Contacts of the strand formed by residues 481 - 485 (chain A) in PDB entry 5ON2
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 MET 481 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A LEU* 4.5 7.4 - - + -
438A GLU* 4.3 15.5 - - + +
439A ASP* 3.3 49.4 - - - +
477A THR* 3.5 10.3 + - - -
478A VAL 3.3 35.2 + - - +
479A ASN* 4.0 9.4 - - + +
480A GLY* 1.3 79.6 - - - +
482A PRO* 1.4 78.6 - - + +
483A ALA* 4.3 0.2 - - - +
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Residues in contact with PRO 482 (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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438A GLU* 3.2 53.2 + - + +
476A THR 3.7 6.7 - - - +
477A THR* 4.9 1.1 - - - -
481A MET* 1.4 94.8 - - + +
483A ALA* 1.3 59.1 + - - +
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Residues in contact with ALA 483 (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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435A VAL* 3.5 25.1 - - + -
436A THR 3.6 5.8 - - - +
437A LEU* 3.6 19.5 - - + +
438A GLU 4.5 0.9 - - - +
475A LYS* 3.6 4.9 - - - +
476A THR* 2.9 41.5 + - + +
478A VAL 4.4 4.5 - - - +
481A MET 4.3 2.9 - - - +
482A PRO* 1.3 76.8 - - - +
484A LEU* 1.3 66.7 + - - +
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Residues in contact with LEU 484 (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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435A VAL* 4.5 1.1 - - - -
436A THR* 2.8 44.3 + - + +
471A PRO 4.9 3.4 - - - +
474A ALA* 3.5 23.1 - - + -
475A LYS* 4.1 19.5 - - + +
483A ALA* 1.3 78.1 - - - +
485A ARG* 1.3 64.9 + - - +
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Residues in contact with ARG 485 (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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432A ILE 5.7 0.9 - - - +
434A MET 3.4 10.8 - - - +
435A VAL* 4.1 14.8 - - + +
445A THR* 5.1 3.4 - - + +
449A GLN* 5.1 5.8 + - - +
452A VAL* 4.2 26.9 - - + +
453A ILE 5.3 1.8 + - - +
473A TRP* 3.0 71.8 + - + +
474A ALA* 3.0 28.7 + - - +
475A LYS 4.4 8.1 + - - -
476A THR* 4.4 18.1 + - + +
483A ALA 4.1 1.2 - - - -
484A LEU* 1.3 77.2 - - - +
486A GLU* 1.3 64.3 + - - +
487A THR* 3.4 5.5 + - - +
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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