Contacts of the strand formed by residues 489 - 496 (chain F) in PDB entry 1D0A
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357F LYS* 4.3 16.8 - - + -
358F ILE 3.3 13.2 - - - +
359F SER* 4.0 15.3 - - - +
361F PHE* 4.4 0.7 - - - -
437F GLN* 3.0 19.9 + - - -
485F VAL* 3.6 3.5 - - - +
486F ARG 3.1 19.1 + - - +
487F ASP* 4.1 5.2 - - + +
488F ASP* 1.3 80.2 - - - +
490F ILE* 1.3 66.1 + - - +
491F PHE* 5.0 4.5 - - + -
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Residues in contact with ILE 490 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357F LYS* 3.6 4.2 - - - +
358F ILE* 3.0 57.8 + - + +
361F PHE* 3.9 27.4 - - + -
394F ILE* 4.8 0.2 - - + -
396F LEU* 4.7 2.2 - - + -
407F LEU* 4.6 8.3 - - + -
434F LEU* 4.3 15.9 - - + -
437F GLN* 4.0 1.3 - - - +
478F MET* 3.8 15.7 - - + -
484F TYR 3.6 13.9 - - - +
485F VAL* 3.6 29.6 - - + -
489F ALA* 1.3 77.8 - - - +
491F PHE* 1.3 66.9 + - - +
492F ILE* 4.5 8.7 - - + -
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Residues in contact with PHE 491 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417E PRO 3.8 13.7 - - - -
418E ASN* 3.4 27.1 - - - -
420E ALA* 4.4 9.9 - - + -
421E LEU* 3.7 28.9 - - + -
355F ILE* 4.0 11.4 - - + -
356F TRP 3.4 3.6 - - - +
357F LYS* 3.7 38.1 - - + -
434F LEU* 3.8 6.7 - - - +
435F LEU* 3.0 49.2 + - + +
437F GLN* 3.6 35.1 - - - +
484F TYR 4.8 1.0 + - - -
489F ALA* 5.0 4.5 - - + -
490F ILE* 1.3 80.8 - - - +
492F ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 492 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354F PHE 3.9 0.3 - - - +
355F ILE* 3.3 4.1 - - - +
356F TRP* 2.6 61.6 + - + +
358F ILE* 4.4 13.7 - - + -
392F LEU* 3.9 22.3 - - + +
394F ILE* 4.3 15.9 - - + -
407F LEU* 4.8 4.0 - - + -
409F LEU* 3.7 32.1 - - + -
433F MET 3.4 8.3 - - - +
434F LEU* 3.7 29.8 - - + -
472F PHE* 4.9 0.2 - - + -
490F ILE* 4.5 4.3 - - + -
491F PHE* 1.3 74.5 - - - +
493F LYS* 1.3 64.3 + - - +
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Residues in contact with LYS 493 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353F VAL* 3.9 24.0 - - - +
354F PHE 3.3 10.3 - - - +
355F ILE* 3.9 24.7 - - + +
431F THR 3.9 0.2 - - - +
432F LEU* 3.5 2.3 - - - -
433F MET* 2.8 62.9 + - + +
435F LEU* 4.3 18.4 - - + -
491F PHE 4.3 0.2 + - - -
492F ILE* 1.3 79.3 - - - +
494F ALA* 1.3 68.4 + - - +
495F ILE* 3.9 21.9 - - + +
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Residues in contact with ALA 494 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352F GLY 3.6 0.8 - - - +
353F VAL* 3.5 4.5 - - - +
354F PHE* 2.8 34.6 + - + +
381F PHE* 4.2 15.5 - - + -
392F LEU* 4.0 23.3 - - + +
411F PHE* 5.9 0.2 - - + -
430F VAL* 5.4 3.4 - - + -
431F THR 3.3 4.7 - - - +
432F LEU* 3.8 19.5 - - + -
493F LYS* 1.3 75.0 - - - +
495F ILE* 1.3 66.2 + - - +
496F VAL* 4.2 1.6 - - + -
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Residues in contact with ILE 495 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352F GLY 3.6 2.2 - - - -
353F VAL* 4.5 16.4 - - + -
429F LYS 3.9 0.3 - - - +
430F VAL* 3.7 1.8 - - - -
431F THR* 2.9 53.1 + - + +
433F MET* 4.4 15.9 - - - -
493F LYS* 3.9 30.7 - - + +
494F ALA* 1.3 79.1 - - - +
496F VAL* 1.3 68.9 + - - +
497F ASP* 3.8 4.0 + - - +
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Residues in contact with VAL 496 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351F ASP 4.8 0.5 - - - +
352F GLY* 2.9 29.6 + - - +
381F PHE* 3.9 13.0 - - + -
383F THR* 3.9 20.4 - - + -
390F MET* 3.8 20.6 - - + -
411F PHE* 4.1 12.8 - - + -
426F PHE* 4.0 9.2 - - + -
428F GLN* 3.9 17.3 - - + -
429F LYS 3.6 4.9 - - - +
430F VAL* 4.6 6.5 - - + +
494F ALA* 5.4 0.9 - - + -
495F ILE* 1.3 79.8 - - - +
497F ASP* 1.3 74.0 + - - +
498F LEU* 3.4 15.2 + - - +
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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