Contacts of the helix formed by residues 465 - 479 (chain A) in PDB entry 6HBU
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 ARG 465 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A SER* 5.7 1.4 - - - +
369A TYR* 3.3 54.0 + - + +
371A THR 4.3 5.4 + - - -
372A SER* 4.8 3.0 - - - +
373A PHE* 3.6 39.0 - - - +
376A GLN* 3.1 30.0 + - - -
464A TYR* 1.3 88.7 - - - +
466A VAL* 1.3 63.4 + - - +
467A SER* 3.7 19.9 + - - +
468A SER* 3.2 15.4 + - - +
469A TYR 3.3 2.1 + - - -
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Residues in contact with VAL 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A PHE* 4.3 17.3 - - + -
459A TYR* 3.5 33.3 + - + +
465A ARG* 1.3 74.4 - - - +
467A SER* 1.3 51.9 + - - +
469A TYR* 3.2 5.8 + - - +
470A PHE* 2.7 34.0 + - - +
645A TYR* 3.6 22.4 + - + +
648A LEU* 4.0 29.6 - - + -
649A LEU* 3.8 29.6 - - + +
653A LYS* 4.5 1.1 - - - +
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Residues in contact with SER 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A PHE* 3.3 22.7 - - - -
465A ARG* 3.7 11.6 + - - +
466A VAL* 1.3 79.8 - - - +
468A SER* 1.3 57.8 + - - +
470A PHE* 4.3 2.2 - - - -
471A LEU* 3.1 37.2 + - - +
645A TYR* 3.6 27.8 + - - -
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Residues in contact with SER 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A PHE* 3.6 24.7 - - - -
376A GLN* 3.2 37.1 + - - +
377A LEU* 4.0 14.2 - - - +
380A VAL* 4.0 8.8 - - - +
464A TYR* 3.3 7.4 - - - +
465A ARG* 3.2 12.3 + - - -
467A SER* 1.3 80.2 + - - +
469A TYR* 1.3 62.1 + - - +
472A GLY* 3.1 24.1 + - - -
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Residues in contact with TYR 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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380A VAL* 3.7 19.2 - - + +
383A ARG* 4.6 9.6 - - - -
447A LEU 4.9 0.3 + - - -
448A PHE* 4.3 20.2 - + + -
451A GLU* 3.8 19.4 + - - +
455A PHE* 3.5 34.6 - + + +
464A TYR* 3.6 44.4 - + + +
465A ARG 3.3 1.2 + - - +
466A VAL 3.2 8.5 + - - +
468A SER* 1.3 81.4 + - - +
470A PHE* 1.3 64.9 + - - +
473A LYS* 2.5 63.5 + - - +
648A LEU* 4.8 8.5 - - + -
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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
----------------------------------------------------------
448A PHE* 3.5 37.1 - + - -
466A VAL 2.7 21.0 + - - +
467A SER* 4.0 3.4 - - - +
469A TYR* 1.3 78.3 - - - +
471A LEU* 1.3 73.3 + - + +
473A LYS* 3.9 1.6 - - - +
474A LEU* 3.1 48.2 + - + +
525A LEU* 5.1 0.2 - - + -
641A LEU* 3.4 52.5 - - + -
644A ALA* 4.0 12.8 - - + -
645A TYR* 4.0 27.8 - + + -
648A LEU* 3.8 14.1 - - + -
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Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A PHE* 3.7 26.9 - - + -
377A LEU* 3.7 14.4 - - + -
467A SER* 3.1 18.0 + - - +
470A PHE* 1.3 87.5 - - + +
472A GLY* 1.3 60.8 + - - +
473A LYS 3.4 0.2 - - - -
474A LEU* 3.8 25.0 + - + +
475A LEU* 3.3 28.1 + - - +
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Residues in contact with GLY 472 (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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377A LEU* 3.5 11.8 - - - +
380A VAL* 4.3 4.6 - - - +
381A SER* 3.3 41.3 - - - -
384A SER* 4.5 0.2 + - - -
468A SER 3.1 20.0 + - - -
469A TYR 4.1 0.2 - - - -
471A LEU* 1.3 77.6 - - - +
473A LYS* 1.3 60.5 + - - +
475A LEU* 3.9 4.8 + - - +
476A SER* 3.8 7.8 + - - -
