Contacts of the helix formed by residues 456 - 463 (chain B) in PDB entry 2EZT
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 ASP 456 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B VAL* 3.4 8.3 - - - +
57B ARG* 2.8 20.0 + - - -
58B HIS 3.3 12.1 + - - -
61B VAL* 3.2 32.3 - - + +
426B ILE* 3.8 9.4 - - + +
430B ILE* 3.7 8.0 - - - +
453B THR 3.0 11.6 + - - +
454B MET 2.9 0.4 + - - -
455B GLN* 1.3 101.3 + - - +
457B LEU* 1.3 59.8 + - - +
458B ALA 3.0 0.9 - - - -
459B THR* 2.5 43.4 + - - +
460B GLN* 3.5 4.5 + - - +
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Residues in contact with LEU 457 (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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426B ILE* 3.9 22.1 - - + +
443B ASN* 5.0 0.2 - - - +
454B MET* 3.0 22.6 + - - +
456B ASP* 1.3 76.9 - - - +
458B ALA* 1.3 61.2 + - - +
460B GLN* 3.3 8.7 + - - +
461B VAL* 3.3 17.0 + - - +
469B ASN* 3.6 36.3 - - + +
502B PHE* 4.6 7.2 - - + -
505B ILE* 4.2 21.1 - - + -
506B ALA* 4.9 4.3 - - + -
509B VAL* 3.8 18.4 - - + -
511B MET* 3.3 19.9 - - + +
539B LEU* 3.8 24.2 - - + -
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Residues in contact with ALA 458 (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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57B ARG* 4.0 29.6 + - - +
455B GLN 3.3 17.6 + - - +
456B ASP 3.0 0.2 - - - -
457B LEU* 1.3 80.0 - - - +
459B THR* 1.3 54.3 + - - +
461B VAL* 3.4 6.9 + - - +
462B GLN* 2.9 28.8 + - - +
509B VAL* 3.9 26.9 - - + +
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Residues in contact with THR 459 (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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54B ILE* 4.0 16.8 - - + -
55B GLN 4.0 6.9 + - - +
56B VAL* 4.0 6.4 - - + -
57B ARG* 3.9 12.3 + - - +
430B ILE* 4.1 20.0 - - + -
456B ASP* 2.5 38.8 + - - +
458B ALA* 1.3 74.5 - - - +
460B GLN* 1.3 64.4 + - - +
462B GLN* 4.4 4.9 - - - -
463B TYR* 3.1 44.8 + - + +
465B LEU* 4.5 1.0 - - - +
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Residues in contact with GLN 460 (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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426B ILE* 4.0 28.9 + - - +
430B ILE* 3.7 17.0 - - + +
456B ASP 3.5 3.1 + - - +
457B LEU* 3.3 15.6 + - - +
459B THR* 1.3 77.2 - - - +
461B VAL* 1.3 57.0 + - - +
464B HIS* 3.0 7.4 + - - -
465B LEU* 2.8 43.9 + - + +
467B VAL* 3.5 31.1 - - + +
469B ASN* 2.9 42.7 + - - -
511B MET* 3.5 5.9 - - - +
537B PRO* 3.6 9.7 - - + +
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Residues in contact with VAL 461 (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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457B LEU 3.3 14.2 + - - +
458B ALA 3.6 6.3 - - - +
460B GLN* 1.3 74.1 - - - +
462B GLN* 1.3 68.4 + - - +
464B HIS* 3.2 25.0 + - + -
509B VAL* 3.4 27.6 - - + +
510B HIS* 3.7 18.4 - - + +
511B MET* 3.8 29.6 - - + -
536B GLU* 4.8 2.1 - - - +
537B PRO* 4.1 10.1 - - + -
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Residues in contact with GLN 462 (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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55B GLN* 2.9 28.4 + - - +
57B ARG* 2.7 30.2 + - - +
458B ALA 2.9 16.4 + - - +
459B THR* 3.9 5.8 - - - +
460B GLN 3.5 0.2 - - - -
461B VAL* 1.3 78.1 - - - +
463B TYR* 1.3 90.0 + - + +
464B HIS* 3.3 16.6 + - - -
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Residues in contact with TYR 463 (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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53B TYR* 3.8 15.5 + - - -
54B ILE* 3.7 28.8 - - + -
55B GLN* 2.8 41.2 + - - +
434B LEU* 5.3 1.1 - - + -
459B THR* 3.1 34.0 + - + +
462B GLN* 1.3 108.5 + - + +
464B HIS* 1.3 72.5 + - - +
465B LEU* 3.3 28.3 - - + +
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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