Contacts of the helix formed by residues 471 - 476 (chain B) 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 GLU 471 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B GLU* 3.3 11.1 - - - +
246B GLU* 2.5 33.4 - - - +
247B SER* 4.5 1.9 + - - -
351B ASN* 3.0 23.0 + - - +
447B TYR* 4.1 14.4 - - + +
449B PHE* 3.6 42.4 - - + -
469B GLY* 3.3 9.6 + - - -
470B ASP* 1.3 72.9 - - - +
472B LEU* 1.3 81.9 + - - +
473B PHE 3.2 0.2 - - - -
474B SER* 3.2 4.5 + - - -
475B VAL* 2.9 33.4 + - + +
500B TRP* 5.3 1.6 - - + -
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Residues in contact with LEU 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE* 3.6 50.7 - - + +
103B ASN* 5.7 1.1 - - - -
138B TRP* 3.5 33.0 - - + -
152B TYR* 4.2 10.3 - - + -
220B GLU* 3.7 11.9 - - + +
246B GLU* 3.7 2.5 - - - +
469B GLY* 2.8 28.7 + - - +
471B GLU* 1.3 98.1 - - - +
473B PHE* 1.3 60.6 + - + +
475B VAL* 4.5 3.1 - - + -
476B PHE* 2.9 41.8 + - + +
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Residues in contact with PHE 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU 3.3 24.2 - - - -
101B PHE* 4.4 7.0 - + - -
102B THR 3.5 22.0 - - - -
103B ASN* 4.9 3.4 - - - -
453B PRO* 4.0 20.6 - - + -
455B PHE* 3.7 51.4 - + + -
456B SER* 5.7 0.9 - - - -
469B GLY 4.0 14.1 - - - -
470B ASP* 3.3 22.0 - - - +
471B GLU 3.2 0.4 - - - -
472B LEU* 1.3 79.2 - - + +
474B SER* 1.3 57.3 + - - +
477B GLY* 3.1 5.9 + - - -
478B ALA* 2.7 47.6 + - + +
479B PRO* 3.4 5.3 - - - +
482B LYS* 4.2 4.5 - - - -
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Residues in contact with SER 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B PHE* 3.8 22.9 - - - -
451B TYR* 5.2 2.3 - - - -
453B PRO* 6.1 0.9 - - - +
470B ASP 4.4 1.2 + - - -
471B GLU 3.2 8.5 + - - -
473B PHE* 1.3 77.4 - - - +
475B VAL* 1.3 65.7 + - - +
477B GLY 3.5 0.5 + - - -
479B PRO* 5.1 0.6 - - - +
489B GLU* 5.4 4.2 + - - +
492B LEU* 3.8 13.9 - - - +
493B SER* 3.1 41.9 + - - +
496B VAL* 3.9 24.8 - - - +
497B MET* 3.7 2.6 - - - +
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Residues in contact with VAL 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B LEU* 3.7 13.7 - - + +
218B PHE* 4.2 14.8 - - + -
246B GLU* 4.1 11.9 - - - +
471B GLU* 2.9 29.5 + - + +
472B LEU* 3.8 5.8 - - + +
474B SER* 1.3 78.4 - - - +
476B PHE* 1.3 66.8 + - + +
477B GLY 3.2 0.4 - - - -
496B VAL* 3.8 19.5 - - + -
497B MET* 3.4 18.8 - - - +
500B TRP* 3.6 48.2 - - + +
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Residues in contact with PHE 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ASN* 2.7 40.2 + - + +
138B TRP* 3.3 65.1 - + + -
152B TYR* 3.7 27.4 - + + -
153B ASP 4.1 16.8 - - - +
154B GLY* 4.8 3.1 - - - -
156B ALA* 4.1 9.6 - - - +
157B LEU* 4.5 18.9 + - + -
165B VAL* 4.6 11.9 - - + -
167B THR* 5.2 1.6 - - + -
218B PHE* 4.2 14.8 - + - -
472B LEU* 2.9 23.8 + - + +
475B VAL* 1.3 82.5 - - + +
477B GLY* 1.3 60.0 + - - +
478B ALA 3.5 1.8 - - - -
497B MET* 4.7 3.1 - - - -
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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