Contacts of the strand formed by residues 530 - 535 (chain A) in PDB entry 1DY7
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 530 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496A ALA* 3.9 27.6 - - + -
498A ILE* 4.0 4.9 - - + -
521A VAL* 2.8 35.3 + - + +
529A SER* 1.3 81.1 - - - +
531A LEU* 1.3 66.3 + - - +
544A VAL* 4.2 2.0 - - + -
545A ILE 3.3 14.6 - - - +
546A LYS* 3.9 10.8 - - + -
550A LEU* 3.5 10.3 - - - +
553A PRO* 3.8 1.6 - - - +
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Residues in contact with LEU 531 (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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171A VAL* 4.1 14.1 - - + -
182A ILE* 3.7 29.4 - - + -
518A TRP* 3.9 26.5 - - + -
519A PHE 3.4 6.1 - - - +
520A SER* 3.7 16.6 - - - +
530A ALA* 1.3 76.9 - - - +
532A VAL* 1.3 64.5 + - - +
533A VAL* 4.2 0.7 - - + -
544A VAL* 3.6 4.5 - - - +
545A ILE* 2.8 48.5 + - + +
550A LEU* 4.0 11.9 - - + -
553A PRO* 3.5 32.3 - - + -
556A LYS* 4.4 3.4 - - + -
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Residues in contact with VAL 532 (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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492A ILE* 3.7 32.8 - - + +
495A TRP* 4.2 12.6 - - + -
496A ALA* 3.7 34.3 - - + +
517A VAL 3.7 1.2 - - - +
518A TRP* 3.4 2.6 - - - -
519A PHE* 2.9 34.7 + - - +
521A VAL* 3.7 11.0 - - + -
531A LEU* 1.3 77.9 - - - +
533A VAL* 1.3 68.1 + - - +
534A VAL* 4.3 0.7 - - + -
541A LEU* 3.7 22.4 - - + -
543A HIS 3.7 2.5 - - - -
544A VAL* 4.5 5.2 - - + -
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Residues in contact with VAL 533 (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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187A TYR* 4.0 16.4 - - + -
516A GLU* 3.5 32.1 - - + +
517A VAL 3.6 3.1 - - - -
518A TRP* 3.8 39.9 - - + +
531A LEU 5.3 0.2 - - - -
532A VAL* 1.3 75.4 - - - +
534A VAL* 1.3 55.7 - - - +
541A LEU* 3.8 4.9 - - - +
542A LYS* 2.8 39.5 + - + -
543A HIS* 2.8 25.6 + - + +
545A ILE* 4.3 12.1 - - + -
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Residues in contact with VAL 534 (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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490A LEU* 4.1 13.2 - - + -
492A ILE* 3.8 28.9 - - + -
495A TRP* 4.1 8.7 - - + -
516A GLU* 3.2 6.4 - - - +
517A VAL* 2.8 52.0 + - + +
519A PHE* 4.1 12.6 - - + -
532A VAL* 4.3 4.0 - - + +
533A VAL* 1.3 75.6 - - - +
535A ASP* 1.3 74.0 + - - +
536A ASP 3.2 1.0 + - - -
539A LEU* 4.1 20.0 - - + -
540A GLU 3.7 12.3 - - - +
542A LYS* 4.2 2.5 - - - -
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Residues in contact with ASP 535 (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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515A THR 4.1 7.1 - - - +
516A GLU* 4.6 5.2 - - - -
534A VAL* 1.3 67.6 - - - +
536A ASP* 1.3 59.2 + - - +
537A LYS* 3.1 21.1 + - - +
538A THR* 3.3 28.3 + - - +
539A LEU* 2.8 30.7 + - - -
540A GLU* 2.9 15.2 + - + +
541A LEU 5.2 0.4 - - - +
542A LYS* 3.9 22.3 - - + +
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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