Contacts of the helix formed by residues 563 - 574 (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 SER 563 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562B SER* 1.3 77.8 - - - +
564B ALA* 1.3 65.9 + - - +
565B ALA* 3.9 9.4 + - - +
566B ASP* 3.1 34.1 + - - +
567B ILE* 3.0 21.6 + - - +
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Residues in contact with ALA 564 (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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562B SER 3.9 1.2 + - - -
563B SER* 1.3 73.3 - - - +
565B ALA* 1.3 57.1 + - - +
567B ILE* 3.8 10.1 - - - +
568B GLU* 2.9 37.9 + - + +
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Residues in contact with ALA 565 (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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563B SER* 3.1 9.9 - - - +
564B ALA* 1.3 75.6 - - - +
566B ASP* 1.3 67.4 + - - +
568B GLU* 3.5 3.7 + - - +
569B ALA* 3.1 25.6 + - - +
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Residues in contact with ASP 566 (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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556B ARG* 3.8 29.4 + - + +
562B SER* 4.5 1.5 - - - -
563B SER* 3.1 27.5 + - - +
565B ALA* 1.3 80.6 - - - +
567B ILE* 1.3 56.4 + - - +
569B ALA* 3.4 6.8 + - - +
570B PHE* 2.9 30.5 + - - +
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Residues in contact with ILE 567 (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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556B ARG 3.4 28.3 - - - +
557B LEU* 3.8 10.1 - - - +
558B ASP 3.8 7.0 - - - -
559B SER* 3.7 33.9 - - - +
562B SER* 3.8 13.9 - - - +
563B SER 3.0 18.0 + - - +
564B ALA* 3.8 8.1 - - - +
566B ASP* 1.3 75.3 - - - +
568B GLU* 1.3 66.6 + - - +
570B PHE* 3.4 1.7 + - - +
571B LYS* 2.9 57.7 + - - +
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Residues in contact with GLU 568 (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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564B ALA* 2.9 26.4 + - + +
565B ALA* 4.3 3.8 - - - +
566B ASP 3.4 0.2 - - - -
567B ILE* 1.3 81.0 - - - +
569B ALA* 1.3 56.9 + - - +
571B LYS* 3.9 26.1 + - - +
572B GLN* 3.0 30.7 + - - +
577B GLN* 6.0 1.4 - - - +
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Residues in contact with ALA 569 (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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565B ALA 3.1 18.6 + - - +
566B ASP* 3.6 7.6 - - - +
567B ILE 3.2 0.2 - - - -
568B GLU* 1.3 76.8 - - - +
570B PHE* 1.3 57.4 + - - +
572B GLN* 3.4 7.2 + - - +
573B ARG* 2.9 30.5 + - - +
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Residues in contact with PHE 570 (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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550B LEU* 3.7 36.1 - - + -
551B PRO* 4.0 8.5 - - + -
554B LYS 3.2 24.2 - - - -
555B LEU* 3.9 11.7 - - + -
556B ARG* 3.4 41.7 - - + +
557B LEU* 3.9 26.5 - - + -
566B ASP 2.9 18.0 + - - +
567B ILE 3.5 0.2 - - - +
569B ALA* 1.3 72.7 - - - +
571B LYS* 1.3 68.3 + - - +
573B ARG* 3.2 1.1 + - - -
574B TYR* 3.0 55.8 + + - +
576B ALA* 4.3 3.4 - - + -
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Residues in contact with LYS 571 (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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557B LEU* 3.7 28.9 - - + +
567B ILE* 2.9 33.9 + - - +
568B GLU* 3.9 28.5 + - - +
570B PHE* 1.3 71.7 - - - +
572B GLN* 1.3 64.1 + - - +
575B GLU* 3.1 4.5 + - - -
576B ALA* 2.9 39.3 + - - +
577B GLN* 3.2 48.7 + - + +
579B LEU 4.1 7.8 + - - -
580B GLN* 5.3 5.5 + - - +
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Residues in contact with GLN 572 (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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568B GLU 3.0 19.1 + - - +
569B ALA* 3.4 7.4 - - - +
571B LYS* 1.3 79.8 - - - +
573B ARG* 1.3 65.1 + - - +
574B TYR 3.3 0.2 + - - -
575B GLU* 3.5 9.7 + - - +
577B GLN* 4.0 17.7 + - - +
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Residues in contact with ARG 573 (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* 5.5 3.8 - - - +
482B ASP* 4.8 1.4 + - - -
485B GLU* 2.7 44.6 + - - -
547B ASP* 6.0 2.8 - - - +
548B ARG* 3.7 27.4 - - - +
569B ALA 2.9 17.7 + - - +
570B PHE* 3.2 0.4 + - - -
572B GLN* 1.3 78.9 - - - +
574B TYR* 1.3 103.6 + - + +
575B GLU* 3.4 7.7 + - - +
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Residues in contact with TYR 574 (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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359B TYR* 2.5 35.9 + - - +
363B LEU* 4.8 0.2 - - - +
548B ARG* 3.2 48.2 + - + -
549B PRO 3.8 3.1 - - - -
550B LEU* 3.6 25.1 - - + +
551B PRO* 3.4 27.7 - - + +
554B LYS* 5.1 2.4 + - - -
570B PHE* 3.0 51.2 + + - +
573B ARG* 1.3 119.9 + - + +
575B GLU* 1.3 71.0 + - - +
576B ALA* 3.1 3.4 - - + -
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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