Contacts of the helix formed by residues 465 - 472 (chain W) in PDB entry 5IY8
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 ASP 465 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463W PRO* 2.8 17.0 + - + +
464W LEU* 1.3 71.7 - - - +
466W ILE* 1.4 54.9 + - - +
467W TYR 3.3 0.2 - - - -
468W PRO* 3.2 10.3 - - - +
469W LYS* 2.8 60.0 + - - +
650W ASP* 4.4 2.4 - - - +
654W PHE* 6.3 0.9 - - + -
690W ARG* 2.9 32.3 + - - +
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Residues in contact with ILE 466 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461W LEU 6.2 0.2 - - - +
463W PRO* 6.3 0.2 - - + -
464W LEU* 5.0 3.4 - - - +
465W ASP* 1.4 78.6 + - - +
467W TYR* 1.3 74.3 + - + +
469W LYS* 3.2 13.2 + - + +
470W ILE* 2.9 53.7 + - + +
650W ASP* 3.8 43.7 - - + +
654W PHE* 3.3 43.6 - - + -
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Residues in contact with TYR 467 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39W VAL* 4.9 6.5 - - + -
236W ALA* 3.6 25.2 - - + +
237W HIS* 2.9 37.4 + + + +
239W ILE* 5.7 4.7 - - + -
456W ILE* 3.7 27.4 - - + -
457W THR 5.1 0.4 - - - -
458W SER* 3.2 31.6 + - - -
461W LEU* 3.8 29.6 - - + -
464W LEU* 3.7 7.0 + - - +
466W ILE* 1.3 91.6 - - + +
468W PRO* 1.4 59.8 - - + +
470W ILE* 3.5 15.9 + - + +
471W LEU* 2.8 41.0 + - + +
475W PRO* 5.8 0.9 - - + -
658W ARG* 5.6 1.6 - - - -
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Residues in contact with PRO 468 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39W VAL* 6.1 2.5 - - + -
464W LEU* 3.1 29.6 - - + +
465W ASP* 3.2 12.6 - - - +
467W TYR* 1.4 78.4 - - + +
469W LYS* 1.4 56.3 + - - +
471W LEU* 4.3 0.4 - - + -
472W ASP* 2.9 29.3 + - - -
473W PHE 3.4 23.8 + - - +
474W HIS* 4.0 23.5 + - + +
475W PRO* 4.3 13.7 - - + -
477W THR* 6.0 5.6 - - + -
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Residues in contact with LYS 469 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465W ASP* 2.8 38.9 + - - +
466W ILE* 3.2 17.0 + - + +
468W PRO* 1.4 74.3 - - - +
470W ILE* 1.3 62.1 + - + +
472W ASP* 3.7 7.4 + - - +
644W PHE* 3.4 57.3 - - + -
646W ILE* 3.8 18.6 - - - +
650W ASP* 2.7 39.8 + - + +
690W ARG* 4.2 3.6 - - - +
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Residues in contact with ILE 470 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237W HIS* 5.6 9.0 - - + +
239W ILE* 5.1 13.2 - - + -
240W ASP* 4.5 28.5 - - + +
441W SER* 5.2 8.7 - - - -
444W ILE* 4.6 10.9 - - + +
466W ILE* 2.9 49.4 + - + +
467W TYR* 3.6 22.0 - - + +
469W LYS* 1.3 71.3 - - - +
471W LEU* 1.3 69.2 + - + +
472W ASP* 3.4 1.2 + - - +
644W PHE* 5.8 0.2 - - - -
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Residues in contact with LEU 471 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37W HIS* 4.0 24.0 - - + +
239W ILE* 5.2 11.9 - - + -
441W SER* 5.7 1.1 - - - -
444W ILE* 3.9 28.4 - - + +
445W LYS* 4.4 10.0 + - - -
456W ILE* 3.9 20.6 - - + -
467W TYR* 2.8 25.6 + - + +
469W LYS 3.4 0.4 - - - -
470W ILE* 1.3 77.8 - - + +
472W ASP* 1.4 68.2 + - - +
473W PHE* 3.2 21.3 + - + +
475W PRO* 3.8 30.5 - - + -
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Residues in contact with ASP 472 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441W SER* 5.8 5.2 - - - -
445W LYS* 4.8 10.5 + - - +
468W PRO 2.9 12.6 + - - -
469W LYS 3.7 5.2 + - - +
470W ILE 3.4 3.9 - - - +
471W LEU* 1.4 78.2 - - - +
473W PHE* 1.3 58.8 + - - +
474W HIS* 5.5 5.0 - - - -
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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