 6.9 - - - +
473G VAL* 4.4 6.2 + - - +
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Residues in contact with LEU 470 (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 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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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