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Residues in contact with LYS 473 (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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380A VAL* 4.4 3.3 - - + +
383A ARG* 5.7 2.7 - - - +
384A SER* 3.6 26.2 - - - +
447A LEU* 3.5 44.6 + - + +
448A PHE* 3.5 24.5 - - + -
451A GLU* 4.4 13.3 - - - +
469A TYR* 2.5 60.8 + - + +
472A GLY* 1.3 74.5 - - - +
474A LEU* 1.3 64.7 + - - +
475A LEU 3.4 0.7 - - - -
476A SER* 3.6 4.4 + - - +
477A ASP 3.6 8.8 + - - -
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Residues in contact with LEU 474 (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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447A LEU* 4.6 4.7 - - + -
448A PHE* 5.1 0.9 - - + -
470A PHE* 3.1 43.7 + - + +
471A LEU* 3.8 25.6 - - + +
472A GLY 3.4 0.2 - - - -
473A LYS* 1.3 78.1 - - - +
475A LEU* 1.3 53.5 + - + +
477A ASP* 2.8 6.7 + - + +
478A LEU* 2.5 51.2 + - + +
525A LEU* 3.7 30.5 - - + -
641A LEU* 3.8 25.8 - - + -
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Residues in contact with LEU 475 (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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377A LEU* 4.7 16.2 - - + -
381A SER* 4.8 12.8 - - - +
385A PHE* 3.4 22.6 - - + -
471A LEU* 3.3 19.5 + - + +
472A GLY 4.1 6.1 - - - +
473A LYS 3.4 0.8 - - - -
474A LEU* 1.3 77.8 - - + +
476A SER* 1.3 56.9 + - - +
477A ASP 3.4 0.2 - - - -
478A LEU* 4.1 22.9 - - + -
479A LEU* 3.6 30.9 + - + +
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Residues in contact with SER 476 (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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381A SER 3.8 8.8 + - - -
384A SER* 3.2 40.2 - - - -
385A PHE* 3.8 15.8 - - - -
388A LEU* 3.5 23.1 - - - +
447A LEU* 5.3 3.1 - - - +
472A GLY 3.8 5.4 + - - -
473A LYS* 3.6 10.6 + - - -
474A LEU 3.1 0.8 - - - -
475A LEU* 1.3 76.9 - - - +
477A ASP* 1.3 58.0 + - - +
480A PRO* 3.4 17.3 - - - +
481A MET* 4.7 1.9 - - - +
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Residues in contact with ASP 477 (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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443A SER 4.9 0.9 - - - +
444A ALA* 3.6 21.5 - - - +
447A LEU* 3.7 37.6 - - + +
473A LYS 3.6 1.0 + - - -
474A LEU* 2.8 7.3 + - + +
476A SER* 1.3 80.0 - - - +
478A LEU* 1.3 63.5 + - - +
480A PRO* 4.2 2.7 - - - -
481A MET* 3.3 24.1 - - - +
482A ARG* 2.7 36.2 + - - -
521A SER* 4.5 5.7 - - - -
525A LEU* 5.0 4.3 - - - +
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Residues in contact with LEU 478 (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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474A LEU* 2.5 34.9 + - + +
475A LEU* 4.3 16.2 - - + -
477A ASP* 1.3 72.2 - - - +
479A LEU* 1.3 82.6 + - + +
482A ARG* 3.1 11.2 + - - +
483A MET* 2.9 31.4 + - + +
518A TYR* 3.4 43.7 - - + +
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Residues in contact with LEU 479 (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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385A PHE* 4.4 13.9 - - + -
475A LEU* 3.6 27.4 + - + +
478A LEU* 1.3 96.8 - - + +
480A PRO* 1.3 71.0 - - + +
481A MET 3.3 0.9 + - - -
483A MET* 3.7 32.2 - - + +
484A LEU* 3.3 26.9 + - - +
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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