Contacts of the helix formed by residues 477 - 488 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A MET* 3.9 11.2 - - + -
448A GLY* 3.7 25.5 + - - -
452A MET* 4.8 10.5 - - + +
476A GLN* 1.3 69.9 - - - +
478A GLY* 1.3 58.8 + - - +
479A TRP 3.3 2.5 - - - -
480A ILE* 3.1 12.4 + - + -
481A LYS* 2.8 27.4 + - - +
494A GLY 3.1 26.5 - - - -
495A VAL* 2.9 12.1 + - + +
497A PHE* 3.4 25.7 - + - -
1611A TDM 3.3 45.5 - - + -
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Residues in contact with GLY 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ASP* 4.1 9.0 - - - -
474A ASN* 4.2 0.7 - - - -
476A GLN* 3.3 22.3 - - - -
477A TYR* 1.3 72.8 - - - +
479A TRP* 1.3 62.6 + - - +
481A LYS* 3.2 3.2 + - - +
482A ASP* 2.9 36.9 + - - -
1611A TDM 2.8 21.5 + - - -
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Residues in contact with TRP 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ARG* 2.9 70.8 + - + +
265A VAL* 3.4 30.1 - - + -
395A GLY* 3.6 17.3 - - - -
396A ASP* 3.3 29.0 + - - -
399A LEU* 3.7 32.1 - - + -
478A GLY* 1.3 77.3 - - - +
480A ILE* 1.3 59.9 + - + +
482A ASP* 4.6 0.2 - - - -
483A GLU* 3.4 31.1 + - - +
1611A TDM 3.0 64.5 + - + +
1612A FAD 4.1 16.5 - + + -
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Residues in contact with ILE 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477A TYR* 3.1 9.6 + - + +
479A TRP* 1.3 74.0 - - + +
481A LYS* 1.3 66.6 + - - +
482A ASP 3.2 1.1 - - - -
483A GLU* 3.2 28.6 + - - +
484A GLN* 2.9 32.3 + - + +
495A VAL* 3.8 17.9 - - + -
1512A PO4 3.3 22.0 - - - +
1611A TDM 3.4 46.0 - - + +
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Residues in contact with LYS 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A GLN* 3.6 30.7 + - + +
477A TYR 2.8 17.8 + - - +
478A GLY* 3.4 9.6 - - - +
480A ILE* 1.3 71.4 - - - +
482A ASP* 1.3 66.6 + - - +
484A GLN* 3.2 2.6 + - - -
485A GLU* 2.9 30.0 + - - +
492A PHE* 3.3 41.3 - - + -
495A VAL* 3.7 23.1 - - + +
496A GLU* 3.7 32.1 - - + -
546A GLY 5.0 7.7 + - - -
573A ARG* 5.5 3.0 - - - +
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Residues in contact with ASP 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ARG* 3.8 15.8 + - - +
396A ASP* 4.1 6.6 - - - +
476A GLN* 5.9 0.2 + - - -
478A GLY* 2.9 25.9 + - - +
481A LYS* 1.3 86.2 + - - +
483A GLU* 1.3 62.2 + - - +
485A GLU* 3.4 7.4 + - - +
486A ASP* 3.2 29.9 + - - +
548A ARG* 3.4 56.2 + - - +
549A PRO* 4.0 11.1 - - - +
573A ARG* 4.9 0.2 + - - -
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Residues in contact with GLU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ARG* 3.0 28.1 + - - +
479A TRP* 3.4 25.3 + - - +
480A ILE* 3.2 30.7 + - + +
482A ASP* 1.3 75.3 - - - +
484A GLN* 1.3 61.4 + - + +
486A ASP* 3.0 12.0 + - - +
487A THR* 2.9 35.0 + - + +
1512A PO4 4.2 14.8 + - - -
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Residues in contact with GLN 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A ILE* 2.9 24.0 + - + +
481A LYS 3.2 8.0 + - - +
483A GLU* 1.3 75.0 - - + +
485A GLU* 1.3 60.1 + - - +
488A ASN* 2.8 65.9 + - + +
492A PHE* 3.3 17.4 - - + -
493A ILE* 3.1 51.8 + - - +
495A VAL* 3.7 16.7 - - - +
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Residues in contact with GLU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A LYS* 2.9 16.0 + - - +
482A ASP* 3.4 13.5 - - - +
483A GLU 3.2 0.2 - - - -
484A GLN* 1.3 76.8 - - - +
486A ASP* 1.3 61.9 + - - +
488A ASN 4.8 4.0 - - - +
492A PHE* 3.7 21.7 - - + -
548A ARG* 3.6 17.0 + - - +
554A LYS* 5.0 3.6 + - - -
573A ARG* 2.6 46.9 + - - -
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Residues in contact with ASP 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ARG* 5.9 1.0 - - - -
482A ASP 3.2 10.0 + - - +
483A GLU* 3.0 11.9 + - - +
485A GLU* 1.3 81.9 - - - +
487A THR* 1.3 67.3 + - + +
548A ARG* 2.9 32.3 + - - -
553A GLU* 4.8 3.5 - - - +
554A LYS* 2.8 36.1 + - + +
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Residues in contact with THR 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A GLU* 2.9 21.3 + - + +
484A GLN* 4.2 0.2 - - - -
486A ASP* 1.3 85.6 - - + +
488A ASN* 1.3 88.3 + - - +
489A GLN* 3.7 15.9 + - - +
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Residues in contact with ASN 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A GLN* 2.8 60.2 + - + +
485A GLU 4.8 4.0 - - - +
487A THR* 1.3 97.4 + - - +
489A GLN* 1.3 64.5 + - - +
490A ASN 4.1 15.4 - - - +
491A ASP 5.5 2.2 + - - -
493A ILE* 5.1 6.5 - - - +
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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