Contacts of the helix formed by residues 470 - 476 (chain A) in PDB entry 1YA8
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 ASP 470 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A ASN* 4.1 1.6 - - - +
449A PHE* 3.7 11.9 - - + -
451A TYR 4.0 6.1 - - - +
452A ARG* 4.4 0.2 - - - -
453A PRO* 3.5 29.5 - - + +
456A SER* 4.4 0.3 + - - -
460A LYS* 3.2 24.6 + - - -
466A GLY* 3.3 9.4 + - - -
467A ASP* 2.7 44.2 + - - +
468A HIS 3.8 3.3 - - - +
469A GLY* 1.3 71.7 - - - +
471A GLU* 1.3 58.8 + - - +
472A LEU 3.0 9.4 + - - -
473A PHE* 3.3 24.4 + - - +
474A SER* 4.4 1.0 + - - -
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Residues in contact with GLU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLU* 3.2 23.0 - - - +
246A GLU* 2.7 33.4 - - - +
247A SER* 4.5 2.5 + - - -
351A ASN* 2.8 22.4 - - - +
447A TYR* 3.9 17.0 - - + +
449A PHE* 3.4 42.9 - - + -
469A GLY* 3.5 3.6 + - - -
470A ASP* 1.3 78.0 + - - +
472A LEU* 1.3 61.1 + - - +
473A PHE 3.3 0.7 - - - -
474A SER* 3.4 4.2 + - - -
475A VAL* 3.1 34.3 + - + +
496A VAL* 6.3 0.9 - - + -
500A TRP* 5.4 2.0 - - + -
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Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A PHE* 4.0 33.2 - - + +
103A ASN* 5.0 1.9 - - - +
138A TRP* 3.4 34.5 - - + -
152A TYR* 4.2 12.6 - - + +
220A GLU* 3.9 21.1 - - + +
246A GLU* 3.6 13.2 - - - +
469A GLY* 3.0 26.2 + - - +
470A ASP 3.0 1.0 - - - -
471A GLU* 1.3 84.8 - - - +
473A PHE* 1.3 67.0 + - + +
475A VAL* 4.4 1.6 - - + -
476A PHE* 3.1 37.3 + - + +
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Residues in contact with PHE 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU 3.4 24.7 - - - -
101A PHE* 4.4 7.6 - + - -
102A THR 3.8 20.4 - - - -
103A ASN* 4.8 3.6 - - - -
453A PRO* 4.0 19.7 - - + -
455A PHE* 3.7 50.5 - + + -
456A SER* 5.5 2.0 - - - -
469A GLY 3.7 16.8 - - - -
470A ASP* 3.3 20.6 - - - +
471A GLU 3.3 0.4 - - - -
472A LEU* 1.3 79.2 - - + +
474A SER* 1.3 62.0 + - - +
477A GLY 3.3 1.7 + - - -
478A ALA* 2.6 47.9 + - + +
479A PRO* 3.4 4.4 - - - +
482A LYS* 4.2 6.1 - - - -
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Residues in contact with SER 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A PHE* 3.8 11.6 - - - -
451A TYR* 5.6 0.9 - - - -
470A ASP 4.4 1.0 + - - -
471A GLU* 3.4 8.8 + - - -
472A LEU 3.2 0.4 - - - -
473A PHE* 1.3 78.4 - - - +
475A VAL* 1.3 66.3 + - - +
477A GLY 3.2 2.4 + - - -
479A PRO* 5.0 1.4 - - - +
489A GLU* 5.1 4.2 + - - +
492A LEU* 3.7 24.3 - - - +
493A SER* 2.9 34.2 + - - +
496A VAL* 4.0 24.7 - - - -
497A MET* 3.5 8.3 - - - +
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Residues in contact with VAL 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU* 4.0 12.9 - - + +
218A PHE* 4.1 9.4 - - + -
246A GLU* 4.0 15.3 - - - +
471A GLU* 3.1 22.6 + - + +
472A LEU* 3.4 5.6 + - - +
474A SER* 1.3 77.1 - - - +
476A PHE* 1.3 79.5 + - + +
477A GLY 3.3 1.8 + - - -
496A VAL* 3.7 23.6 - - + -
497A MET* 3.5 16.8 - - - +
500A TRP* 3.9 37.8 - - + +
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Residues in contact with PHE 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASN* 2.7 43.7 + - + +
138A TRP* 3.3 67.3 - + + -
152A TYR* 3.9 26.2 - + + -
153A ASP 3.8 17.1 - - - +
154A GLY* 4.6 5.2 - - - -
156A ALA* 4.1 8.9 - - - +
157A LEU* 4.8 12.5 + - + -
165A VAL* 4.6 15.5 - - + -
167A THR* 4.9 2.7 - - + -
218A PHE* 4.1 7.2 - + - -
472A LEU* 3.1 21.8 + - + +
473A PHE 3.9 0.2 - - - -
475A VAL* 1.3 88.6 - - + +
477A GLY* 1.3 60.4 + - - +
478A ALA 3.4 2.5 - - - -
497A MET* 4.6 2.5 - - - -
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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