Contacts of the strand formed by residues 490 - 496 (chain H) 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 ILE 490 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357H LYS* 3.5 5.4 - - - +
358H ILE* 3.0 53.9 + - + +
361H PHE* 3.7 29.6 - - + -
394H ILE* 4.8 2.0 - - + -
396H LEU* 5.1 0.2 - - + -
407H LEU* 4.8 7.2 - - + -
434H LEU* 4.2 12.1 - - + -
437H GLN* 4.2 1.3 - - - +
478H MET* 3.7 9.0 - - + -
484H TYR 3.6 11.4 - - - +
485H VAL* 3.6 30.1 - - + -
489H ALA* 1.3 79.3 - - - +
491H PHE* 1.3 67.7 + - - +
492H ILE* 4.0 23.8 - - + -
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Residues in contact with PHE 491 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417G PRO 4.1 6.1 - - - -
418G ASN* 3.5 21.5 - - - -
420G ALA* 4.0 16.4 - - + -
421G LEU* 3.4 41.7 - - + -
355H ILE* 4.0 10.5 - - + -
356H TRP 3.4 3.6 - - - +
357H LYS* 3.4 48.0 - - + -
434H LEU* 3.7 5.2 - - - +
435H LEU* 3.1 39.7 + - + +
437H GLN* 3.9 29.6 - - + -
484H TYR 4.7 1.8 + - - -
486H ARG 6.0 0.2 - - - -
489H ALA* 5.1 3.6 - - + -
490H ILE* 1.3 78.3 - - - +
492H ILE* 1.3 63.4 + - - +
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Residues in contact with ILE 492 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354H PHE 3.9 0.5 - - - +
355H ILE* 3.4 3.6 - - - +
356H TRP* 2.7 64.5 + - + +
358H ILE* 4.2 13.0 - - + -
392H LEU* 4.0 20.0 - - + -
394H ILE* 4.0 15.9 - - + -
407H LEU* 5.3 1.6 - - + -
409H LEU* 3.6 27.1 - - + -
433H MET 3.3 9.9 - - - +
434H LEU* 3.8 27.8 - - + -
472H PHE* 5.1 2.5 - - + -
490H ILE* 4.0 11.7 - - + -
491H PHE* 1.3 75.3 - - - +
493H LYS* 1.3 63.9 + - - +
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Residues in contact with LYS 493 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353H VAL* 4.0 23.5 - - - +
354H PHE 3.3 11.0 - - - +
355H ILE* 4.0 19.4 - - + +
392H LEU* 5.2 0.4 - - - -
431H THR 3.9 0.2 - - - +
432H LEU* 3.5 2.4 - - - -
433H MET* 2.7 63.6 + - + +
435H LEU* 4.2 22.4 - - + -
491H PHE 4.1 0.2 + - - -
492H ILE* 1.3 79.9 - - - +
494H ALA* 1.3 67.7 + - - +
495H ILE* 4.0 20.7 - - + +
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Residues in contact with ALA 494 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352H GLY 3.4 4.7 - - - +
353H VAL* 3.5 2.8 - - - +
354H PHE* 2.8 37.8 + - + +
381H PHE* 4.4 15.0 - - + -
392H LEU* 3.9 30.3 - - + +
411H PHE* 5.9 0.4 - - + -
430H VAL* 5.6 1.6 - - + -
431H THR 3.3 7.6 - - - +
432H LEU* 4.0 8.7 - - + -
493H LYS* 1.3 75.3 - - - +
495H ILE* 1.3 66.8 + - - +
496H VAL* 5.4 2.0 - - + -
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Residues in contact with ILE 495 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352H GLY 3.5 2.7 - - - -
353H VAL* 4.6 17.3 - - + -
429H LYS 4.5 0.2 - - - -
430H VAL* 3.6 1.1 - - - -
431H THR* 2.8 52.0 + - + +
433H MET* 4.0 26.9 - - + -
493H LYS* 4.0 26.2 - - + +
494H ALA* 1.3 79.9 - - - +
496H VAL* 1.3 69.7 + - - +
497H ASP* 3.8 5.0 + - - +
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Residues in contact with VAL 496 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351H ASP 5.0 0.3 - - - +
352H GLY* 3.0 25.8 + - - +
381H PHE* 4.1 9.2 - - + -
383H THR* 4.1 14.4 - - + -
390H MET* 3.9 20.0 - - - -
411H PHE* 4.0 16.6 - - + -
426H PHE* 3.7 13.9 - - + -
428H GLN* 3.6 25.8 - - + -
429H LYS 3.5 6.1 - - - +
430H VAL* 4.4 7.0 - - + -
494H ALA* 5.4 1.1 - - + -
495H ILE* 1.3 78.9 - - - +
497H ASP* 1.3 66.8 + - - +
498H LEU* 3.3 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