Contacts of the strand formed by residues 489 - 496 (chain A) in PDB entry 1D00
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 489 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A LYS* 4.1 24.7 - - + -
358A ILE 3.2 13.7 - - - +
359A SER* 4.0 9.6 - - - +
361A PHE* 4.3 2.0 - - - -
437A GLN* 3.0 20.1 + - - -
485A VAL* 4.2 1.6 - - - +
486A ARG 3.0 16.7 + - - +
487A ASP 3.9 7.2 - - - +
488A ASP* 1.3 79.6 - - - +
490A ILE* 1.3 67.8 + - - +
491A PHE* 5.2 3.6 - - + -
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Residues in contact with ILE 490 (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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357A LYS* 3.4 5.4 - - - +
358A ILE* 2.9 55.5 + - + -
361A PHE* 3.8 28.3 - - + -
394A ILE* 4.7 2.2 - - + -
396A LEU* 4.9 0.4 - - + -
407A LEU* 4.6 8.7 - - + -
434A LEU* 4.4 4.9 - - + -
437A GLN* 4.1 1.6 - - - +
478A MET* 3.4 26.7 - - + -
484A TYR 3.4 21.5 - - - +
485A VAL* 3.5 11.2 - - + -
489A ALA* 1.3 77.5 - - - +
491A PHE* 1.3 65.1 - - - +
492A ILE* 4.2 24.7 - - + -
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Residues in contact with PHE 491 (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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355A ILE* 4.0 17.9 - - + -
356A TRP 3.5 2.2 - - - -
357A LYS* 3.6 50.9 - - + -
434A LEU* 3.7 6.6 - - - +
435A LEU* 3.0 52.9 + - + +
437A GLN* 3.7 38.8 - - + +
484A TYR 4.7 1.2 + - - -
489A ALA* 5.1 2.7 - - + -
490A ILE* 1.3 80.1 - - - +
492A ILE* 1.3 62.5 + - - +
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Residues in contact with ILE 492 (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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354A PHE* 4.0 0.5 - - - +
355A ILE* 3.4 3.5 - - - +
356A TRP* 2.7 52.5 + - + +
358A ILE* 4.3 15.0 - - + -
392A LEU* 3.9 21.8 - - + -
394A ILE* 4.2 18.2 - - + -
407A LEU* 5.1 2.5 - - + -
409A LEU* 3.6 31.0 - - + -
433A MET 3.3 7.4 - - - +
434A LEU* 3.9 28.5 - - + -
472A PHE* 4.8 2.2 - - + -
490A ILE* 4.2 15.0 - - + -
491A PHE* 1.3 74.3 - - - +
493A LYS* 1.3 63.6 + - - +
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Residues in contact with LYS 493 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A VAL* 4.0 23.4 - - - +
354A PHE 3.3 10.1 - - - +
355A ILE* 4.0 22.1 - - + +
392A LEU* 5.7 0.2 - - - -
431A THR 4.0 0.2 - - - +
432A LEU* 3.5 4.0 - - - +
433A MET* 2.7 58.7 + - + +
435A LEU* 4.0 28.9 - - + -
491A PHE 4.2 0.4 + - - -
492A ILE* 1.3 78.6 - - - +
494A ALA* 1.3 68.1 + - - +
495A ILE* 4.1 17.4 - - + +
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Residues in contact with ALA 494 (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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352A GLY 4.2 1.3 - - - -
353A VAL* 3.5 2.6 - - - +
354A PHE* 2.8 35.1 + - + +
381A PHE* 4.2 19.7 - - + -
392A LEU* 4.0 18.6 - - + -
411A PHE* 5.9 0.2 - - + -
430A VAL* 5.7 1.8 - - + -
431A THR 3.3 9.4 - - - +
432A LEU* 3.9 15.0 - - + -
493A LYS* 1.3 75.1 - - - +
495A ILE* 1.3 68.9 + - - +
496A VAL* 5.5 1.6 - - + -
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Residues in contact with ILE 495 (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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352A GLY 3.5 3.4 - - - -
353A VAL* 4.6 16.6 - - + -
429A LYS 3.9 0.2 - - - +
430A VAL* 5.5 0.2 - - - -
431A THR* 2.9 50.8 + - + +
433A MET* 4.4 16.8 - - - -
493A LYS* 4.1 28.0 - - + +
494A ALA* 1.3 80.3 - - - +
496A VAL* 1.3 69.7 + - - +
497A ASP* 3.7 5.6 + - - +
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Residues in contact with VAL 496 (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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351A ASP 4.8 0.3 - - - +
352A GLY* 2.8 29.8 + - - +
353A VAL* 6.0 0.2 - - - +
381A PHE* 3.8 22.0 - - + -
383A THR* 3.9 21.5 - - + -
390A MET* 3.8 12.6 - - - -
411A PHE* 4.1 13.9 - - + -
426A PHE* 3.9 21.5 - - + -
428A GLN* 3.9 4.5 - - + -
429A LYS 3.7 5.4 - - - +
430A VAL* 4.8 5.4 - - + -
494A ALA* 5.5 0.7 - - + -
495A ILE* 1.3 78.9 - - - +
497A ASP* 1.3 72.3 + - - +
498A LEU* 3.4 14.9 + - - +
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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