Contacts of the strand formed by residues 474 - 478 (chain L) 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 TYR 474 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422L ALA* 4.0 4.9 - - + -
460L ILE* 3.9 27.4 - - + +
471L HIS* 3.2 49.9 + + + +
472L ALA 3.4 0.8 - - - -
473L PHE* 1.3 84.4 - - + +
475L GLN* 1.3 73.1 + - - +
518L ILE* 3.9 13.2 - - + -
519L LEU 3.3 12.3 - - - -
520L LYS* 3.3 36.4 - - + +
539L ASN 3.8 11.0 - - - -
540L THR* 3.7 22.3 - - - +
542L VAL* 3.3 19.3 - - + -
569L CYS* 3.4 33.0 + - + +
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Residues in contact with GLN 475 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460L ILE* 3.7 8.0 + - - +
471L HIS 4.5 2.9 - - - +
472L ALA 5.6 0.2 - - - -
474L TYR* 1.3 88.7 - - - +
476L VAL* 1.3 66.0 + - - +
495L ASN 2.6 28.8 + - - -
496L THR* 3.7 11.4 + - - +
497L LYS* 3.4 38.3 + - + +
518L ILE* 3.4 4.5 - - - -
519L LEU* 2.8 41.3 + - + -
521L LEU* 3.4 33.2 - - + +
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Residues in contact with VAL 476 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458L ILE* 3.9 11.2 - - + +
459L PHE* 3.2 42.4 - - - +
460L ILE* 3.6 11.7 - - + +
475L GLN* 1.3 84.2 - - - +
477L HIS* 1.3 63.6 + - - +
497L LYS* 3.2 43.0 + - + +
499L LEU* 3.9 28.9 - - + +
516L ALA* 5.4 2.5 - - + -
517L GLY 3.1 7.4 - - - +
519L LEU* 4.8 1.2 - - - +
544L LEU* 5.2 1.1 - - + -
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Residues in contact with HIS 477 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423L HIS* 3.5 33.3 + + + -
428L GLY 4.5 4.7 + - - -
429L SER* 4.1 20.0 + - - -
476L VAL* 1.3 75.4 - - - +
478L ARG* 1.3 75.7 + - - +
479L ILE* 3.4 7.0 + - + +
490L GLU* 5.3 0.4 - - - -
497L LYS* 5.5 8.1 - - - -
499L LEU* 4.9 1.3 - - - -
515L CYS 3.1 7.3 - - - +
516L ALA* 3.3 1.5 - - - -
517L GLY* 2.4 59.7 + - - +
518L ILE 4.0 0.4 - - - +
519L LEU* 4.1 20.7 - - + +
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Residues in contact with ARG 478 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476L VAL 4.2 0.6 - - - -
477L HIS* 1.3 86.5 + - - +
479L ILE* 1.3 63.2 + - - +
480L THR* 3.4 36.7 + - - +
487L THR* 4.7 3.0 + - - +
488L SER* 2.6 57.8 + - - +
489L TYR* 4.2 0.8 - - - +
490L GLU* 3.2 43.0 + - - +
499L LEU* 3.5 16.6 - - + +
515L CYS 3.4 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