Contacts of the strand formed by residues 494 - 498 (chain A) in PDB entry 2ADC
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 ALA 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457A HIS* 3.7 5.5 - - - -
458A LEU* 2.9 40.8 + - + +
461A ILE* 3.8 14.6 - - + +
470A LEU* 5.0 1.1 - - + -
484A PHE* 3.8 24.0 - - + -
485A LYS 3.6 11.7 - - - +
486A PHE* 4.1 7.4 - - + -
487A PHE* 4.1 11.2 - - - +
493A MET* 1.3 75.9 - - - +
495A LEU* 1.3 59.2 + - - +
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Residues in contact with LEU 495 (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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456A LEU 3.6 1.6 - - - +
457A HIS* 3.5 30.1 - - + -
484A PHE* 3.3 4.2 - - - -
485A LYS* 2.8 56.8 + - + +
487A PHE* 3.7 18.9 - - + -
494A ALA* 1.3 72.3 - - - +
496A ILE* 1.3 61.4 + - - +
527A SER* 3.8 12.6 - - - +
529A SER* 4.0 13.2 - - - +
530A THR 3.9 14.6 - - - +
531A ILE* 3.4 32.5 - - + -
536B C 3.7 12.8 - - - +
537B U 4.1 4.3 - - - +
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Residues in contact with ILE 496 (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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455A THR* 3.5 5.7 - - - +
456A LEU* 2.8 41.2 + - + +
458A LEU* 3.7 25.8 - - + -
470A LEU* 4.7 6.1 - - + +
471A LYS* 5.8 0.2 - - - -
474A PHE* 4.0 41.5 - - + -
481A VAL* 4.9 5.8 - - + -
483A GLY 3.4 9.2 - - - +
484A PHE* 3.4 46.0 - - + +
494A ALA* 4.4 0.4 + - + -
495A LEU* 1.3 77.9 - - - +
497A GLN* 1.3 68.7 + - - +
498A MET* 4.6 2.7 - - - -
531A ILE* 3.8 2.6 - - - +
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Residues in contact with GLN 497 (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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454A ALA* 3.5 17.5 - - + +
455A THR* 2.9 26.4 + - - +
456A LEU* 4.4 0.9 - - - -
481A VAL* 3.5 5.4 - - - +
482A LYS* 2.8 66.2 + - + +
483A GLY* 2.8 19.7 + - - +
496A ILE* 1.3 76.0 - - - +
498A MET* 1.3 67.9 + - - +
530A THR* 5.0 9.9 - - - +
531A ILE* 3.8 19.3 - - + +
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Residues in contact with MET 498 (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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454A ALA* 2.9 23.0 + - - +
456A LEU* 3.9 17.3 - - + -
474A PHE* 3.6 43.7 - - + +
477A ASN* 5.0 3.1 - - + -
479A GLY* 3.6 19.5 - - - +
480A VAL 3.2 20.2 - - - +
481A VAL* 3.8 15.9 - - + +
482A LYS* 3.5 14.1 - - - +
496A ILE* 4.6 2.5 - - - -
497A GLN* 1.3 84.5 - - - +
499A GLY* 1.3 63.1 + - - +
500A SER 3.3 16.8 + - - +
503A GLU* 3.8 16.4 - - + +
504A ALA* 4.1 10.8 - - - +
507A ALA* 5.5 0.2 - - + -
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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