Contacts of the strand formed by residues 461 - 465 (chain A) in PDB entry 2ODP
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 HIS 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A GLN* 3.2 28.0 + - - +
458A THR* 3.1 23.7 + - - +
459A PRO 3.2 1.3 - - - +
460A TRP* 1.3 88.2 - + + +
462A VAL* 1.3 68.7 + - - +
463A THR* 4.9 2.8 + - - -
473A ARG* 3.6 43.9 - - + +
474A GLY 3.9 10.8 - - - -
501A ASN 4.5 0.3 - - - +
503A GLY 4.3 4.7 + - - -
598A VAL* 3.3 46.0 + - + +
599A ALA 4.5 3.1 - - - -
600A LEU 6.0 0.2 - - - -
602A GLY* 5.4 3.6 - - - -
661A GLY* 5.0 6.7 - - - -
662A ALA 5.3 2.2 - - - -
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Residues in contact with VAL 462 (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 TRP 3.7 9.6 - - - +
461A HIS* 1.3 82.5 - - - +
463A THR* 1.3 62.1 + - - +
464A ILE* 4.4 3.6 - - + -
473A ARG* 3.4 10.8 - - - +
474A GLY* 3.1 53.2 + - - +
476A LEU* 3.9 17.5 - - + +
482A VAL* 3.7 18.4 - - + -
500A VAL* 3.7 14.6 - - + -
501A ASN 3.3 10.8 - - - +
502A VAL* 3.8 26.2 - - + -
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Residues in contact with THR 463 (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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461A HIS* 4.9 3.1 + - - -
462A VAL* 1.3 74.2 - - - +
464A ILE* 1.3 64.5 + - - +
465A LYS* 3.8 23.5 - - - +
471A THR* 4.1 10.8 - - - +
472A CYS 3.7 3.4 - - - +
473A ARG* 3.5 39.3 + - - +
500A VAL* 3.5 3.8 - - - +
501A ASN* 2.8 41.1 + - - -
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Residues in contact with ILE 464 (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 VAL* 4.4 8.3 - - + -
463A THR* 1.3 76.6 - - - +
465A LYS* 1.3 65.0 + - - +
466A PRO* 3.5 14.0 - - + +
471A THR* 3.5 6.9 + - - -
472A CYS* 2.8 38.9 + - + +
473A ARG 3.6 14.6 - - - +
474A GLY* 4.1 4.3 - - - +
482A VAL* 4.3 3.6 - - + -
484A THR* 3.4 37.7 - - + +
488A CYS* 5.7 0.2 - - + -
489A PHE* 4.0 24.7 - - + -
498A TRP* 5.6 3.1 - - + -
499A ARG 3.7 7.0 - - - +
500A VAL* 4.5 6.1 - - + -
545A LEU* 3.8 22.0 - - + -
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Residues in contact with LYS 465 (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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463A THR* 3.8 22.8 - - - +
464A ILE* 1.3 74.0 - - - +
466A PRO* 1.3 64.5 - - - +
471A THR* 4.8 8.1 - - - +
498A TRP* 3.3 4.2 - - - +
499A ARG* 2.8 59.9 + - + +
501A ASN* 3.5 29.6 - - - +
512A GLU* 3.6 17.4 + - - +
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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