Contacts of the strand formed by residues 470 - 474 (chain B) in PDB entry 1DY7
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 VAL 470 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438B LEU* 3.7 4.7 - - - -
455B TYR* 4.1 8.1 - - + -
456B VAL 3.4 19.7 - - - +
457B ASP* 4.3 8.7 - - + -
469B SER* 1.3 80.9 - - - +
471B ALA* 1.3 75.3 + - - +
472B VAL* 4.6 1.8 - - + -
488B LYS 3.7 0.2 - - - +
489B THR* 3.5 4.2 - - - -
490B LEU* 2.9 34.0 + - + +
492B ILE* 3.9 12.6 - - + -
505B VAL* 3.8 19.7 - - + -
519B PHE* 3.7 39.9 - - + -
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Residues in contact with ALA 471 (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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437B ALA* 4.1 18.4 - - + -
438B LEU* 3.8 16.6 - - + +
454B LEU 3.6 1.1 - - - +
455B TYR* 3.4 4.0 - - - -
456B VAL* 2.8 38.2 + - + +
470B VAL* 1.3 74.8 - - - +
472B VAL* 1.3 59.6 + - - +
473B PHE* 4.2 4.3 - - + -
487B PHE* 3.7 27.8 - - + -
488B LYS 3.5 4.9 - - - -
489B THR* 4.8 0.2 - - - +
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Residues in contact with VAL 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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453B TYR* 3.5 39.0 - - + -
454B LEU 3.3 5.2 - - - +
455B TYR* 3.6 20.2 - - + -
470B VAL* 4.5 1.6 - - + +
471B ALA* 1.3 77.5 - - - +
473B PHE* 1.3 63.5 + - - +
474B ASP 4.2 0.7 + - - -
487B PHE* 3.3 3.3 - - - +
488B LYS* 2.8 41.5 + - + +
490B LEU* 3.5 42.2 - - + -
539B LEU* 4.0 13.4 - - + +
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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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414B VAL* 4.4 0.7 - - + -
435B PHE* 3.6 31.0 - + - -
436B PRO 3.4 18.4 - - - -
437B ALA* 3.9 12.3 - - + -
453B TYR* 3.3 10.4 - - - -
454B LEU* 2.9 47.8 + - + +
456B VAL* 3.8 24.5 - - + -
471B ALA* 4.3 2.7 - - + -
472B VAL* 1.3 75.4 - - - +
474B ASP* 1.3 60.1 + - - +
475B ILE 3.5 0.7 + - - -
478B MET* 3.8 17.7 - - + -
485B PRO* 3.5 30.5 - - + -
486B GLU 3.4 16.8 - - - +
487B PHE* 3.7 21.1 - + + -
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Residues in contact with ASP 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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452B GLN* 2.9 31.9 - - - +
453B TYR* 3.8 17.4 + - + -
472B VAL 4.2 0.6 + - - -
473B PHE* 1.3 69.9 - - - +
475B ILE* 1.3 65.1 + - - +
476B LYS* 3.1 13.4 + - - +
477B ALA* 3.1 32.3 + - + +
478B MET* 3.5 13.1 + - - +
485B PRO* 6.0 0.5 - - - +
486B GLU 4.7 4.2 + - - -
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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