Contacts of the strand formed by residues 496 - 503 (chain O) in PDB entry 2O93
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 THR 496 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397O LEU* 3.9 25.7 - - + +
459O PHE* 4.4 12.8 - - + -
460O ILE 5.4 2.2 - - - +
470O PRO* 4.1 23.1 - - + +
471O HIS 5.4 4.2 + - - +
475O GLN* 3.9 9.6 - - - +
492O ILE* 3.5 5.1 - - - +
493O VAL 2.8 39.2 + - - -
494O GLY 3.1 0.4 - - - -
495O ASN* 1.3 83.9 + - - +
497O LYS* 1.3 67.8 + - - +
498O VAL* 3.7 1.2 + - + +
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Residues in contact with LYS 497 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425O GLU* 6.0 0.2 + - - -
459O PHE* 4.3 5.5 - - - +
460O ILE 5.3 0.2 + - - -
475O GLN* 3.2 37.4 + - + +
476O VAL* 3.5 39.4 + - + +
477O HIS* 5.7 4.0 - - - -
490O GLU* 3.7 34.6 + - + +
491O LYS 3.9 2.7 - - - +
492O ILE* 3.7 32.8 - - + -
496O THR* 1.3 75.4 - - - +
498O VAL* 1.3 63.4 + - - +
519O LEU* 5.5 8.3 - - - +
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Residues in contact with VAL 498 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397O LEU* 4.6 8.5 - - + -
457O GLN* 4.3 9.4 - - + +
458O ILE 3.7 15.9 - - - +
459O PHE* 4.2 15.0 - - + -
490O GLU* 3.4 2.9 - - - +
491O LYS* 2.5 71.9 + - + +
493O VAL* 3.5 28.7 - - + -
496O THR* 3.7 10.1 + - + +
497O LYS* 1.3 77.8 - - - +
499O LEU* 1.3 75.3 + - - +
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Residues in contact with LEU 499 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457O GLN* 3.3 2.3 - - - -
458O ILE* 2.7 52.3 + - + +
476O VAL* 3.4 24.7 - - + +
477O HIS 4.4 3.8 - - - +
478O ARG* 3.6 33.4 - - + +
488O SER* 4.8 4.7 - - - -
489O TYR 3.4 4.5 - - - +
490O GLU* 3.5 34.8 - - + +
491O LYS* 4.9 0.2 - - - -
498O VAL* 1.3 76.8 - - - +
500O GLU* 1.3 63.7 + - - +
501O ILE* 5.5 2.0 - - + -
515O CYS* 4.2 24.0 - - - +
516O ALA* 4.7 9.4 - - + -
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Residues in contact with GLU 500 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455O GLY* 3.4 21.8 - - - -
456O LEU 3.8 13.9 - - - +
457O GLN* 4.1 11.2 - - + +
488O SER* 3.8 0.2 - - - -
489O TYR* 2.7 55.7 + - + +
491O LYS* 4.0 28.8 + - - +
499O LEU* 1.3 79.2 - - - +
501O ILE* 1.3 69.2 + - - +
502O PRO* 5.3 0.5 - - - +
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Residues in contact with ILE 501 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455O GLY* 3.5 4.3 - - - -
456O LEU* 2.9 45.0 + - + +
458O ILE* 4.7 7.4 - - + +
486O THR* 4.8 7.9 - - + +
487O THR 3.1 20.2 - - - +
488O SER* 3.5 15.0 - - - +
499O LEU* 5.5 2.0 - - + -
500O GLU* 1.3 79.3 - - - +
502O PRO* 1.3 75.2 - - + +
511O ALA* 3.9 23.1 - - + -
512O THR 4.7 6.5 - - - +
513O ILE* 3.6 28.5 - - + -
515O CYS* 3.8 14.8 - - - -
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Residues in contact with PRO 502 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453O PRO* 5.7 2.5 - - + -
454O LEU 3.7 4.0 - - - +
455O GLY* 4.6 1.8 - - - -
486O THR* 5.6 5.4 - - + +
487O THR* 3.5 39.7 - - + +
488O SER* 4.7 0.4 - - - +
489O TYR* 5.8 2.7 - - + -
500O GLU* 4.8 0.9 - - - +
501O ILE* 1.3 101.4 - - + +
503O LEU* 1.3 60.0 + - - +
504O GLU* 3.5 33.0 + - + +
510O ARG 4.7 0.5 - - - +
511O ALA* 4.5 5.7 - - - +
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Residues in contact with LEU 503 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410O LEU* 5.1 2.9 - - + -
443O VAL* 5.6 0.2 - - + -
444O GLN* 4.9 2.9 - - - -
445O LEU* 4.2 21.8 - - + +
453O PRO* 4.5 0.4 - - - -
454O LEU 2.4 39.3 + - - +
456O LEU* 3.9 35.7 - - + -
501O ILE 4.0 0.4 + - - -
502O PRO* 1.3 69.2 - - - +
504O GLU* 1.3 60.9 + - - +
509O MET* 3.0 48.9 - - + +
510O ARG 3.0 31.9 - - - +
511O ALA* 4.2 2.9 - - + -
548O VAL* 4.1 22.2 - - + -
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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