Contacts of the strand formed by residues 573 - 579 (chain B) in PDB entry 2DX0
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 573 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563B VAL* 3.6 24.7 - - + -
564B ARG* 3.2 10.8 - - - +
565B GLU* 3.6 38.5 + - + -
566B SER* 3.9 3.1 - - - +
572B ASP* 1.3 84.8 - - - +
574B THR* 1.3 65.1 + - - +
587B ARG* 3.8 4.3 + - - +
588B ILE* 2.8 37.8 + - + +
599B TYR* 4.0 25.0 + + - -
610B ILE* 4.0 24.9 - - + +
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Residues in contact with THR 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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562B LEU 3.9 0.7 - - - +
563B VAL* 3.5 7.1 - - - -
564B ARG* 2.7 40.0 + - + +
566B SER* 4.7 3.6 - - - +
573B TYR* 1.3 76.5 + - - +
575B LEU* 1.3 72.5 + - - +
576B SER* 4.0 11.4 + - - +
585B HIS* 4.2 10.5 - - + -
586B CYS 3.8 10.1 - - - +
587B ARG* 4.8 7.8 + - - +
588B ILE* 4.6 0.7 - - - +
1003B SO4 3.6 22.4 + - - -
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Residues in contact with LEU 575 (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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631A LEU* 4.0 18.6 - - + -
561B PHE* 3.9 22.7 - - + -
562B LEU 3.8 4.7 - - - +
563B VAL* 3.8 23.3 - - + -
574B THR* 1.3 74.3 - - - +
576B SER* 1.3 65.4 + - - +
577B PHE* 3.3 38.4 - - + -
585B HIS* 3.0 8.0 - - - +
586B CYS* 2.9 43.5 + - + +
588B ILE* 4.2 18.1 - - + +
601B LEU* 4.9 10.3 - - + -
613B LEU* 6.1 1.1 - - + -
614B ILE* 5.2 2.5 - - + -
622B LEU* 4.7 8.1 - - + -
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Residues in contact with SER 576 (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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543B ALA* 5.7 3.4 - - - +
544B GLU* 3.4 17.9 + - - -
547B LEU* 3.6 10.1 - - - -
561B PHE* 2.9 26.0 - - - +
562B LEU* 3.0 34.7 + - - +
574B THR* 4.0 9.3 + - - +
575B LEU* 1.3 77.5 + - - +
577B PHE* 1.3 61.1 + - - +
583B VAL* 4.3 4.3 - - - -
584B GLN 3.2 8.5 - - - -
585B HIS* 3.9 7.6 - - - +
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Residues in contact with PHE 577 (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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626A GLU 3.5 24.0 - - - -
627A PHE* 3.9 21.3 - + - -
629A LEU* 3.9 11.4 - - + -
631A LEU* 4.0 9.0 - - + -
547B LEU* 3.9 6.0 - - - +
559B GLY* 4.4 3.6 - - - -
560B THR 3.0 11.7 - - - +
561B PHE* 3.8 9.9 - - + -
575B LEU* 3.3 25.8 - - + -
576B SER* 1.3 75.0 - - - +
578B TRP* 1.3 71.6 + - - +
579B ARG* 4.0 5.4 - - + -
583B VAL* 3.5 2.6 - - - -
584B GLN* 2.9 58.6 + - + -
585B HIS* 4.5 2.5 - - - -
586B CYS* 5.3 0.4 - - + -
622B LEU* 3.4 29.2 - - + -
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Residues in contact with TRP 578 (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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547B LEU* 4.4 3.0 - - + +
548B GLN* 3.3 30.5 - - - -
551B CYS* 3.3 44.9 + - + +
552B ALA* 4.6 9.9 - - + -
556B ALA 3.3 26.3 + - - -
557B LYS 3.8 6.7 - - - -
558B ASP* 3.1 13.4 + - - +
559B GLY 2.8 28.2 + - - -
560B THR* 2.7 19.0 + - - +
577B PHE* 1.3 71.5 - - - +
579B ARG* 1.3 63.4 + - - +
581B GLY* 3.1 49.0 - - - +
582B ARG 3.7 5.8 - - - -
583B VAL* 3.7 23.3 - - + -
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Residues in contact with ARG 579 (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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589A ARG* 5.4 5.2 - - - +
625A ALA* 2.6 33.3 + - - +
626A GLU* 3.5 29.8 + - + +
628A GLU* 3.7 15.2 + - - +
629A LEU* 3.8 30.6 - - - +
558B ASP* 3.3 20.3 + - - +
577B PHE* 4.0 6.5 - - + -
578B TRP* 1.3 78.0 - - - +
580B SER* 1.3 82.9 + - - +
581B GLY 3.4 0.9 - - - -
582B ARG* 2.8 27.8 + - - +
584B GLN* 3.9 18.4 - - + +
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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