Contacts of the helix formed by residues 565 - 572 (chain A) in PDB entry 2ODP
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 THR 565 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562A LEU* 2.7 30.8 + - + +
563A PRO 3.2 4.0 - - - +
564A CYS* 1.3 83.1 - - - +
566A MET* 1.3 64.2 + - - +
567A GLU* 3.7 12.2 + - - +
568A ALA 3.2 13.3 + - - -
569A ASN* 3.0 21.8 + - - +
583A HIS* 3.7 2.6 + - - -
727A LEU* 4.2 27.8 - - + -
728A ASN 3.3 13.0 - - - +
729A PHE* 4.2 13.7 - - + -
730A LEU* 3.9 4.7 - - - +
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Residues in contact with MET 566 (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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565A THR* 1.3 72.1 - - - +
567A GLU* 1.3 66.5 + - - +
569A ASN* 3.3 17.8 + - - +
570A LEU* 3.0 26.3 + - + +
576A GLN* 3.8 37.2 - - - +
728A ASN* 2.8 23.8 + - + +
729A PHE 5.7 0.9 - - - +
730A LEU* 3.7 24.8 - - + +
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Residues in contact with GLU 567 (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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268A GLU* 4.5 3.5 - - - +
443A CYS* 3.9 24.0 - - + +
565A THR* 3.2 9.9 - - - +
566A MET* 1.3 77.0 + - - +
568A ALA* 1.3 56.9 + - - +
570A LEU* 3.4 8.0 + - - +
571A ALA* 3.0 26.9 + - - +
670A ARG* 4.6 0.2 + - - -
727A LEU* 5.4 1.6 - - - +
728A ASN* 2.6 54.1 + - - +
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Residues in contact with ALA 568 (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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443A CYS* 4.5 1.4 - - - -
561A CYS* 4.3 5.8 - - + -
562A LEU 3.1 30.7 - - - +
563A PRO* 4.1 8.5 - - + -
565A THR* 3.2 8.1 + - - +
567A GLU* 1.3 75.6 - - - +
569A ASN* 1.3 66.0 + - - +
571A ALA* 3.2 2.2 + - - +
572A LEU* 2.8 29.7 + - + +
583A HIS* 4.1 7.2 - - + +
672A PHE* 4.0 21.8 - - + -
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Residues in contact with ASN 569 (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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565A THR 3.0 14.2 + - - +
566A MET* 3.3 27.7 + - - +
568A ALA* 1.3 75.5 - - - +
570A LEU* 1.3 58.9 + - - +
572A LEU* 3.4 1.9 + - - -
573A ARG 3.1 21.0 + - - -
574A ARG* 3.2 30.9 + - - +
575A PRO 3.0 19.0 - - - +
576A GLN* 4.0 7.4 + - - +
578A SER* 3.3 22.0 + - - -
583A HIS* 2.7 34.1 + - - +
730A LEU* 4.2 5.8 - - + -
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Residues in contact with LEU 570 (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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268A GLU* 3.7 33.5 - - + +
566A MET* 3.0 18.6 + - + +
567A GLU* 3.7 7.6 - - - +
568A ALA 3.2 0.2 - - - -
569A ASN* 1.3 74.9 - - - +
571A ALA* 1.3 64.7 + - - +
573A ARG* 2.9 24.4 + - + +
574A ARG 5.8 0.2 - - - -
576A GLN* 5.6 9.4 - - - +
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Residues in contact with ALA 571 (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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268A GLU* 3.9 1.0 + - - -
561A CYS* 4.4 2.2 - - - -
567A GLU 3.0 12.6 + - - +
568A ALA* 3.5 9.0 - - - +
570A LEU* 1.3 76.1 - - - +
572A LEU* 1.3 61.3 + - - +
573A ARG* 3.6 17.7 + - - -
668A ARG* 4.2 9.2 - - - +
670A ARG* 3.5 45.9 + - + +
672A PHE* 3.6 22.7 - - + -
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Residues in contact with LEU 572 (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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568A ALA* 2.8 24.9 + - + +
569A ASN 3.9 4.0 - - - +
571A ALA* 1.3 75.0 - - - +
573A ARG* 1.3 72.2 + - - +
574A ARG* 3.4 19.1 + - + +
583A HIS* 4.4 22.9 - - + +
586A GLU* 4.1 23.9 - - + +
587A LEU* 3.8 27.6 - - + -
667A ARG* 4.2 13.0 - - + +
668A ARG* 3.9 14.3 + - - +
672A PHE* 3.5 35.2 - - + -
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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