Contacts of the strand formed by residues 474 - 478 (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 TYR 474 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422O ALA* 3.7 12.6 - - + -
460O ILE* 3.7 27.8 + - + +
471O HIS* 3.4 33.5 + + + +
472O ALA 4.7 0.2 - - - -
473O PHE* 1.3 93.8 - - + +
475O GLN* 1.3 73.6 + - - +
518O ILE* 3.4 19.3 - - + -
519O LEU 3.4 3.8 - - - -
520O LYS* 3.5 31.5 - - + +
521O LEU* 3.1 2.6 - - - +
539O ASN 4.2 2.0 - - - -
540O THR* 3.6 24.4 - - - +
542O VAL* 3.3 24.0 - - + -
569O CYS* 3.2 42.0 + - + +
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Residues in contact with GLN 475 (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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460O ILE* 4.2 4.7 - - - +
471O HIS 4.8 2.1 - - - +
472O ALA* 5.8 0.7 - - - -
474O TYR* 1.3 88.1 - - - +
476O VAL* 1.3 66.0 + - - +
492O ILE* 5.8 1.0 - - - +
495O ASN 3.4 17.9 + - - -
496O THR* 3.9 11.1 - - - +
497O LYS* 3.2 48.6 + - + +
518O ILE* 3.4 4.3 - - - +
519O LEU* 2.6 51.0 + - + +
521O LEU* 3.6 28.3 - - + +
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Residues in contact with VAL 476 (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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458O ILE* 3.7 17.5 - - + +
459O PHE* 3.5 12.1 - - - +
460O ILE* 3.3 40.6 - - + +
475O GLN* 1.3 76.0 - - - +
477O HIS* 1.3 59.4 + - - +
478O ARG 4.0 0.3 + - - -
497O LYS* 3.5 40.7 + - + +
499O LEU* 3.4 33.2 - - + +
516O ALA* 5.6 3.4 - - + -
517O GLY 3.3 7.2 - - - +
519O LEU* 5.3 0.9 - - - +
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Residues in contact with HIS 477 (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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423O HIS* 3.6 28.9 + + + -
428O GLY 5.0 2.8 + - - -
429O SER* 3.8 24.7 + - - -
476O VAL* 1.3 74.2 - - - +
478O ARG* 1.3 73.3 + - - +
479O ILE* 3.4 19.7 + - + +
490O GLU* 5.0 0.4 - - - -
497O LYS* 6.0 3.1 - - - -
499O LEU* 4.4 3.7 - - - +
516O ALA* 3.6 5.2 - - - -
517O GLY* 2.6 49.7 + - - -
518O ILE 4.1 0.2 - - - +
519O LEU* 4.6 12.1 - - + +
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Residues in contact with ARG 478 (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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476O VAL 4.0 0.6 + - - -
477O HIS* 1.3 83.1 + - - +
479O ILE* 1.3 62.1 + - - +
480O THR* 4.1 28.6 + - - +
488O SER* 3.1 45.5 + - - +
489O TYR* 4.4 0.9 - - - +
490O GLU* 3.0 52.3 + - - +
499O LEU* 3.6 17.9 - - + +
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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