Contacts of the strand formed by residues 489 - 496 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357D LYS* 4.3 17.7 - - + -
358D ILE 3.2 14.1 - - - +
359D SER* 4.1 14.1 - - - +
361D PHE* 4.2 3.4 - - - +
437D GLN* 3.1 7.7 + - - +
485D VAL* 3.5 1.6 - - - +
486D ARG 2.9 35.7 + - - +
487D ASP* 4.1 3.6 - - + +
488D ASP* 1.3 76.6 - - - +
490D ILE* 1.3 67.5 + - - +
491D PHE* 5.4 2.9 - - + -
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Residues in contact with ILE 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D TRP 3.7 0.2 - - - +
357D LYS* 3.5 4.5 - - - +
358D ILE* 2.9 53.0 + - + -
361D PHE* 3.6 31.9 - - + -
394D ILE* 4.9 7.2 - - + -
396D LEU* 4.9 0.7 - - + -
407D LEU* 5.0 3.6 - - + -
434D LEU* 4.3 11.2 - - + -
437D GLN* 4.1 1.8 - - - +
478D MET* 4.2 8.1 - - + -
484D TYR 3.5 20.2 - - - +
485D VAL* 3.8 21.3 - - + -
489D ALA* 1.3 80.3 - - - +
491D PHE* 1.3 65.5 + - - +
492D ILE* 4.2 21.3 - - + -
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Residues in contact with PHE 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417C PRO 3.6 18.4 - - - -
418C ASN* 3.4 29.2 - - - -
420C ALA* 4.5 6.5 - - + -
421C LEU* 3.9 23.8 - - + -
355D ILE* 3.9 12.6 - - + -
356D TRP 3.4 1.6 - - - -
357D LYS* 3.7 33.9 - - + -
434D LEU* 3.7 6.7 - - - +
435D LEU* 3.0 50.8 + - + -
437D GLN* 3.6 39.0 - - + -
484D TYR 4.8 1.8 + - - -
489D ALA* 5.4 2.5 - - + -
490D ILE* 1.3 79.3 - - - +
492D ILE* 1.3 62.5 + - - +
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Residues in contact with ILE 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D PHE* 3.8 0.7 - - - +
355D ILE* 3.3 3.1 - - - +
356D TRP* 2.5 60.4 + - + +
358D ILE* 4.1 22.4 - - + -
392D LEU* 4.1 20.9 - - + -
394D ILE* 4.4 13.2 - - + -
407D LEU* 5.0 3.6 - - + -
409D LEU* 3.8 25.8 - - + -
433D MET 3.4 10.1 - - - +
434D LEU* 3.8 29.8 - - + -
472D PHE* 5.3 0.2 - - + -
490D ILE* 4.2 11.0 - - + -
491D PHE* 1.3 73.5 - - - +
493D LYS* 1.3 64.3 + - - +
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Residues in contact with LYS 493 (chain D).
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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353D VAL* 4.1 19.8 - - - +
354D PHE 3.2 10.3 - - - +
355D ILE* 3.8 22.4 - - + +
392D LEU* 5.1 0.2 - - - -
431D THR 3.8 0.2 - - - +
432D LEU* 3.5 4.0 - - - +
433D MET* 2.8 62.5 + - + +
435D LEU* 4.1 28.0 - - + +
491D PHE 4.2 0.4 - - - -
492D ILE* 1.3 78.1 - - - +
494D ALA* 1.3 67.6 + - - +
495D ILE* 4.1 20.2 - - + +
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Residues in contact with ALA 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D GLY 3.6 1.2 - - - +
353D VAL* 3.6 1.4 - - - +
354D PHE* 2.8 34.9 + - + +
381D PHE* 4.3 14.4 - - + -
392D LEU* 3.9 30.3 - - + +
430D VAL* 5.6 2.2 - - + -
431D THR 3.2 7.9 - - - +
432D LEU* 3.9 10.5 - - + -
493D LYS* 1.3 75.8 - - - +
495D ILE* 1.3 67.8 + - - +
496D VAL* 4.2 2.5 - - + -
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Residues in contact with ILE 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D GLY 3.6 3.1 - - - -
353D VAL* 4.6 16.8 - - + -
429D LYS 3.9 0.2 - - - +
430D VAL* 3.7 2.0 - - - -
431D THR* 2.9 53.7 + - + +
433D MET* 4.4 15.3 - - - -
493D LYS* 4.1 28.7 - - + +
494D ALA* 1.3 78.9 - - - +
496D VAL* 1.3 69.8 + - - +
497D ASP* 3.7 3.4 + - - +
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Residues in contact with VAL 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D ASP 4.9 0.3 - - - +
352D GLY* 2.9 21.0 + - - +
353D VAL* 5.9 0.2 - - - +
381D PHE* 3.8 20.4 - - + -
383D THR* 4.1 14.6 - - + -
390D MET* 3.8 21.1 - - - -
411D PHE* 3.9 13.2 - - + -
426D PHE* 3.8 14.6 - - + -
428D GLN* 3.8 24.0 - - + -
429D LYS 3.6 5.4 - - - +
430D VAL* 4.7 5.4 - - + -
494D ALA* 5.4 0.9 - - + -
495D ILE* 1.3 79.7 - - - +
497D ASP* 1.3 69.6 + - - +
498D LEU* 3.4 14.7 + - - +
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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