Contacts of the strand formed by residues 449 - 454 (chain A) in PDB entry 1BFD
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 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421A GLN* 3.5 22.9 - - + +
422A VAL 3.0 12.3 + - - +
423A ILE* 3.4 12.3 - - + -
424A ALA 2.9 25.8 + - - -
447A PRO 4.4 2.2 - - - +
448A THR* 1.3 77.8 - - - +
450A PHE* 1.3 62.6 + - - +
451A VAL* 4.1 19.7 + - + -
507A LEU* 5.2 4.9 - - + -
510A ALA* 3.8 43.3 - - + +
511A LEU* 3.8 25.6 - - + -
517A VAL* 3.3 13.0 - - + +
519A ILE* 4.4 7.4 - - + -
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Residues in contact with PHE 450 (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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407A LEU* 3.7 40.4 - - + -
410A ALA* 4.3 1.1 - - + -
411A ILE* 4.0 16.8 - - + -
424A ALA* 3.6 15.0 - - + +
426A ILE* 4.4 1.8 - - + -
438A LEU* 3.7 27.1 - - + -
441A ALA* 4.4 4.5 - - + -
448A THR* 3.6 41.1 - - + -
449A ILE* 1.3 73.4 - - - +
451A VAL* 1.3 58.0 + - - +
452A ILE* 3.9 8.6 + - + -
492A VAL* 5.0 2.0 - - + -
516A PRO* 4.3 13.0 - - + -
517A VAL 2.8 22.8 + - - +
518A LEU* 3.3 16.1 - - + +
519A ILE* 2.8 33.4 + - - +
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Residues in contact with VAL 451 (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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358A VAL* 4.6 11.2 - - + -
362A LEU* 4.7 11.2 - - + -
423A ILE* 4.0 25.1 - - + -
424A ALA 2.7 12.7 + - - +
425A VAL* 3.5 9.6 - - + +
426A ILE 2.9 28.1 + - - +
449A ILE* 4.2 10.1 - - + -
450A PHE* 1.3 75.2 - - - +
452A ILE* 1.3 62.5 + - - +
453A MET* 3.7 16.4 + - - -
503A LEU* 5.7 2.2 - - + -
507A LEU* 4.9 2.5 - - + -
519A ILE* 3.5 13.9 - - + -
521A VAL* 3.7 25.6 - - + -
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Residues in contact with ILE 452 (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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407A LEU* 5.3 3.1 - - + -
426A ILE* 3.2 21.8 - - + +
427A GLY 4.4 0.7 - - - +
428A ASP* 4.0 23.8 - - + -
431A ALA* 4.2 17.7 - - + -
435A ILE* 6.5 0.2 - - + -
450A PHE* 4.5 9.4 - - + -
451A VAL* 1.3 76.5 - - - +
453A MET* 1.3 59.6 + - - +
454A ASN* 3.3 4.4 + - + +
483A PHE* 4.0 27.4 - - + -
518A LEU* 3.9 39.5 - - + -
519A ILE 2.8 13.4 + - - +
520A GLU* 4.3 5.6 - - - -
521A VAL* 2.8 34.2 + - - +
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Residues in contact with MET 453 (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 PRO* 4.2 27.8 - - + -
358A VAL* 4.1 24.5 - - + -
359A PHE* 4.0 26.2 - - + -
376A SER* 3.7 23.1 - - - +
379A THR* 4.6 1.8 - - + +
425A VAL* 3.8 20.2 - - + -
426A ILE 2.8 14.4 + - - +
427A GLY* 3.7 3.4 - - - -
428A ASP* 3.1 24.7 + - - +
451A VAL* 4.4 9.0 - - - +
452A ILE* 1.3 67.2 - - - +
454A ASN* 1.3 59.6 + - - +
455A ASN* 3.5 5.0 + - - +
521A VAL* 3.9 5.4 - - - -
523A THR* 3.9 21.0 + - + +
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Residues in contact with ASN 454 (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 ARG* 2.8 24.3 + - - -
428A ASP* 3.2 18.6 - - + +
452A ILE* 3.3 1.7 + - + +
453A MET* 1.3 72.6 - - - +
455A ASN* 1.3 58.0 + - - +
456A GLY* 3.0 19.4 + - - -
481A ILE 4.1 6.9 + - - -
483A PHE* 4.1 11.6 - - + -
520A GLU* 2.9 36.8 + - + +
521A VAL 2.7 18.4 + - - +
522A SER* 3.7 1.5 - - - -
523A THR* 3.0 13.5 + - - -
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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