Contacts of the strand formed by residues 454 - 459 (chain A) in PDB entry 3BRF
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 VAL 454 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A LEU* 3.8 5.9 - - - +
430A PHE* 3.0 55.3 + - + +
445A ARG* 4.0 6.8 + - - +
452A GLY 4.9 1.1 - - - +
453A SER* 1.3 73.1 - - - +
455A VAL* 1.3 61.6 + - - +
468A ARG* 4.0 6.5 - - + +
469A LEU 3.3 4.9 - - - +
470A ARG* 4.2 23.3 - - + +
501A ILE* 3.1 36.1 - - + -
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Residues in contact with VAL 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 3.6 38.4 - - + -
428A HIS 3.1 13.0 - - - +
429A LEU* 3.8 21.8 - - + -
430A PHE* 4.7 1.3 - - - -
449A VAL* 3.8 11.4 - - + -
453A SER 4.4 5.2 - - - +
454A VAL* 1.3 73.2 - - - +
456A LYS* 1.3 68.4 + - - +
457A LEU* 4.3 9.8 + - + -
467A PRO 4.4 0.5 - - - +
468A ARG* 3.6 3.6 - - - -
469A LEU* 2.6 40.3 + - + +
471A ILE* 4.8 6.1 - - + -
498A PHE* 4.5 13.9 - - + -
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Residues in contact with LYS 456 (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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426A THR 3.2 5.2 - - - +
427A ILE* 3.4 1.7 - - - -
428A HIS* 2.7 44.8 + - + +
430A PHE* 4.2 15.7 - - + -
439A THR* 3.9 15.1 + - - +
442A PHE* 3.6 48.9 - - + -
455A VAL* 1.3 77.2 - - - +
457A LEU* 1.3 63.6 + - - +
458A VAL* 4.4 1.1 - - + -
465A ALA* 4.5 7.1 - - + +
466A LEU 3.4 13.5 + - - +
467A PRO* 4.5 0.9 - - - +
468A ARG* 3.4 35.3 - - + +
944D VAL* 3.4 30.7 - - - +
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Residues in contact with LEU 457 (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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392A VAL* 4.0 27.1 - - + -
394A LEU* 3.7 25.4 - - + -
408A LEU* 4.9 0.9 - - + -
415A PHE* 4.4 2.1 - - + -
425A PHE* 4.1 19.3 - - + -
426A THR 3.6 0.4 - - - -
427A ILE* 4.0 20.0 - - + -
455A VAL* 4.3 6.5 + - + -
456A LYS* 1.3 74.8 - - - +
458A VAL* 1.3 59.7 + - - +
459A ASP 4.3 0.2 - - - -
464A ILE 4.2 0.2 - - - +
465A ALA* 3.3 6.2 - - - +
466A LEU* 3.1 56.5 + - + +
467A PRO 5.4 1.0 + - - -
469A LEU* 4.7 8.2 - - + +
498A PHE* 4.1 24.2 - - + -
508A LEU* 6.4 0.7 - - + -
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Residues in contact with VAL 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A PHE* 3.4 5.6 - - - +
426A THR* 2.7 43.8 + - - +
428A HIS* 3.6 30.3 - - + +
442A PHE* 4.1 14.8 - - + -
456A LYS* 4.3 3.1 - - + +
457A LEU* 1.3 78.8 - - - +
459A ASP* 1.3 75.3 + - - +
460A SER 3.4 0.2 + - - -
463A GLY* 4.2 18.6 - - - +
464A ILE 3.7 3.4 - - - +
465A ALA* 4.1 10.3 - - + -
940D ILE* 4.9 7.0 - - + -
941D ASN 5.4 1.1 - - - +
942D ALA* 4.3 8.5 - - + -
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Residues in contact with ASP 459 (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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409A HIS* 6.0 0.5 - - - -
410A VAL* 3.3 31.5 + - + +
423A GLY* 4.8 5.9 - - - -
424A ALA 4.4 3.5 + - - +
425A PHE* 3.6 18.0 - - - -
426A THR* 5.2 0.6 + - - -
458A VAL* 1.3 76.4 - - - +
460A SER* 1.3 70.3 + - - +
461A VAL* 3.4 16.3 + - - +
462A THR* 2.6 44.8 + - - +
463A GLY* 3.3 15.6 + - - -
464A ILE 2.9 19.2 + - - +
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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