Contacts of the helix formed by residues 476 - 480 (chain C) in PDB entry 5UHC
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 HIS 476 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369C ASP* 2.9 29.1 + - - -
371C ASP* 3.7 21.1 - - + +
372C HIS* 3.6 26.2 - + - +
474C ASP* 3.4 7.5 + - - +
475C VAL* 1.3 73.8 - - - +
477C PRO* 1.3 90.1 - - + +
478C SER* 2.7 39.1 + - - -
479C HIS* 3.2 43.3 + - + +
850D PHE* 3.7 8.6 - - - -
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Residues in contact with PRO 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475C VAL 4.1 3.8 - - - +
476C HIS* 1.3 109.3 - - + +
478C SER* 1.3 55.0 + - - +
479C HIS 3.0 5.2 + - - -
480C TYR* 3.3 19.2 + - - +
562C ARG* 5.3 2.3 + - - -
565C ALA* 4.5 7.9 - - - -
566C GLY* 3.8 34.3 - - - +
850D PHE* 4.1 11.2 - - + -
854D HIS* 5.9 1.6 - - + -
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Residues in contact with SER 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C HIS* 4.0 16.6 - - - -
373C PHE* 3.0 35.5 + - - +
476C HIS* 2.7 31.7 + - - -
477C PRO* 1.3 72.9 - - - +
479C HIS* 1.3 61.2 + - - +
480C TYR 3.0 6.1 - - - -
482C ARG* 3.1 31.1 + - - +
533C ALA* 4.2 4.5 - - - -
537C ASP* 5.8 1.1 - - - -
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Residues in contact with HIS 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C ASP 4.7 2.9 - - - -
373C PHE* 3.4 44.0 - + - -
376C ARG* 4.9 7.5 + - - -
474C ASP 4.5 6.0 + - - -
475C VAL* 4.6 11.0 - - + -
476C HIS* 3.3 47.2 + - + +
477C PRO 3.0 1.4 - - - -
478C SER* 1.3 78.0 + - - +
480C TYR* 1.3 62.9 + - - +
481C GLY 3.2 0.5 + - - -
482C ARG 3.1 1.7 + - - -
483C MET* 2.8 67.0 + - + +
484C CYS 5.0 3.1 - - - -
485C PRO* 5.7 1.1 - - + -
586C MET 5.1 0.2 - - - +
850D PHE* 4.2 8.7 - - + -
857D ARG* 5.7 3.8 + - - -
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Residues in contact with TYR 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477C PRO 3.3 13.9 + - - +
478C SER 3.0 2.9 - - - -
479C HIS* 1.3 77.2 - - - +
481C GLY* 1.3 59.6 + - - +
482C ARG* 3.0 26.0 + - - +
514C THR* 4.4 0.3 - - - +
516C TYR* 3.7 7.0 + - - -
536C GLU* 5.2 0.7 - - - +
543C GLN* 5.3 1.2 - - - +
544C ALA* 5.4 0.5 + - - +
562C ARG* 3.4 45.0 - - - +
580C ASP* 2.7 38.7 + - - +
582C SER 4.8 2.6 + - - -
583C PRO 4.9 2.1 + - - -
585C GLN* 4.6 14.4 - - + +
586C MET* 3.8 25.8 - - + -
846D VAL* 4.0 24.7 - - + +
847D LEU* 5.1 4.0 - - + +
850D PHE* 3.7 29.4 - + + -
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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