Contacts of the strand formed by residues 568 - 573 (chain A) in PDB entry 2D2O
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 GLN 568 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542A LEU* 4.1 36.1 - - + +
543A LEU 3.2 6.7 - - - +
544A GLN* 2.5 40.3 + - - +
545A VAL* 3.4 3.7 - - - +
564A GLY* 2.7 29.3 - - - -
565A LYS* 2.7 25.2 + - + +
566A GLN* 3.7 9.2 - - - +
567A GLY* 1.3 87.9 - - - +
569A LEU* 1.3 59.1 + - - +
570A LYS 4.2 0.2 - - - -
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Residues in contact with LEU 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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508A TRP* 4.4 9.2 - - + -
541A VAL 3.4 2.3 - - - +
542A LEU* 3.2 7.5 - - - -
543A LEU* 2.7 40.5 + - + +
544A GLN 4.0 0.7 - - - +
545A VAL* 3.2 40.4 - - + -
546A PRO* 3.9 10.8 - - + -
553A TRP* 4.0 21.8 - - + +
562A VAL* 3.7 20.2 - - + -
563A HIS 4.0 4.5 - - - +
564A GLY* 3.4 28.0 - - - +
568A GLN* 1.3 73.3 - - - +
570A LYS* 1.3 60.5 + - - +
571A LEU* 3.7 16.3 + - + +
581A LEU* 5.6 2.7 - - + -
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Residues in contact with LYS 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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540A THR* 3.9 22.0 - - + -
541A VAL 3.4 3.6 - - - +
542A LEU* 3.6 12.7 - - + +
562A VAL* 4.4 9.9 - - - +
564A GLY* 5.2 0.4 - - - -
565A LYS* 3.2 38.5 - - - +
568A GLN 4.1 1.6 + - - -
569A LEU* 1.3 71.1 - - - +
571A LEU* 1.3 69.8 + - - +
572A THR* 4.4 6.4 + - + +
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Residues in contact with LEU 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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508A TRP* 4.8 1.6 - - + -
531A VAL* 3.6 33.4 - - + -
539A GLN 3.8 0.5 - - - +
540A THR* 2.9 3.7 - - - +
541A VAL* 2.5 48.1 + - + +
543A LEU* 4.1 15.3 - - + -
560A GLU* 5.3 0.7 - - - +
562A VAL* 4.2 27.8 - - + -
569A LEU* 4.2 12.6 - - + +
570A LYS* 1.3 85.0 - - - +
572A THR* 1.3 62.7 + - - +
573A LEU* 3.6 13.7 - - + -
579A MET* 4.0 21.1 - - + -
581A LEU* 3.9 16.2 - - + -
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Residues in contact with THR 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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538A LYS* 4.8 16.8 - - - -
539A GLN 3.2 5.4 - - - -
540A THR* 2.9 34.8 - - + +
560A GLU* 5.4 5.4 + - - -
570A LYS* 5.1 8.1 - - + -
571A LEU* 1.3 71.9 - - - +
573A LEU* 1.3 64.0 + - - +
574A ARG* 4.1 1.9 + - - +
577A GLN* 4.1 4.7 + - - +
579A MET* 4.6 10.6 - - - +
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Residues in contact with LEU 573 (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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516A LEU* 4.4 7.0 - - + -
531A VAL* 4.4 14.1 - - + +
533A ASN* 3.2 29.7 + - + +
538A LYS* 3.3 3.6 - - - -
539A GLN* 2.5 41.3 + - + +
541A VAL* 4.3 11.2 - - + -
571A LEU* 3.6 30.7 - - + +
572A THR* 1.3 77.4 - - - +
574A ARG* 1.3 64.3 + - - +
577A GLN* 3.7 23.1 - - + +
579A MET* 3.4 34.1 - - + -
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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