Contacts of the helix formed by residues 596 - 604 (chain A) in PDB entry 2O1S
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 596 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425A GLY* 4.9 0.2 - - - -
595A GLY* 1.3 74.9 - - - -
597A GLN* 1.3 57.6 + - - +
598A GLU* 3.0 15.9 - - + +
599A GLU* 2.9 45.3 + - + +
600A MSE 2.7 32.1 + - - +
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Residues in contact with GLN 597 (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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423A ILE* 3.5 39.2 - - + +
424A VAL 3.7 15.3 - - - +
425A GLY* 4.1 1.5 - - - -
478A ARG* 2.9 51.9 + - - +
479A GLY* 4.8 4.8 - - - -
595A GLY 3.7 1.0 + - - -
596A THR* 1.3 74.4 - - - +
598A GLU* 1.3 57.7 + - - +
600A MSE 3.4 1.2 + - - +
601A ARG* 2.9 58.8 + - - +
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Residues in contact with GLU 598 (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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596A THR* 3.0 11.3 - - + +
597A GLN* 1.3 78.7 - - - +
599A GLU* 1.3 59.6 + - - +
601A ARG* 3.3 10.6 + - - +
602A ALA* 3.0 32.1 + - + +
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Residues in contact with GLU 599 (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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101A LYS* 3.6 45.0 + - + +
595A GLY* 3.8 0.7 - - - -
596A THR* 2.9 42.8 + - + +
598A GLU* 1.3 79.0 - - - +
600A MSE 1.3 59.5 + - + +
602A ALA* 4.0 4.9 - - - +
603A GLU* 3.3 21.1 + - - +
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Residues in contact with MSE 600 (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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101A LYS* 3.8 21.5 - - + -
423A ILE* 4.1 14.8 - - + -
592A ILE* 3.8 18.8 - - + -
593A PRO* 3.5 28.3 - - - +
594A GLN 2.9 28.3 - - - +
595A GLY* 3.2 19.7 - - - -
596A THR 2.7 18.2 + - - +
597A GLN 4.0 2.5 - - - +
599A GLU* 1.3 72.9 - - - +
601A ARG* 1.3 65.6 + - - +
602A ALA 3.2 0.2 - - - -
603A GLU* 3.4 27.4 + - - +
604A LEU* 3.1 36.2 + - + +
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Residues in contact with ARG 601 (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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423A ILE* 3.7 18.8 + - + +
477A PRO* 4.2 18.0 - - - +
478A ARG 4.8 1.2 + - - -
513A THR* 5.3 0.4 + - - -
514A LEU* 4.5 10.4 - - + +
558A GLU* 2.9 42.0 + - - +
597A GLN* 2.9 53.8 + - - +
598A GLU* 3.8 7.3 - - - +
600A MSE 1.3 73.9 - - - +
602A ALA* 1.3 61.8 + - - +
604A LEU* 3.4 1.1 + - - -
605A GLY 3.2 3.3 + - - -
606A LEU* 2.7 61.9 + - + +
607A ASP* 5.1 2.0 - - + -
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Residues in contact with ALA 602 (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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598A GLU* 3.0 19.5 + - + +
599A GLU* 4.0 6.3 - - - +
601A ARG* 1.3 78.0 - - - +
603A GLU* 1.3 62.6 + - - +
605A GLY* 3.0 14.9 + - - -
607A ASP* 3.4 27.6 - - + +
610A GLY* 5.7 0.3 - - - -
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Residues in contact with GLU 603 (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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101A LYS* 2.5 40.4 + - - +
593A PRO* 5.5 5.9 - - - +
599A GLU 3.3 16.6 + - - +
600A MSE 3.6 20.2 - - - +
601A ARG 3.3 0.4 - - - -
602A ALA* 1.3 81.0 - - - +
604A LEU* 1.3 64.5 + - + +
605A GLY 3.3 0.8 + - - -
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Residues in contact with LEU 604 (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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423A ILE* 4.8 3.8 - - + -
586A GLY 5.2 1.1 - - - +
587A LEU* 4.0 24.5 - - + -
588A PRO* 3.9 27.2 - - + +
590A PHE* 4.1 20.4 - - + -
592A ILE* 4.0 28.3 - - + -
593A PRO* 5.7 1.8 - - + -
600A MSE 3.1 22.8 + - + +
601A ARG 3.4 0.6 + - - +
602A ALA 3.2 0.2 - - - -
603A GLU* 1.3 86.4 - - + +
605A GLY* 1.3 59.4 + - - +
606A LEU* 4.0 17.9 - - + +
614A LYS* 2.8 22.9 + - - -
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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