Contacts of the helix formed by residues 492 - 497 (chain B) in PDB entry 2PDA
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 PRO 492 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489B CYS* 4.9 0.2 - - - -
490B HIS 4.1 0.2 - - - +
491B ASN* 1.3 90.2 - - - +
493B ALA* 1.3 56.8 + - - +
494B TYR 2.9 0.7 + - - -
495B VAL* 2.7 35.0 + - - +
512B LEU* 4.2 8.1 - - + -
513B ASN* 3.2 38.5 - - - +
514B SER* 4.1 15.5 - - - -
515B PRO* 4.9 6.5 - - + -
516B TRP* 4.0 16.2 - - + -
547B VAL* 6.2 2.5 - - + -
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Residues in contact with ALA 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B ASN* 3.0 21.3 - - - +
492B PRO* 1.3 78.1 - - - +
494B TYR* 1.3 66.6 + - + +
495B VAL* 3.6 1.3 + - - -
496B GLY* 3.9 5.5 + - - -
497B ILE* 3.3 23.4 + - + +
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Residues in contact with TYR 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B TRP* 3.9 28.0 - + + -
424B GLY 2.9 40.0 + - - -
425B LEU* 3.4 20.1 - - + +
463B ILE* 3.6 25.1 - - + +
489B CYS* 3.7 4.7 - - - -
491B ASN* 3.0 35.8 + - + +
492B PRO 2.9 0.4 + - - -
493B ALA* 1.3 82.8 - - + +
495B VAL* 1.3 66.7 + - - +
497B ILE* 2.9 10.4 + - + -
498B TYR* 2.9 47.6 + + + +
500B ILE* 3.5 18.8 - - + -
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Residues in contact with VAL 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B CYS* 4.5 3.3 - - - -
492B PRO* 2.7 27.5 + - + +
493B ALA 4.5 0.7 - - - -
494B TYR* 1.3 74.1 - - - +
496B GLY* 1.3 72.8 + - - +
498B TYR 3.7 7.6 - - - +
500B ILE* 4.0 13.8 - - - +
510B PHE* 6.2 2.0 - - + -
512B LEU* 5.0 9.6 - - + -
516B TRP* 3.5 23.3 - - + -
525B HIS 5.3 2.7 - - - +
526B LEU* 3.8 20.6 - - + -
527B PRO* 3.4 26.1 - - + +
530B ILE* 3.6 25.2 - - + +
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Residues in contact with GLY 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B ALA 3.9 3.7 + - - -
494B TYR 3.2 0.8 - - - -
495B VAL* 1.3 89.7 - - - +
497B ILE* 1.3 62.6 + - - +
498B TYR 4.7 0.9 - - - +
525B HIS 5.5 1.1 - - - -
527B PRO* 3.7 22.6 - - - +
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Residues in contact with ILE 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B ALA* 3.3 28.9 + - + +
494B TYR* 2.9 7.7 + - + +
496B GLY* 1.3 74.9 - - - +
498B TYR* 1.3 92.9 + - + +
648B THR* 4.7 16.5 - - + +
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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