Contacts of the helix formed by residues 447 - 453 (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 447 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446B GLY* 1.3 69.2 - - - -
448B GLY* 1.3 60.2 + - - -
450B ALA* 4.5 0.2 - - - -
451B SER* 3.0 29.6 + - - -
471B VAL* 3.7 11.2 - - + +
472B PHE 3.1 11.6 + - - +
473B THR* 3.6 24.4 - - + +
474B ASN* 3.2 3.8 + - - -
475B CYS* 2.8 32.4 + - - -
476B GLN 3.3 1.4 - - - +
497B PHE* 3.8 12.0 - - + -
500B ILE* 6.0 1.3 - - + +
502B PHE* 3.9 10.2 - - + -
1513B MG 2.1 32.5 - - - -
1614B TDM 2.8 4.2 + - - -
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Residues in contact with GLY 448 (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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422B MET* 3.4 7.9 - - - +
447B ASP* 1.3 76.0 + - - +
449B GLY* 1.3 57.4 + - - +
451B SER* 3.1 17.9 + - - -
452B MET* 3.5 17.7 + - - +
477B TYR* 3.7 23.5 + - - -
497B PHE* 4.4 5.2 - - - -
1614B TDM 2.8 23.0 + - - -
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Residues in contact with GLY 449 (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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393B ASP* 3.6 27.1 - - - -
422B MET* 3.4 9.8 - - - +
423B GLY* 3.6 21.2 - - - -
446B GLY 3.3 1.3 + - - -
448B GLY* 1.3 70.1 - - - +
450B ALA* 1.3 65.3 + - - +
451B SER 3.2 1.3 - - - -
452B MET* 3.1 10.9 + - - +
453B THR* 3.7 2.4 + - - -
1614B TDM 2.8 17.5 + - - -
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Residues in contact with ALA 450 (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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393B ASP* 4.9 0.9 - - - -
426B ILE* 3.9 14.8 - - + +
443B ASN* 5.7 0.9 - - - +
445B ALA* 4.0 17.2 - - + +
446B GLY 2.8 21.6 + - - +
447B ASP 4.2 0.2 - - - +
449B GLY* 1.3 71.4 - - - +
451B SER* 1.3 56.9 + - - +
453B THR* 3.4 3.0 + - - -
454B MET* 2.9 30.1 + - - +
471B VAL* 3.9 18.6 - - + -
502B PHE* 3.8 22.0 - - + -
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Residues in contact with SER 451 (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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447B ASP 3.0 22.4 + - - -
448B GLY* 3.1 12.5 + - - -
449B GLY 3.2 0.2 - - - -
450B ALA* 1.3 73.5 - - - +
452B MET* 1.3 66.4 + - - +
453B THR 3.3 0.5 + - - -
454B MET* 3.4 40.3 - - - +
455B GLN* 5.0 0.2 - - - +
477B TYR* 5.6 0.9 + - - -
500B ILE* 4.1 14.3 - - - +
502B PHE* 3.6 5.1 - - - -
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Residues in contact with MET 452 (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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60B GLU* 4.3 10.6 - - - +
422B MET* 3.7 38.8 - - + +
423B GLY* 4.5 7.9 - - - -
448B GLY 3.5 9.9 - - - +
449B GLY 3.1 9.6 + - - +
451B SER* 1.3 79.1 + - - +
453B THR* 1.3 60.4 - - + +
455B GLN* 4.3 0.2 + - - -
477B TYR* 4.9 11.0 - - + +
1511B NA 2.7 26.9 - - - -
1614B TDM 3.7 37.0 - - + +
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Residues in contact with THR 453 (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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60B GLU* 4.2 19.5 - - + -
61B VAL* 3.7 26.7 - - + -
64B MET* 4.4 2.2 - - - -
393B ASP* 4.8 0.5 + - - -
423B GLY* 2.8 41.4 + - - +
426B ILE* 3.4 23.3 + - - +
427B PRO* 4.5 2.0 - - - -
449B GLY 3.7 3.3 + - - -
450B ALA* 3.4 2.5 + - - -
451B SER 3.2 0.4 - - - -
452B MET* 1.3 82.8 - - + +
454B MET* 1.3 65.2 + - - +
455B GLN* 3.2 11.1 + - - +
456B ASP* 3.0 15.4 + - - +
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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