Contacts of the strand formed by residues 573 - 579 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520A ASP 5.4 0.9 + - - -
522A PRO* 3.5 29.8 - - + +
533A PHE* 3.9 31.4 - + - -
563A VAL* 4.2 9.0 - - + -
564A ARG 3.2 16.2 - - - +
565A GLU* 3.8 29.3 + - + -
566A SER* 3.5 3.3 - - - +
571A ASN 3.4 20.2 - - - -
572A ASP* 1.3 78.5 - - - +
574A THR* 1.3 67.2 + - - +
587A ARG* 3.6 5.9 - - - +
588A ILE* 2.8 41.3 + - + +
590A SER* 4.6 0.4 - - - -
597A MET* 5.9 2.4 - - + +
599A TYR* 4.1 22.2 + + - -
610A ILE* 4.2 11.4 - - + -
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Residues in contact with THR 574 (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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563A VAL* 3.4 4.9 - - - +
564A ARG* 2.6 73.6 + - - +
566A SER* 3.5 8.3 + - - -
573A TYR* 1.3 79.0 + - - +
575A LEU* 1.3 70.2 + - - +
585A HIS* 3.8 14.8 - - + -
586A CYS 3.4 12.8 - - - +
587A ARG* 4.7 2.7 - - - +
588A ILE* 4.2 4.3 - - - +
1001A SO4 3.3 26.4 + - - +
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Residues in contact with LEU 575 (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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561A PHE* 3.5 34.3 - - + -
562A LEU 3.5 8.7 - - - +
563A VAL* 4.0 9.6 - - + +
574A THR* 1.3 72.5 - - - +
576A SER* 1.3 59.9 + - - +
577A PHE* 3.1 40.6 - - + -
584A GLN 3.5 0.7 - - - +
585A HIS* 3.1 4.2 - - - -
586A CYS* 2.7 52.5 + - + +
588A ILE* 3.9 16.5 - - + +
601A LEU* 5.0 3.8 - - + -
613A LEU* 5.7 2.2 - - + -
614A ILE* 4.2 4.0 - - + -
622A LEU* 4.3 9.2 - - + -
631B LEU* 4.0 21.1 - - + -
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Residues in contact with SER 576 (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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543A ALA* 4.4 2.2 - - - -
547A LEU* 3.7 15.1 - - - +
561A PHE* 3.1 2.5 - - - -
562A LEU* 3.0 49.8 + - - +
564A ARG* 2.6 33.8 + - - -
574A THR 3.9 0.2 + - - -
575A LEU* 1.3 71.9 - - - +
577A PHE* 1.3 60.5 + - - +
584A GLN 3.2 5.2 - - - -
585A HIS* 2.8 19.5 + - - -
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Residues in contact with PHE 577 (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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547A LEU* 4.1 5.8 - - - +
559A GLY* 4.3 4.9 - - - +
560A THR 3.1 13.0 - - - +
561A PHE* 3.6 12.1 - - + -
575A LEU* 3.1 26.2 - - + -
576A SER* 1.3 74.6 - - - +
578A TRP* 1.3 71.0 + - - +
579A ARG* 4.8 1.7 - - + +
583A VAL* 3.2 7.3 - - - +
584A GLN* 3.1 63.1 + - + -
586A CYS* 3.9 15.3 - - - -
622A LEU* 3.5 23.6 - - + -
624A CYS* 5.2 0.7 - - - -
627B PHE* 4.1 17.0 - + + -
629B LEU* 3.4 28.5 - - + -
631B LEU* 4.0 8.1 - - + -
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Residues in contact with TRP 578 (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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547A LEU* 4.2 8.9 - - + +
548A GLN* 4.1 19.7 - - + -
551A CYS* 3.4 40.2 + - + +
552A ALA* 3.9 27.8 - - + -
556A ALA 4.3 8.1 + - - -
557A LYS 3.9 13.2 - - - -
558A ASP* 3.4 12.7 + - - +
559A GLY* 2.7 31.0 + - - -
560A THR* 2.7 17.2 + - - +
577A PHE* 1.3 76.1 - - - +
579A ARG* 1.3 64.4 + - - +
580A SER* 3.7 9.2 - - - +
581A GLY* 3.2 37.5 - - - -
582A ARG 3.4 16.4 - - - -
583A VAL* 3.9 15.5 - - + +
629B LEU* 4.5 0.2 - - - +
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Residues in contact with ARG 579 (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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558A ASP* 3.7 18.1 + - - -
577A PHE* 4.8 3.4 - - + +
578A TRP* 1.3 76.0 - - - +
580A SER* 1.3 82.8 + - - +
581A GLY 3.6 0.7 - - - -
582A ARG* 2.9 24.8 + - + +
584A GLN 6.2 0.2 - - - +
589B ARG* 3.6 23.4 - - - +
625B ALA 4.2 4.8 + - - -
626B GLU* 3.0 40.0 + - + +
627B PHE* 3.8 33.0 - - + -
629B LEU* 4.1 22.8 - - + +
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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