Contacts of the helix formed by residues 477 - 488 (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 TYR 477 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422B MET* 3.9 10.5 - - + -
448B GLY* 3.7 22.8 + - - -
451B SER* 5.6 0.9 + - - -
452B MET* 4.9 9.0 - - + +
476B GLN* 1.3 69.5 - - - +
478B GLY* 1.3 60.6 + - - +
479B TRP 3.3 2.5 - - - -
480B ILE* 3.1 13.3 + - + -
481B LYS* 2.8 27.0 + - - +
494B GLY 3.1 27.4 - - - -
495B VAL* 2.8 13.2 + - + +
497B PHE* 3.4 26.4 - + - -
1614B TDM 3.3 46.4 - - + -
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Residues in contact with GLY 478 (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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396B ASP* 3.9 14.8 - - - -
474B ASN* 4.2 0.7 - - - -
476B GLN* 3.2 23.4 - - - -
477B TYR* 1.3 72.5 - - - +
479B TRP* 1.3 61.7 + - - +
481B LYS* 3.2 3.8 + - - +
482B ASP* 3.0 30.5 + - - -
1614B TDM 2.8 21.0 + - - -
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Residues in contact with TRP 479 (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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264B ARG* 2.9 74.7 + - + +
265B VAL* 3.5 27.4 - - + -
395B GLY* 3.6 18.2 - - - -
396B ASP* 3.2 28.3 + - - -
399B LEU* 3.6 32.3 - - + -
478B GLY* 1.3 74.0 - - - +
480B ILE* 1.3 64.0 + - + +
482B ASP 3.7 0.2 + - - -
483B GLU* 3.3 32.0 + - - +
1614B TDM 3.0 64.5 + - + +
1615B FAD 4.2 15.6 - + + +
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Residues in contact with ILE 480 (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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477B TYR* 3.1 9.7 + - + +
479B TRP* 1.3 76.0 - - + +
481B LYS* 1.3 59.3 + - - +
482B ASP 3.2 2.0 - - - -
483B GLU* 3.2 22.1 + - + +
484B GLN* 2.9 38.2 + - + +
495B VAL* 3.7 17.9 - - + -
1515B PO4 3.4 24.9 - - - +
1614B TDM 3.5 50.0 - - + +
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Residues in contact with LYS 481 (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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476B GLN* 3.7 30.1 + - + +
477B TYR 2.8 19.7 + - - +
478B GLY* 3.2 7.4 + - - +
480B ILE* 1.3 71.8 - - - +
482B ASP* 1.3 67.2 + - - +
484B GLN* 3.2 3.3 + - - +
485B GLU* 2.9 29.9 + - - +
492B PHE* 3.2 47.0 - - + -
495B VAL* 3.7 21.2 - - + +
496B GLU* 3.7 30.7 - - + -
546B GLY 4.8 9.3 + - - -
573B ARG* 5.5 3.4 - - - +
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Residues in contact with ASP 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ARG* 3.9 9.7 + - - +
396B ASP* 4.2 6.9 - - - +
478B GLY* 3.0 22.2 + - - +
479B TRP 3.8 5.2 - - - +
481B LYS* 1.3 85.5 + - - +
483B GLU* 1.3 65.1 + - - +
485B GLU* 3.4 11.5 + - - +
486B ASP* 3.1 28.9 + - - -
546B GLY 5.6 1.0 - - - +
548B ARG* 3.4 52.7 + - - +
549B PRO* 4.0 11.3 - - - +
573B ARG* 4.8 0.5 + - - -
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Residues in contact with GLU 483 (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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264B ARG* 2.9 33.0 + - - +
479B TRP* 3.3 21.9 + - - +
480B ILE* 3.2 30.2 + - + +
482B ASP* 1.3 78.6 - - - +
484B GLN* 1.3 56.6 + - + +
486B ASP* 3.2 10.3 + - - +
487B THR* 3.0 36.3 + - + +
1515B PO4 4.1 11.1 + - - -
1614B TDM 5.6 0.2 - - - +
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Residues in contact with GLN 484 (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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480B ILE* 2.9 22.7 + - + +
481B LYS 3.2 8.5 + - - +
483B GLU* 1.3 73.9 - - + +
485B GLU* 1.3 62.9 + - - +
488B ASN* 2.9 64.0 + - + +
491B ASP 5.3 0.7 - - - -
492B PHE* 3.4 16.3 - - + -
493B ILE* 3.0 52.6 + - - +
495B VAL* 3.6 19.1 - - - +
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Residues in contact with GLU 485 (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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481B LYS* 2.9 16.6 + - - +
482B ASP* 3.5 13.3 - - - +
483B GLU 3.3 0.2 - - - -
484B GLN* 1.3 75.9 - - - +
486B ASP* 1.3 62.4 + - - +
488B ASN 4.7 4.9 - - - +
492B PHE* 3.6 22.6 - - + -
548B ARG* 3.0 18.7 + - - +
554B LYS* 5.0 1.0 + - - -
573B ARG* 2.7 47.6 + - - -
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Residues in contact with ASP 486 (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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264B ARG* 6.1 0.2 - - - -
482B ASP 3.1 11.0 + - - +
483B GLU* 3.2 10.8 + - - +
485B GLU* 1.3 80.4 - - - +
487B THR* 1.3 64.9 + - + +
488B ASN 5.5 0.2 - - - -
489B GLN* 5.8 0.2 + - - -
548B ARG* 2.9 30.9 + - - -
553B GLU* 4.9 1.9 - - - +
554B LYS* 2.8 34.3 + - - -
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Residues in contact with THR 487 (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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483B GLU* 3.0 21.7 + - + +
486B ASP* 1.3 82.7 - - + +
488B ASN* 1.3 85.7 + - - +
489B GLN* 3.7 15.3 + - - +
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Residues in contact with ASN 488 (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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484B GLN* 2.9 58.6 + - + +
485B GLU 4.7 4.0 - - - +
487B THR* 1.3 100.4 + - - +
489B GLN* 1.3 66.5 + - - +
490B ASN* 3.4 15.0 - - + +
491B ASP 5.4 1.9 + - - +
493B ILE* 5.0 7.5 - - - +
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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