Contacts of the helix formed by residues 522 - 534 (chain A) in PDB entry 3BK0
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 SER 522 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451A VAL 4.4 3.2 + - - -
513A TYR* 3.8 11.2 - - - -
520A PHE* 3.1 6.5 - - - +
521A PRO* 1.3 81.8 - - - +
523A ILE* 1.3 63.5 + - - +
524A PRO* 3.4 13.5 - - - +
525A LEU* 3.0 34.7 + - - +
526A LEU* 3.1 17.5 + - - +
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Residues in contact with ILE 523 (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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455A LEU* 4.0 26.5 - - + -
460A TRP* 4.3 0.7 - - + -
482A VAL* 4.3 6.1 - - + -
491A TYR* 3.4 46.4 - - + -
506A ILE* 3.8 27.4 - - + -
513A TYR* 3.7 32.3 - - + -
522A SER* 1.3 69.1 - - - +
524A PRO* 1.4 68.5 - - + +
526A LEU* 3.1 8.4 + - + +
527A ILE* 2.8 40.7 + - + +
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Residues in contact with PRO 524 (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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451A VAL* 3.4 27.9 - - + +
453A LYS 3.8 9.6 - - - +
455A LEU* 4.3 13.5 - - + +
458A GLN* 3.6 37.0 - - + +
460A TRP* 3.8 17.6 - - + -
522A SER* 3.4 11.9 - - - +
523A ILE* 1.4 93.4 - - + +
525A LEU* 1.3 56.1 + - - +
527A ILE* 3.4 1.7 + - - +
528A ASP* 2.9 29.8 + - - +
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Residues in contact with LEU 525 (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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451A VAL* 3.7 23.1 - - + +
520A PHE* 3.8 18.9 - - + -
521A PRO* 3.6 31.9 - - + -
522A SER* 3.0 27.9 + - - +
524A PRO* 1.3 75.7 - - - +
526A LEU* 1.3 57.7 + - - +
528A ASP* 3.4 7.4 + - - +
529A HIS* 3.0 28.1 + - - +
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Residues in contact with LEU 526 (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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493A LEU* 6.1 0.7 - - + -
506A ILE* 3.8 34.8 - - + -
513A TYR* 4.0 4.5 - - + +
514A ARG* 3.8 22.2 - - - +
515A LEU* 4.5 12.3 - - + +
518A GLU 4.2 9.0 - - - +
520A PHE* 3.6 32.6 - - + +
522A SER 3.1 12.9 + - - +
523A ILE* 3.5 10.5 - - + +
525A LEU* 1.3 73.4 - - - +
527A ILE* 1.3 67.8 + - + +
529A HIS* 3.2 7.1 + - + +
530A LEU* 3.0 45.2 + - + +
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Residues in contact with ILE 527 (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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460A TRP* 3.7 33.7 - - + +
480A PHE* 3.7 28.7 - - + -
482A VAL* 3.8 19.7 - - + -
493A LEU* 4.0 27.8 - - + -
506A ILE* 5.2 2.5 - - + -
523A ILE* 2.8 29.3 + - + +
524A PRO 3.8 3.8 - - - +
526A LEU* 1.3 74.3 - - + +
528A ASP* 1.3 65.2 + - - +
530A LEU* 3.3 6.9 + - + +
531A LEU* 2.9 29.3 + - + +
545A LEU* 4.3 6.4 - - + +
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Residues in contact with ASP 528 (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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451A VAL* 4.4 25.6 - - + +
524A PRO 2.9 18.1 + - - +
525A LEU* 3.6 8.3 - - - +
527A ILE* 1.3 78.5 - - - +
529A HIS* 1.3 52.4 + - - +
531A LEU* 3.9 5.4 - - - +
532A SER* 2.7 49.5 + - - -
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Residues in contact with HIS 529 (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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518A GLU* 3.5 34.2 + - + +
520A PHE* 3.3 36.8 - + + -
525A LEU 3.0 10.2 + - - +
526A LEU* 3.3 10.8 - - + +
528A ASP* 1.3 78.9 + - - +
530A LEU* 1.3 68.1 + - + +
532A SER* 3.8 4.7 - - - -
533A THR* 2.7 57.9 + - + +
535A GLN* 3.0 27.8 + - - -
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Residues in contact with LEU 530 (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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493A LEU* 4.0 13.9 - - + -
515A LEU* 3.8 27.4 - - + -
526A LEU* 3.0 37.3 + - + +
527A ILE* 3.8 4.7 - - + +
529A HIS* 1.3 89.1 - - + +
531A LEU* 1.3 63.5 + - - +
533A THR* 4.1 2.7 - - - -
534A GLN* 3.0 24.9 + - - -
535A GLN* 3.8 20.1 + - + +
536A PRO 4.7 2.7 - - - +
537A LEU* 3.8 27.1 - - + +
545A LEU* 3.8 20.8 + - + +
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Residues in contact with LEU 531 (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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480A PHE* 3.8 26.5 - - + -
527A ILE* 2.9 20.9 + - + +
528A ASP* 3.9 4.7 - - - +
530A LEU* 1.3 78.6 - - - +
532A SER* 1.3 61.7 + - - +
533A THR 3.5 0.3 + - - -
534A GLN* 2.8 27.4 + - - +
545A LEU* 3.6 34.5 - - + +
546A HIS 3.6 21.8 - - - +
548A ALA* 5.1 6.7 - - + +
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Residues in contact with SER 532 (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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528A ASP* 2.7 35.8 + - - -
529A HIS* 3.4 7.1 + - - -
531A LEU* 1.3 77.9 - - - +
533A THR* 1.3 65.6 + - - +
534A GLN* 3.4 3.3 - - - +
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Residues in contact with THR 533 (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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529A HIS* 2.7 46.7 + - + +
530A LEU* 3.9 0.3 + - - -
532A SER* 1.3 82.4 - - - +
534A GLN* 1.3 69.4 + - - +
535A GLN* 3.2 35.4 + - - +
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Residues in contact with GLN 534 (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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530A LEU 3.0 12.2 + - - -
531A LEU* 2.8 30.0 + - - +
532A SER 3.4 2.9 - - - +
533A THR* 1.3 80.0 - - - +
535A GLN* 1.3 64.7 + - - +
536A PRO* 3.6 4.2 - - - +
544A VAL* 3.3 31.6 - - + +
545A LEU 2.9 24.3 + - - +
546A HIS* 4.8 10.0 + - - +
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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