Contacts of the helix formed by residues 596 - 605 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425B GLY* 4.6 2.5 - - - -
426B ALA* 4.9 2.4 - - - +
595B GLY* 1.3 75.9 - - - +
597B GLN* 1.3 67.1 + - - +
598B GLU* 3.9 10.4 + - + +
599B GLU* 3.1 50.1 + - + +
600B MSE 2.9 18.0 + - - +
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Residues in contact with GLN 597 (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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423B ILE* 3.2 27.8 - - - +
424B VAL* 3.6 26.6 + - - +
425B GLY* 3.8 1.5 - - - +
478B ARG* 3.2 44.4 + - - +
479B GLY* 4.8 3.6 - - - -
595B GLY 3.4 2.4 + - - -
596B THR* 1.3 73.9 + - - +
598B GLU* 1.3 58.7 + - + +
600B MSE 3.4 0.9 + - - +
601B ARG* 2.8 73.2 + - - +
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Residues in contact with GLU 598 (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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596B THR* 3.3 10.7 + - + +
597B GLN* 1.3 76.0 - - + +
599B GLU* 1.3 58.6 + - - +
601B ARG* 3.3 11.1 + - - +
602B ALA* 2.8 33.4 + - - +
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Residues in contact with GLU 599 (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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595B GLY* 4.1 6.1 - - - -
596B THR* 3.1 40.1 + - + +
598B GLU* 1.3 79.4 - - + +
600B MSE 1.3 70.2 + - + +
602B ALA* 3.7 5.4 - - - +
603B GLU* 2.8 30.5 + - - +
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Residues in contact with MSE 600 (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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423B ILE* 4.0 22.9 - - + -
425B GLY 5.7 0.2 - - - +
592B ILE* 4.7 6.5 - - + -
593B PRO* 3.6 38.4 - - + +
594B GLN 3.9 13.9 - - - +
595B GLY* 3.7 20.4 - - - +
596B THR 2.9 9.6 + - - +
597B GLN 3.9 2.9 - - - +
599B GLU* 1.3 91.9 - - + +
601B ARG* 1.3 57.6 + - - +
603B GLU* 3.5 32.8 - - - +
604B LEU* 2.9 42.0 + - + +
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Residues in contact with ARG 601 (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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423B ILE* 3.6 26.4 + - + +
477B PRO* 4.3 12.9 - - - +
513B THR* 5.3 2.0 + - - -
514B LEU* 4.6 10.3 - - - -
558B GLU* 2.9 38.1 + - - +
597B GLN* 2.8 65.0 + - - +
598B GLU* 3.8 9.7 - - - +
600B MSE 1.3 70.7 - - - +
602B ALA* 1.3 63.6 + - - +
604B LEU* 3.4 1.0 + - - -
605B GLY 3.2 3.3 + - - -
606B LEU* 2.8 49.6 + - + +
607B ASP* 5.9 0.2 - - - -
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Residues in contact with ALA 602 (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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598B GLU 2.8 18.7 + - - +
599B GLU* 3.7 5.6 - - - +
601B ARG* 1.3 76.1 - - - +
603B GLU* 1.3 62.9 + - - +
605B GLY* 3.3 12.0 + - - -
607B ASP* 3.6 29.2 - - - +
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Residues in contact with GLU 603 (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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593B PRO* 5.9 4.2 - - - +
599B GLU 2.8 17.4 + - - +
600B MSE 3.5 33.1 - - - +
601B ARG 3.3 0.2 - - - -
602B ALA* 1.3 77.9 - - - +
604B LEU* 1.3 66.0 + - + +
605B GLY 3.3 0.6 + - - -
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Residues in contact with LEU 604 (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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423B ILE* 3.8 14.1 - - + -
586B GLY 5.4 0.7 - - - +
587B LEU* 3.7 29.4 - - + -
588B PRO* 4.1 27.6 - - + +
590B PHE* 4.1 17.3 - - + -
592B ILE* 4.1 19.5 - - + -
593B PRO* 6.1 1.1 - - + -
600B MSE 2.9 29.1 + - + +
602B ALA 3.3 0.2 - - - -
603B GLU* 1.3 86.6 - - + +
605B GLY* 1.3 59.0 + - - +
606B LEU* 4.1 13.4 - - + +
614B LYS* 2.9 20.8 + - - -
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Residues in contact with GLY 605 (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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601B ARG 3.2 3.9 + - - -
602B ALA 3.3 10.4 + - - -
603B GLU 3.3 1.0 + - - -
604B LEU* 1.3 79.8 - - - +
606B LEU* 1.3 57.6 + - - +
607B ASP* 2.9 10.2 + - - -
610B GLY* 3.5 14.4 - - - -
611B MSE 3.4 21.5 + - - +
614B LYS* 3.2 20.3 + - - -
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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