Contacts of the helix formed by residues 414 - 419 (chain B) in PDB entry 2OKC
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 VAL 414 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325B LEU* 4.2 24.5 - - + +
359B THR* 3.4 38.4 - - + +
360B LYS* 2.8 24.9 + - + +
361B GLU* 5.3 0.4 - - - +
412B TYR 3.6 1.2 + - - -
413B PRO* 1.3 69.7 - - - +
415B ASP* 1.3 69.6 + - - +
417B ILE* 3.0 12.7 + - + +
418B ILE* 2.9 44.1 + - + +
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Residues in contact with ASP 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B PRO* 4.0 15.6 - - + +
414B VAL* 1.3 80.4 - - - +
416B GLU* 1.3 65.4 + - + +
418B ILE* 3.3 8.8 + - - +
419B ALA* 3.0 23.9 + - - +
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B ARG* 4.9 6.7 + - - -
411B LYS 5.4 0.3 - - - +
412B TYR* 3.5 33.5 - - + -
413B PRO* 3.1 35.4 + - + +
415B ASP* 1.3 81.3 - - + +
417B ILE* 1.3 58.1 + - + +
419B ALA* 3.3 10.0 + - - +
420B ARG* 3.1 30.4 + - + +
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Residues in contact with ILE 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B LEU* 4.0 19.7 - - + -
362B ILE* 3.3 37.2 - - + -
364B PHE* 4.9 1.8 - - + -
412B TYR* 4.0 15.7 - - + +
413B PRO 3.6 18.4 - - - +
414B VAL* 3.0 9.8 + - - +
416B GLU* 1.3 74.5 - - + +
418B ILE* 1.3 62.1 + - - +
419B ALA 3.1 1.1 - - - -
420B ARG* 2.8 30.7 + - - +
423B THR* 3.8 14.5 - - + -
424B SER 4.1 7.6 - - - +
425B LEU* 3.7 23.3 - - + -
427B ILE* 4.3 20.6 - - + -
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Residues in contact with ILE 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B LYS* 6.5 0.9 - - - -
325B LEU* 4.4 13.7 - - + -
414B VAL* 2.9 44.3 + - + +
415B ASP* 3.7 6.7 - - - +
417B ILE* 1.3 75.8 - - - +
419B ALA* 1.3 61.0 + - - +
420B ARG 3.4 5.9 + - - +
423B THR* 4.2 15.3 + - + +
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Residues in contact with ALA 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B ASP 3.0 14.0 + - - +
416B GLU* 3.4 13.9 - - - +
417B ILE 3.1 0.2 - - - -
418B ILE* 1.3 76.0 - - - +
420B ARG* 1.3 63.2 + - - +
421B ASP 3.7 0.7 + - - -
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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