Contacts of the helix formed by residues 472 - 480 (chain C) 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 ARG 472 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460C GLY* 2.8 23.2 + - - +
462C LEU* 4.0 11.6 - - - +
470C LEU 3.8 0.2 + - - -
471C HIS* 1.3 79.6 + - + +
473C LEU* 1.3 88.6 + - - +
475C CYS* 3.2 13.2 + - - +
476C VAL* 3.4 13.1 + - - +
483C ILE* 3.7 19.0 - - + +
484C ASP* 3.3 26.7 + - - +
487C VAL* 3.8 39.7 - - + -
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Residues in contact with LEU 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C GLN 5.9 0.2 - - - +
389C ALA 5.4 3.8 - - - +
390C ASN* 4.8 20.4 - - + +
471C HIS* 3.1 30.3 + - + +
472C ARG* 1.3 106.3 - - - +
474C GLN* 1.3 62.3 + - + +
476C VAL* 3.3 27.0 - - + +
477C ARG 4.8 0.2 + - - -
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Residues in contact with GLN 474 (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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386C ARG 3.0 22.8 + - - -
387C PHE* 3.6 0.9 - - - -
388C GLN* 2.9 45.4 + - + +
402C HIS* 3.4 32.0 - - - +
405C GLN* 4.0 8.3 + - - +
470C LEU* 3.6 23.5 - - + +
471C HIS* 2.9 35.2 + - + +
473C LEU* 1.3 77.3 - - + +
475C CYS* 1.3 59.4 + - - +
476C VAL 3.4 0.4 + - - -
477C ARG 4.7 0.2 + - - -
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Residues in contact with CYS 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C GLN* 4.9 3.1 - - - +
462C LEU* 3.7 19.5 - - + -
464C PHE* 4.1 12.3 - - - -
470C LEU* 4.0 27.8 - - - -
471C HIS 3.7 12.6 - - - -
472C ARG 3.2 9.7 + - - +
474C GLN* 1.3 78.9 - - - +
476C VAL* 1.3 54.5 - - - +
477C ARG 3.5 0.4 - - - -
478C GLY 3.3 2.9 + - - -
479C PHE* 2.8 52.3 + - + +
483C ILE* 3.7 14.4 - - + -
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Residues in contact with VAL 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C ARG* 3.4 8.7 + - - +
473C LEU* 3.3 22.2 - - + +
474C GLN 3.4 0.6 - - - -
475C CYS* 1.3 76.7 - - - +
477C ARG* 1.3 68.6 + - + +
480C GLY* 2.8 41.5 + - - +
481C GLU* 4.8 3.4 - - - +
483C ILE* 3.9 24.2 - - + -
484C ASP* 5.2 4.7 - - - +
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Residues in contact with ARG 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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399C ASP* 3.3 49.1 + - - +
402C HIS* 3.8 38.5 + - + -
403C ILE* 4.3 5.2 - - - +
473C LEU 4.8 0.2 + - - -
474C GLN 4.7 1.2 + - - -
475C CYS 3.5 0.6 - - - -
476C VAL* 1.3 89.0 - - + +
478C GLY* 1.3 57.9 + - - +
480C GLY* 4.9 0.2 - - - -
572C ARG* 2.8 20.8 + - - -
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Residues in contact with GLY 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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402C HIS* 3.4 35.4 - - - +
403C ILE* 4.1 3.5 - - - +
405C GLN* 5.2 1.1 - - - -
406C PHE* 3.7 20.8 - - - -
475C CYS 3.3 5.5 + - - -
477C ARG* 1.3 77.2 - - - +
479C PHE* 1.3 60.3 + - - +
572C ARG* 2.9 24.3 + - - -
576C LEU* 4.7 0.2 - - - +
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Residues in contact with PHE 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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405C GLN* 5.2 3.4 - - - -
406C PHE* 3.6 39.9 - + + -
409C LEU* 4.0 21.1 - - + -
447C PHE* 4.1 22.9 - + - -
451C LEU* 4.9 1.6 - - + -
464C PHE* 3.8 25.4 - + - -
475C CYS* 2.8 41.7 + - + +
478C GLY* 1.3 75.2 - - - -
480C GLY* 1.3 58.1 + - - +
482C TRP* 3.6 29.2 - + + +
483C ILE* 3.7 33.2 - - + +
486C ILE* 4.3 5.2 - - + -
572C ARG* 3.4 21.6 - - - +
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Residues in contact with GLY 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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476C VAL* 2.8 28.5 + - - +
477C ARG 4.9 0.2 - - - -
478C GLY 3.4 2.4 + - - -
479C PHE* 1.3 71.3 - - - +
481C GLU* 1.3 63.3 + - - -
482C TRP 3.0 7.2 + - - -
483C ILE* 3.2 22.2 - - - +
572C ARG* 3.8 13.3 - - - +
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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