Contacts of the strand formed by residues 566 - 570 (chain A) in PDB entry 1D0N
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 ALA 566 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541A VAL* 2.7 43.4 + - - +
565A ASP* 1.3 74.5 - - - +
567A PHE* 1.3 60.3 + - - +
577A LEU* 6.3 0.7 - - + -
578A TRP 3.5 13.7 - - - +
579A VAL* 3.9 15.0 - - + -
580A GLY 4.3 2.0 - - - +
583A ALA* 4.2 5.8 - - + -
587A GLU* 4.0 26.2 - - + +
588A LYS* 4.7 2.0 - - + +
591A ALA* 4.6 8.7 - - + -
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Residues in contact with PHE 567 (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 LEU* 3.6 20.0 - - + -
539A PHE 2.9 7.9 - - - +
540A GLN* 3.4 34.8 - - + -
554A ILE* 4.1 5.4 - - + -
560A ALA 3.4 17.3 - - - -
561A LEU* 3.4 19.1 - - + -
562A ASN* 3.0 39.5 - - + -
565A ASP* 3.2 24.7 - - - -
566A ALA* 1.3 77.8 - - - +
568A VAL* 1.3 71.4 + - - +
569A LEU 4.3 0.4 - - - -
577A LEU* 3.6 2.3 - - - +
578A TRP* 2.8 56.7 + + + +
614A PHE* 6.4 0.2 - - + -
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Residues in contact with VAL 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A ARG 3.8 0.7 - - - +
538A LEU* 3.8 2.8 - - - -
539A PHE* 2.8 41.2 + - + +
541A VAL* 4.5 2.9 - - + -
567A PHE* 1.3 80.7 - - - +
569A LEU* 1.3 65.5 + - - +
570A LYS* 3.7 3.3 + - - +
575A ALA* 5.2 0.2 - - + -
576A TYR 3.3 8.7 - - - +
577A LEU* 3.6 10.1 - - + -
591A ALA* 3.4 31.0 - - + +
594A LEU* 4.4 5.2 - - + -
595A LEU* 3.4 37.9 - - + -
598A LEU* 4.4 13.0 - - + -
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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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536A THR* 3.8 16.8 - - + -
537A ARG 3.4 17.0 - - - +
538A LEU* 4.0 19.1 - - + -
556A PRO* 5.1 0.4 - - + -
567A PHE 4.3 0.4 - - - -
568A VAL* 1.3 72.6 - - - +
570A LYS* 1.3 62.5 + - - +
571A THR* 5.4 0.9 - - - -
574A ALA 3.8 6.1 - - - +
575A ALA* 3.9 0.5 - - - -
576A TYR* 3.0 47.8 + - + +
578A TRP* 5.9 0.6 - - + +
614A PHE* 4.0 27.6 - - + +
617A ALA* 3.3 44.2 - - + +
618A LEU* 3.9 12.3 - - + -
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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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533A PRO* 6.4 2.9 - - - -
534A ALA 4.3 9.8 + - - -
535A SER 3.7 13.3 + - - +
536A THR* 3.7 5.4 - - - +
537A ARG* 2.9 54.1 + - + +
539A PHE* 5.4 1.6 - - + -
568A VAL* 3.7 3.7 + - - +
569A LEU* 1.3 76.9 - - - +
571A THR* 1.3 99.2 + - - +
572A PRO* 3.8 4.4 - - - +
574A ALA 4.8 1.3 - - - -
575A ALA* 5.3 4.3 - - + +
595A LEU* 6.4 0.2 - - - -
598A LEU* 4.8 30.5 - - + +
600A ALA* 5.4 11.2 - - + -
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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