Contacts of the helix formed by residues 492 - 500 (chain B) in PDB entry 5DO7
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 492 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402B LEU* 4.0 3.1 - - + -
405B ARG* 5.6 3.4 - - - -
474B GLU* 3.5 11.4 + - - +
477B MET* 3.0 45.5 - - + +
480B TYR* 5.5 3.6 - + - -
486B LEU* 3.2 31.9 - - + -
487B TYR 4.0 14.1 - - - +
488B THR* 4.7 4.7 - - + -
491B PRO* 1.3 78.9 - - + +
493B PHE* 1.3 65.6 + - - +
494B PHE 2.9 1.1 - - - -
495B ALA* 2.5 30.9 + - + +
496B LYS* 2.8 44.5 + - + +
658B TYR* 4.1 4.2 - - - -
662B LEU* 4.0 14.4 - - + -
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Residues in contact with PHE 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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488B THR* 4.2 16.2 - - + +
492B TYR* 1.3 79.1 - - - +
494B PHE* 1.3 88.2 + + + +
497B ILE* 3.2 39.9 + - + +
655B MET* 2.8 55.2 - - + -
656B VAL* 5.1 0.2 - - - -
658B TYR* 3.3 26.0 - + + -
659B TYR* 2.9 50.7 - + + -
662B LEU* 4.1 8.5 - - + -
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Residues in contact with PHE 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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399B PHE* 3.2 30.6 - + + -
489B THR 5.2 4.0 - - - -
490B GLY* 4.4 25.1 - - - +
491B PRO* 4.8 0.7 - - + +
492B TYR* 2.9 1.4 - - - +
493B PHE* 1.3 105.8 - + + +
495B ALA* 1.3 66.6 + - - +
496B LYS 3.4 0.6 + - - -
497B ILE* 4.8 0.9 - - + -
498B LEU* 3.4 38.6 + - + +
659B TYR* 5.8 2.0 - + - -
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Residues in contact with ALA 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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399B PHE* 3.4 11.2 - - - -
402B LEU* 3.8 24.7 - - + -
403B ILE* 3.4 13.7 - - + +
406B GLN* 4.5 6.2 - - + +
491B PRO 3.5 6.3 - - - +
492B TYR* 2.5 45.2 + - + +
494B PHE* 1.3 76.2 - - - +
496B LYS* 1.3 62.4 + - - +
499B GLY* 3.1 15.4 + - - -
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Residues in contact with LYS 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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406B GLN* 4.9 17.9 - - - +
467B VAL* 5.3 0.2 - - + -
470B LYS* 5.8 1.1 - - + -
471B CYS* 4.4 10.4 - - - +
474B GLU* 3.3 26.4 + - - -
477B MET* 4.1 6.1 - - - +
492B TYR* 2.8 42.3 + - + +
495B ALA* 1.3 71.3 - - - +
497B ILE* 1.3 59.3 + - - +
498B LEU 3.0 2.9 - - - -
499B GLY* 2.6 23.3 + - - +
500B GLU* 3.2 40.9 + - - +
547B LEU* 3.9 25.4 - - + -
658B TYR* 2.9 29.8 + - + +
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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 PHE* 3.2 52.6 + - + +
494B PHE* 3.8 1.4 + - - -
495B ALA 3.6 0.6 - - - -
496B LYS* 1.3 76.0 - - - +
498B LEU* 1.3 72.1 + - + +
500B GLU* 4.5 4.9 + - - +
501B LEU* 3.9 18.2 + - + +
540B PHE* 3.8 30.3 - - + -
544B ILE* 4.7 9.4 - - + -
547B LEU* 4.2 22.0 - - + -
655B MET* 4.0 18.8 - - + -
658B TYR* 4.1 8.1 - - + -
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Residues in contact with LEU 498 (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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399B PHE* 3.7 27.4 - - + -
403B ILE* 4.6 7.6 - - + -
407B ILE* 4.8 2.4 - - - +
494B PHE* 3.4 30.7 + - + +
495B ALA 4.4 0.7 - - - +
496B LYS 3.0 0.6 - - - -
497B ILE* 1.3 93.9 - - + +
499B GLY* 1.3 54.9 + - - +
500B GLU 3.3 0.4 - - - -
501B LEU* 2.8 40.0 + - + +
502B PRO* 3.5 5.2 - - - +
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Residues in contact with GLY 499 (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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403B ILE* 4.7 3.7 - - - +
406B GLN* 4.1 27.0 + - - -
407B ILE* 3.7 24.4 - - - +
410B ASP* 4.8 2.9 - - - +
411B PHE* 5.8 1.6 - - - -
495B ALA 3.1 15.0 + - - -
496B LYS 2.6 12.7 + - - -
498B LEU* 1.3 71.1 - - - +
500B GLU* 1.3 59.3 + - - +
502B PRO* 3.7 8.1 - - - +
503B GLU* 5.3 0.3 + - - +
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Residues in contact with GLU 500 (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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406B GLN* 4.6 4.1 + - - +
410B ASP* 5.0 5.8 - - - +
467B VAL* 3.8 25.3 - - - +
470B LYS* 3.8 24.9 - - - +
496B LYS* 3.2 41.4 + - - +
497B ILE* 4.8 4.9 - - - +
499B GLY* 1.3 75.0 - - - +
501B LEU* 1.3 68.0 + - - +
503B GLU* 2.8 24.0 + - - +
504B HIS* 3.1 6.9 + - + -
543B ARG* 3.5 37.0 - - - +
547B LEU* 4.2 9.9 - - - +
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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