Contacts of the helix formed by residues 452 - 458 (chain G) in PDB entry 6IY6
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 ILE 452 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401G PHE* 4.4 20.0 - - + -
442G ALA* 3.9 23.8 - - + -
447G ILE* 4.0 24.5 - - + -
448G ASP 4.0 2.0 - - - +
449G LEU* 3.5 18.8 - - + +
451G LYS* 1.3 84.5 - - + +
453G LYS* 1.3 64.4 + - - +
454G ALA* 3.3 2.9 - - - -
455G TYR* 3.3 17.2 + - + +
456G ILE* 3.2 42.6 + - + +
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Residues in contact with LYS 453 (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 LEU 2.7 11.3 + - - +
450G GLU* 3.4 29.3 + - - +
451G LYS 3.6 0.4 - - - -
452G ILE* 1.3 76.2 - - - +
454G ALA* 1.3 57.3 - - - +
456G ILE* 3.4 8.8 + - - +
457G ASP* 3.0 55.9 + - - +
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Residues in contact with ALA 454 (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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451G LYS 5.5 1.1 - - - +
452G ILE* 3.3 1.3 - - - -
453G LYS* 1.3 78.9 - - - +
455G TYR* 1.3 60.8 + - - +
457G ASP* 3.3 11.2 + - - +
458G SER 3.3 16.1 + - - -
179H ARG 5.9 1.8 - - - +
180H LEU* 3.5 43.3 - - + +
181H ASP 4.8 0.7 + - - -
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Residues in contact with TYR 455 (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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252G LEU* 4.5 33.2 - - + -
255G GLN* 2.5 40.3 + - + -
256G MET* 6.2 2.2 - - + -
401G PHE* 4.2 20.6 - + - -
402G TYR* 3.8 19.1 - + + +
432G ILE 5.2 0.5 + - - -
438G LEU* 3.8 27.6 - - + +
452G ILE* 3.3 18.6 + - + +
454G ALA* 1.3 77.6 - - - +
456G ILE* 1.3 69.4 + - + +
458G SER* 3.1 22.2 - - - -
459G PHE* 3.2 28.2 - + - -
180H LEU* 4.5 9.5 - - + +
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Residues in contact with ILE 456 (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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435G PRO* 4.0 12.9 - - + +
438G LEU* 4.3 17.0 - - + -
439G THR* 3.7 40.4 - - + +
442G ALA* 5.2 0.2 - - + -
449G LEU* 4.3 10.1 - - + +
452G ILE* 3.2 40.4 + - + +
453G LYS* 3.7 8.1 - - - +
455G TYR* 1.3 76.7 - - + +
457G ASP* 1.3 63.2 - - - +
459G PHE* 3.2 26.6 + - - +
460G ARG* 3.7 28.9 - - - +
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Residues in contact with ASP 457 (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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453G LYS* 3.0 57.2 + - - +
454G ALA* 3.5 9.1 + - - +
455G TYR 3.3 0.2 - - - -
456G ILE* 1.3 74.6 - - - +
458G SER* 1.3 60.8 + - - +
459G PHE 3.3 1.0 + - - -
460G ARG* 3.1 47.7 + - - +
461G PHE* 4.6 6.6 - - - -
181H ASP* 3.9 27.5 - - + +
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Residues in contact with SER 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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255G GLN 5.2 0.2 - - - -
256G MET* 4.0 9.3 - - - +
259G CYS* 3.7 27.4 - - - +
454G ALA 3.3 4.8 + - - -
455G TYR* 3.1 18.3 + - - -
456G ILE 3.1 0.4 - - - -
457G ASP* 1.3 77.1 - - - +
459G PHE* 1.3 60.4 - - - +
460G ARG 3.8 0.3 + - - -
461G PHE* 4.3 9.5 + - - +
180H LEU* 3.9 21.3 - - - -
181H ASP* 4.3 6.5 - - - +
184H VAL* 3.5 27.6 - - - +
188H ARG* 4.6 0.5 + - - -
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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