Contacts of the strand formed by residues 472 - 478 (chain A) in PDB entry 1WBB
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 GLY 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467A PHE* 3.7 14.6 - - - -
468A ASN* 3.0 29.6 + - - +
469A ALA 4.5 1.9 + - - -
470A VAL 3.7 0.8 - - - -
471A HIS* 1.3 79.9 - - - +
473A TYR* 1.3 66.0 + - - -
474A TYR* 3.5 10.6 - - - +
492A ARG* 5.1 0.2 - - - -
510A GLU* 3.2 13.0 - - - -
514A LEU* 6.1 0.9 - - - -
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Residues in contact with TYR 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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443A ALA* 5.5 3.3 - - - +
447A LEU* 3.5 43.9 - - + +
465A VAL* 5.1 0.7 - - + -
466A GLY 3.5 14.1 - - - -
467A PHE* 3.5 33.3 - + + -
472A GLY* 1.3 71.2 - - - -
474A TYR* 1.3 60.2 + - - +
492A ARG* 2.9 26.6 + - - +
502A ILE* 3.5 7.5 - - + +
506A LEU* 3.4 23.6 - - + +
509A TYR* 3.7 14.1 + + - -
510A GLU* 2.8 44.3 + - + +
513A VAL* 3.5 25.5 - - + +
514A LEU* 4.8 4.3 - - + +
517A LYS* 5.2 3.3 + - - -
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Residues in contact with TYR 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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464A LYS* 5.4 0.9 - - + -
465A VAL* 3.4 11.0 - - - +
466A GLY* 2.9 56.6 + - - -
467A PHE 3.7 16.7 + - - -
468A ASN* 4.0 4.3 - - + -
471A HIS* 6.1 0.7 - - + -
472A GLY 3.5 12.6 - - - -
473A TYR* 1.3 76.6 - - - +
475A ILE* 1.3 59.7 + - - +
476A GLN* 3.8 20.2 + - + -
492A ARG* 4.8 6.3 - - - -
493A GLN* 4.7 4.7 - - + -
500A ARG* 3.2 71.4 + - + -
501A TYR 3.3 11.7 - - - +
506A LEU* 3.8 8.0 - - - +
28F G 4.8 1.6 + - - -
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Residues in contact with ILE 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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450A LEU* 5.3 3.4 - - + -
454A GLU* 4.9 7.0 - - + -
463A LEU* 3.6 29.2 - - + -
464A LYS 3.5 3.6 - - - -
465A VAL* 4.4 11.9 - - + -
474A TYR* 1.3 75.7 - - - +
476A GLN* 1.3 61.7 + - - +
477A ILE* 4.6 1.1 - - + -
489A TYR* 3.5 40.2 - - + +
500A ARG* 3.3 1.4 - - - -
501A TYR* 2.7 46.3 + - + +
503A ILE* 3.8 38.4 - - + +
506A LEU* 4.0 13.5 - - + -
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Residues in contact with GLN 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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462A THR 3.7 4.2 + - - +
463A LEU* 3.0 7.6 - - - +
464A LYS* 2.7 60.5 + - + +
474A TYR* 3.8 17.8 + - + -
475A ILE* 1.3 72.1 - - - +
477A ILE* 1.3 65.7 + - - +
478A SER* 5.7 0.6 - - - +
495A LEU* 5.3 0.5 - - - +
498A ALA* 3.9 25.2 - - + +
499A GLU 3.6 3.1 - - - -
500A ARG* 3.0 44.5 + - + -
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Residues in contact with ILE 477 (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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460A LEU* 3.8 17.7 - - + -
462A THR* 3.8 8.7 - - - +
463A LEU* 4.1 17.3 - - + +
475A ILE* 3.9 1.3 + - + -
476A GLN* 1.3 83.0 - - - +
478A SER* 1.3 72.8 + - - +
481A GLN* 3.7 30.7 - - + +
482A SER* 3.8 1.6 - - - +
485A ALA* 3.4 32.1 - - + -
486A PRO* 4.7 0.2 - - + -
489A TYR* 3.9 20.9 - - + -
498A ALA* 3.6 3.3 - - - +
499A GLU* 2.9 34.1 + - - +
501A TYR* 4.1 9.6 - - + -
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Residues in contact with SER 478 (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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462A THR* 3.1 39.9 + - - +
476A GLN* 5.7 0.8 - - - +
477A ILE* 1.3 77.3 - - - +
479A ARG* 1.3 59.1 + - - +
480A GLY* 3.4 5.0 + - - -
481A GLN* 3.3 16.6 + - - +
482A SER* 2.8 26.0 + - - -
497A ASN 3.9 10.1 - - - -
498A ALA* 4.2 3.4 - - - +
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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