Contacts of the helix formed by residues 475 - 480 (chain D) in PDB entry 5YD6
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 CYS 475 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462D LEU* 3.8 18.6 - - + -
464D PHE* 3.9 22.4 - - - -
470D LEU* 4.0 20.0 - - - -
471D HIS 3.1 14.1 + - - +
472D ARG 3.8 7.4 - - - +
473D LEU 3.3 0.4 - - - -
474D GLN* 1.3 76.4 - - - +
476D VAL* 1.3 58.7 + - - +
477D ARG 3.4 1.8 - - - -
478D GLY* 3.4 3.4 + - - -
479D PHE* 3.0 44.8 + - + +
483D ILE* 3.8 22.0 - - + -
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Residues in contact with VAL 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D ARG 3.5 8.1 + - - +
473D LEU* 3.3 26.5 - - + +
474D GLN 3.4 0.6 - - - -
475D CYS* 1.3 77.6 - - - +
477D ARG* 1.3 66.0 + - + +
480D GLY* 3.0 34.0 + - - +
481D GLU* 5.2 2.9 - - - +
483D ILE* 3.7 21.1 - - + -
484D ASP* 4.6 7.0 - - - +
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Residues in contact with ARG 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399D ASP* 3.2 51.9 + - - +
402D HIS* 4.0 29.3 + - + +
403D ILE* 4.3 7.1 - - - +
474D GLN 4.8 1.8 + - - -
475D CYS 3.4 0.8 - - - -
476D VAL* 1.3 84.8 - - + +
478D GLY* 1.3 56.9 + - - +
480D GLY* 5.1 0.2 - - - -
572D ARG* 3.0 17.3 + - - -
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Residues in contact with GLY 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D HIS* 3.4 33.7 - - - +
403D ILE* 4.2 2.3 - - - +
406D PHE* 3.5 22.1 - - - +
475D CYS 3.4 4.9 + - - -
476D VAL 3.3 0.2 - - - -
477D ARG* 1.3 77.3 - - - +
479D PHE* 1.3 60.6 + - - +
480D GLY 3.3 1.3 - - - -
572D ARG* 2.9 22.3 + - - -
576D LEU* 4.5 1.2 - - - +
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Residues in contact with PHE 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D HIS 5.9 0.4 - - - -
406D PHE* 3.4 42.0 - + + -
409D LEU* 4.0 20.9 - - + -
447D PHE* 4.1 22.9 - + - -
451D LEU* 5.1 1.3 - - + -
464D PHE* 3.6 26.7 - + - -
475D CYS* 3.0 39.6 + - + +
478D GLY* 1.3 75.9 - - - +
480D GLY* 1.3 60.2 + - - +
482D TRP* 3.4 28.5 - + + +
483D ILE* 3.7 32.3 - - + +
486D ILE* 4.4 4.7 - - + -
572D ARG* 3.4 18.7 - - - +
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Residues in contact with GLY 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476D VAL* 3.0 22.7 + - - +
477D ARG 5.1 0.2 - - - -
478D GLY 3.3 2.8 - - - -
479D PHE* 1.3 77.0 - - - +
481D GLU* 1.3 55.3 + - - -
482D TRP 2.8 17.0 + - - -
483D ILE* 3.5 20.1 - - - +
572D ARG* 3.6 17.6 - - - +
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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