Contacts of the strand formed by residues 463 - 471 (chain A) in PDB entry 1B0P
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 463 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A TRP* 3.5 33.9 - - + -
424A GLY 4.2 0.2 - - - +
455A TYR 3.7 3.4 - - - +
456A ASP* 2.9 49.6 + - + +
461A GLY 4.0 0.6 + - - -
462A GLY* 1.3 74.1 - - - -
464A THR* 1.3 71.5 + - - +
465A ILE* 3.6 19.1 - - + -
494A TYR* 3.5 21.3 + - + +
498A TYR* 4.4 15.3 - - + +
649A GLN* 4.2 30.3 - - + +
1199B ASP* 5.0 1.2 - - - +
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Residues in contact with THR 464 (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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423A TRP* 3.4 4.3 - - - -
424A GLY* 2.8 45.8 + - - +
425A LEU 5.1 4.9 - - - +
426A GLY* 5.3 4.2 - - - -
430A THR* 4.7 8.1 - - + -
431A VAL* 3.8 25.3 - - + +
453A PHE* 5.9 0.2 - - + -
454A SER 3.4 12.4 + - - +
455A TYR* 3.9 16.3 - - - -
462A GLY 5.1 0.9 - - - -
463A ILE* 1.3 80.2 + - - +
465A ILE* 1.3 66.7 + - - +
466A SER* 3.9 12.8 - - - +
1199B ASP* 5.5 2.4 + - - +
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Residues in contact with ILE 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A GLN* 3.8 16.4 - - + +
422A PHE 3.1 14.8 - - - +
423A TRP* 3.8 35.0 - - + +
453A PHE* 4.7 0.2 - - - -
454A SER* 2.9 45.4 + - - +
463A ILE* 3.6 23.1 - - + -
464A THR* 1.3 76.8 - - - +
466A SER* 1.3 71.9 + - - +
467A HIS* 3.4 28.2 + - + +
649A GLN* 5.6 2.9 - - + +
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Residues in contact with SER 466 (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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420A CYS 3.5 0.3 - - - +
421A GLN* 3.2 8.1 - - - -
422A PHE* 2.7 40.5 + - - +
430A THR* 4.2 1.2 - - - +
431A VAL* 4.3 1.2 - - - +
434A ASN* 2.7 35.0 + - - -
452A TYR 3.8 0.2 - - - -
453A PHE* 3.3 25.3 - - - -
464A THR* 3.9 14.2 - - - +
465A ILE* 1.3 77.9 - - - +
467A HIS* 1.3 61.1 + - - +
468A LEU* 4.2 2.0 - - - -
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Residues in contact with HIS 467 (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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420A CYS 3.5 5.4 - - - -
421A GLN* 4.1 10.1 + - + -
450A GLN* 4.6 3.9 - - - +
451A GLY* 3.5 1.7 - - - -
452A TYR* 2.7 54.8 + - + +
454A SER* 4.2 6.7 + - - -
465A ILE* 3.4 37.3 + - + +
466A SER* 1.3 74.8 - - - +
468A LEU* 1.3 62.0 + - - +
469A ARG* 5.8 0.4 - - - +
479A TYR 5.8 0.4 - - - +
480A LEU* 3.6 38.2 - - + +
481A VAL* 3.3 46.6 + - + +
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Residues in contact with LEU 468 (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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418A ILE 3.7 0.3 - - - +
419A GLN* 3.5 0.2 - - - -
420A CYS* 2.9 34.4 + - + +
422A PHE* 3.9 28.3 - - + -
434A ASN* 4.1 17.0 - - + +
437A ALA* 4.7 6.1 - - + -
438A ILE* 3.6 31.0 - - + -
450A GLN* 3.4 6.3 - - - +
451A GLY* 3.8 4.9 - - - -
453A PHE* 4.0 19.7 - - + -
466A SER* 4.6 0.2 - - - -
467A HIS* 1.3 83.5 - - - +
469A ARG* 1.3 67.6 + - - +
470A PHE* 3.8 31.4 - - + -
481A VAL* 4.1 1.2 - - - +
567A PHE* 5.0 1.3 - - + -
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Residues in contact with ARG 469 (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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413A THR* 3.8 8.0 - - - +
417A THR* 4.1 11.7 - - + -
418A ILE 3.1 5.2 - - - +
419A GLN* 2.4 49.5 + - + +
449A ALA* 3.4 2.8 - - - -
450A GLN* 3.0 55.3 + - + +
467A HIS* 5.8 0.6 - - - +
468A LEU* 1.3 80.5 - - - +
470A PHE* 1.3 67.2 + - - +
475A ILE* 3.4 17.3 - - + +
477A SER* 3.3 28.3 + - - -
479A TYR* 2.6 37.0 + - - -
480A LEU 2.9 18.0 + - - -
481A VAL* 3.6 13.5 - - + +
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Residues in contact with PHE 470 (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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417A THR* 3.2 3.5 - - - -
418A ILE* 2.7 46.2 + - + +
420A CYS* 4.5 5.4 - - - -
437A ALA 4.8 0.4 - - - -
438A ILE* 4.2 13.7 - - + -
441A ILE* 3.6 41.3 - - + -
447A LEU* 4.5 12.1 - - + -
448A PHE 3.3 6.1 - - - +
449A ALA* 3.8 24.7 - - + -
450A GLN 5.0 0.4 - - - -
468A LEU* 3.8 41.3 - - + -
469A ARG* 1.3 80.1 - - - +
471A GLY* 1.3 58.9 + - - +
475A ILE* 4.4 2.5 - - - -
567A PHE* 4.0 17.0 - + - -
573A VAL* 3.8 26.2 - - + -
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Residues in contact with GLY 471 (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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416A GLY 3.6 12.3 - - - -
417A THR* 4.3 8.1 - - - -
418A ILE* 5.7 0.4 - - - -
447A LEU* 3.5 12.6 - - - +
448A PHE* 2.6 41.7 + - - +
470A PHE* 1.3 77.7 - - - +
472A GLU* 1.3 58.4 + - - -
473A LYS 3.2 9.8 + - - -
475A ILE* 4.2 2.5 - - - +
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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