Contacts of the helix formed by residues 474 - 479 (chain C) in PDB entry 2W93
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 TYR 474 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415C ILE* 4.9 1.6 - - + -
445C GLY* 3.6 20.5 + - - -
448C GLN* 5.0 2.9 + - - -
449C LEU* 4.8 5.0 - - - +
473C GLY* 1.3 71.6 - - - -
475C THR* 1.3 65.1 + - - +
476C ILE* 3.3 2.7 - - - -
477C GLN* 3.2 17.5 + - + +
478C LYS* 3.1 24.2 + - - +
487C TYR 3.5 26.0 - - - -
488C ASN* 3.0 25.2 + - - +
489C GLU 4.9 0.9 - - - -
490C ILE* 3.4 26.7 - - + +
600C TPP 3.3 44.4 - - + -
25D LEU* 4.1 18.2 - - - +
26D PRO* 3.6 15.1 - - + +
48D ASN 4.5 7.1 + - - -
49D ALA* 5.9 0.5 - - - -
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Residues in contact with THR 475 (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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390C THR* 4.0 5.4 - - - +
471C ASN* 3.1 42.0 - - + +
473C GLY 4.1 1.6 - - - +
474C TYR* 1.3 72.3 - - - +
476C ILE* 1.3 64.8 + - - +
478C LYS* 3.0 18.0 + - + +
479C LEU* 3.0 23.4 + - - +
542C VAL* 2.6 35.0 + - + +
543C PHE* 4.4 0.3 - - - -
544C ASP 3.7 13.6 + - - +
600C TPP 2.9 13.1 + - - -
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Residues in contact with ILE 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C PHE* 6.1 1.6 - - + -
389C GLY* 3.7 24.9 - - - +
390C THR* 4.2 2.2 - - - +
393C PHE* 3.6 32.8 - - + -
475C THR* 1.3 77.0 + - - +
477C GLN* 1.3 65.0 + - + +
479C LEU* 3.7 12.1 + - - +
480C ILE* 3.4 28.6 - - + +
549C LEU* 4.0 17.5 - - + -
600C TPP 3.0 58.1 + - + +
602C PY0 4.3 14.1 - - + +
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Residues in contact with GLN 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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474C TYR* 3.2 9.9 + - - +
475C THR 3.1 0.6 - - - -
476C ILE* 1.3 75.8 - - + +
478C LYS* 1.3 60.9 + - - +
479C LEU 3.1 1.8 - - - -
480C ILE* 3.1 4.5 + - - -
481C HIS* 2.8 35.5 + - - +
488C ASN* 2.8 34.4 + - - +
600C TPP 3.1 34.0 + - + -
602C PY0 2.9 39.4 + - - +
26D PRO* 3.7 24.7 - - - +
27D GLY* 3.6 5.9 - - - -
31D LEU* 4.1 17.3 - - + +
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Residues in contact with LYS 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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471C ASN 4.6 0.2 + - - -
472C ASP 3.0 20.0 + - - -
473C GLY* 4.2 0.4 - - - -
474C TYR 3.1 17.7 + - - +
475C THR* 3.0 13.5 + - - +
477C GLN* 1.3 76.0 - - - +
479C LEU* 1.3 59.9 + - - +
480C ILE 3.3 0.7 + - - -
481C HIS 4.0 1.6 + - - -
483C PRO* 3.5 45.6 + - + +
488C ASN* 3.4 35.7 - - + +
489C GLU* 2.8 39.7 + - - -
542C VAL* 3.5 31.1 - - + +
543C PHE* 3.8 17.0 - - + -
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Residues in contact with LEU 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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475C THR* 3.0 24.8 + - - +
476C ILE* 3.8 6.1 - - - +
477C GLN 3.1 0.2 - - - -
478C LYS* 1.3 76.7 - - - +
480C ILE* 1.3 60.2 + - + +
543C PHE* 3.5 40.8 - - + +
545C ALA* 3.6 28.9 - - + -
549C LEU* 3.9 27.1 - - + +
550C VAL* 5.3 5.4 - - + +
553C ALA* 3.7 24.4 - - + +
554C LYS 4.7 3.6 + - - -
557C ALA* 4.9 2.1 - - - +
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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