Contacts of the strand formed by residues 490 - 496 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356E TRP 3.6 0.2 - - - +
357E LYS* 3.6 4.2 - - - +
358E ILE* 2.8 62.1 + - + -
361E PHE* 3.5 35.7 - - + -
394E ILE* 4.9 0.7 - - + -
396E LEU* 4.7 6.3 - - + -
407E LEU* 4.8 4.5 - - + -
434E LEU* 4.3 10.3 - - + -
437E GLN* 4.2 1.1 - - - +
478E MET* 3.7 7.9 - - + -
484E TYR 3.3 21.5 - - - +
485E VAL* 3.6 17.7 - - + -
489E ALA* 1.3 77.9 - - - +
491E PHE* 1.3 65.7 + - - +
492E ILE* 4.3 16.2 - - + -
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Residues in contact with PHE 491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417D PRO 3.7 14.4 - - - -
418D ASN* 3.5 26.0 - - - -
420D ALA* 4.2 13.0 - - + -
421D LEU* 3.9 23.8 - - + -
355E ILE* 4.0 12.6 - - + -
356E TRP 3.5 1.1 - - - -
357E LYS* 3.5 44.9 - - + -
434E LEU* 3.8 5.5 - - - +
435E LEU* 3.1 48.4 + - + +
437E GLN* 3.7 33.1 - - + +
484E TYR 4.6 2.2 + - - -
489E ALA* 5.4 2.7 - - + -
490E ILE* 1.3 78.4 - - - +
492E ILE* 1.3 64.3 + - - +
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Residues in contact with ILE 492 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354E PHE* 3.9 0.3 - - - +
355E ILE* 3.4 3.5 - - - +
356E TRP* 2.6 53.2 + - + +
358E ILE* 4.3 23.8 - - + -
392E LEU* 4.2 17.7 - - + +
394E ILE* 4.5 13.2 - - + -
407E LEU* 5.2 1.6 - - + -
409E LEU* 3.6 27.6 - - + -
432E LEU* 5.7 0.2 - - + -
433E MET 3.2 11.0 - - - +
434E LEU* 3.5 33.4 - - + -
472E PHE* 4.9 2.5 - - + -
490E ILE* 4.3 9.2 - - + -
491E PHE* 1.3 74.7 - - - +
493E LYS* 1.3 65.7 + - - +
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Residues in contact with LYS 493 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353E VAL* 4.1 19.8 - - - +
354E PHE 3.2 10.5 - - - +
355E ILE* 3.8 24.3 - - + +
392E LEU* 5.3 0.2 - - - -
431E THR 3.9 0.5 - - - +
432E LEU* 3.6 1.7 - - - -
433E MET* 2.8 51.3 + - + +
435E LEU* 3.9 31.0 - - + -
491E PHE 4.2 0.2 + - - -
492E ILE* 1.3 80.0 - - - +
494E ALA* 1.3 67.8 + - - +
495E ILE* 4.0 22.5 - - + +
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Residues in contact with ALA 494 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352E GLY 4.2 1.6 - - - -
353E VAL* 3.5 0.9 - - - -
354E PHE* 2.7 37.5 + - + +
381E PHE* 4.3 15.9 - - + -
392E LEU* 3.9 29.3 - - + +
411E PHE* 6.1 0.2 - - + -
430E VAL* 5.6 2.7 - - + -
431E THR 3.3 8.7 - - - +
432E LEU* 4.0 9.0 - - + -
493E LYS* 1.3 75.5 - - - +
495E ILE* 1.3 69.8 + - - +
496E VAL* 5.6 1.3 - - + -
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Residues in contact with ILE 495 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352E GLY 3.5 3.6 - - - -
353E VAL* 4.6 18.2 - - + -
429E LYS 4.6 0.2 - - - -
430E VAL* 3.8 0.2 - - - -
431E THR* 2.9 45.0 + - + +
433E MET* 3.9 28.3 - - + -
493E LYS* 4.0 24.7 - - + +
494E ALA* 1.3 80.3 - - - +
496E VAL* 1.3 69.1 + - - +
497E ASP* 3.7 5.2 + - - +
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Residues in contact with VAL 496 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351E ASP 4.8 0.5 - - - +
352E GLY* 2.8 22.5 + - - +
381E PHE* 4.1 14.8 - - + -
383E THR* 3.9 16.4 - - + -
390E MET* 3.8 20.9 - - - -
411E PHE* 3.9 16.8 - - + -
426E PHE* 3.9 12.8 - - + -
428E GLN* 3.8 16.4 - - + -
429E LYS 3.6 5.8 - - - +
430E VAL* 4.5 8.7 - - + -
494E ALA* 5.6 0.9 - - + -
495E ILE* 1.3 78.5 - - - +
497E ASP* 1.3 74.9 + - - +
498E LEU* 3.3 15.6 + - - +
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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