Contacts of the helix formed by residues 414 - 422 (chain G) in PDB entry 4Y49
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 ALA 414 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402G SER* 3.8 19.3 - - - +
405G PHE* 3.3 27.6 - - + +
406G LEU* 4.9 2.0 - - + -
411G PHE* 2.7 23.2 + - - +
413G LYS* 1.3 71.2 - - - +
415G GLN* 1.3 62.7 + - - +
416G GLU 3.1 1.2 + - - -
417G TYR 3.7 1.2 + - - +
418G ILE* 3.6 21.5 + - - +
438G ILE* 4.3 24.6 - - + +
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Residues in contact with GLN 415 (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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163A TRP* 6.4 0.2 - - + -
164A GLU* 4.2 24.2 - - + -
411G PHE 2.8 12.0 + - - +
412G PRO* 4.5 0.9 - - + +
414G ALA* 1.3 74.1 - - - +
416G GLU* 1.3 63.8 + - - +
418G ILE* 5.3 1.3 - - - -
419G ASP* 3.0 30.3 + - + +
438G ILE* 3.7 26.2 - - + +
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Residues in contact with GLU 416 (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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164A GLU* 6.4 0.2 - - - -
412G PRO 3.4 20.7 + - - +
413G LYS* 3.7 13.9 - - + -
414G ALA 3.1 0.4 - - - -
415G GLN* 1.3 79.3 - - - +
417G TYR* 1.3 75.9 + - + +
419G ASP* 4.2 1.6 - - - +
420G ALA* 3.4 16.8 + - - +
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Residues in contact with TYR 417 (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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379G LEU* 5.3 8.1 - - - +
398G ASN* 3.5 31.6 - - - +
401G LEU* 3.6 31.4 - - + -
402G SER* 3.5 17.7 - - - -
413G LYS* 4.1 17.7 - - + -
414G ALA 3.7 2.9 + - - +
416G GLU* 1.3 87.6 - - + +
418G ILE* 1.3 57.0 + - - +
419G ASP 2.6 3.0 + - - -
420G ALA* 2.4 35.3 + - - -
421G ALA 2.7 9.4 + - - -
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Residues in contact with ILE 418 (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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399G TYR* 5.7 0.7 - - - +
402G SER* 3.3 20.5 - - - +
414G ALA 3.6 9.9 + - - +
415G GLN* 4.8 1.8 - - - +
417G TYR* 1.3 76.8 - - - +
419G ASP* 1.3 50.3 + - - +
421G ALA* 3.1 12.0 - - - +
422G LEU* 2.4 39.7 + - - +
431G PHE* 4.3 22.0 - - + +
434G LEU* 4.7 6.7 - - + +
435G LYS* 4.7 16.2 - - + +
438G ILE* 6.1 0.4 - - + -
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Residues in contact with ASP 419 (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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415G GLN 3.0 21.0 + - - +
416G GLU 4.2 1.8 - - - +
417G TYR 2.6 3.6 + - - -
418G ILE* 1.3 76.1 - - - +
420G ALA* 1.3 50.7 + - - +
422G LEU* 3.0 10.6 + - - +
423G ASP* 2.8 32.6 + - - +
435G LYS* 5.9 1.2 - - - +
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Residues in contact with ALA 420 (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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394G PHE* 6.0 2.1 - - - -
398G ASN* 4.4 5.4 - - - +
416G GLU 3.4 12.9 + - - +
417G TYR* 2.4 23.5 + - - +
419G ASP* 1.3 68.1 - - - +
421G ALA* 1.3 62.8 + - - +
423G ASP* 3.3 18.6 + - - +
424G HIS* 3.7 7.8 + - - +
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Residues in contact with ALA 421 (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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394G PHE* 5.4 2.5 - - - -
395G ILE* 4.2 15.1 - - - +
398G ASN* 3.5 36.1 - - + +
399G TYR* 4.5 4.3 - - - +
417G TYR 2.7 9.3 + - - -
418G ILE* 3.1 21.1 - - - +
420G ALA* 1.3 72.5 - - - +
422G LEU* 1.3 54.6 + - - +
423G ASP 3.2 0.2 - - - -
424G HIS* 3.3 23.0 + - - +
425G THR 3.7 7.3 + - - +
431G PHE* 4.8 12.2 - - + -
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Residues in contact with LEU 422 (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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418G ILE 2.4 30.9 + - - +
419G ASP* 3.0 11.6 + - - +
421G ALA* 1.3 66.5 - - - +
423G ASP* 1.3 55.8 + - - +
424G HIS 3.3 3.5 + - - -
425G THR 3.8 15.1 - - - +
426G PRO* 4.2 14.0 - - - +
431G PHE* 4.7 10.3 - - + +
432G TYR* 4.5 22.9 - - + -
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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