Contacts of the helix formed by residues 465 - 477 (chain A) in PDB entry 1HS6
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 THR 465 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A PHE* 3.4 29.0 + - - +
343A LEU* 3.9 29.8 - - + +
461A ASP 4.7 2.9 + - - -
462A MET* 3.1 15.6 + - + -
464A LEU* 1.3 77.2 - - - +
466A ASN* 1.3 66.6 + - - +
467A ALA 3.2 0.4 - - - -
468A CYS* 2.8 17.2 + - - +
469A ILE* 3.1 32.6 + - + +
501A GLU* 5.2 3.8 - - + +
505A GLN* 4.0 14.8 - - - +
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Residues in contact with ASN 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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462A MET* 3.1 49.5 + - - +
463A THR* 4.1 9.0 + - - +
464A LEU 3.5 0.4 - - - -
465A THR* 1.3 77.7 - - - +
467A ALA* 1.3 62.8 + - - +
469A ILE* 3.3 9.0 + - - +
470A ALA* 3.0 23.9 + - - +
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Residues in contact with ALA 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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463A THR 4.8 1.6 + - - +
464A LEU 4.1 2.6 + - - -
465A THR 3.1 1.0 + - - -
466A ASN* 1.3 77.9 - - - +
468A CYS* 1.3 61.9 + - - +
470A ALA* 3.7 6.8 - - - +
471A LEU* 3.1 26.0 + - - +
494A LEU* 3.6 29.3 - - + +
498A GLN* 4.3 11.2 - - - +
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Residues in contact with CYS 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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340A PHE* 4.2 2.5 - - - -
464A LEU 3.7 17.9 - - - -
465A THR 2.8 7.8 + - - +
467A ALA* 1.3 75.1 - - - +
469A ILE* 1.3 59.7 + - - +
471A LEU* 3.4 2.6 + - - +
472A SER* 2.9 30.5 + - - -
494A LEU* 5.3 2.9 - - - -
498A GLN* 3.4 41.3 - - - -
501A GLU* 4.0 13.9 - - + -
502A PHE* 4.1 13.0 - - - +
505A GLN* 3.2 22.0 - - - +
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Residues in contact with ILE 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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343A LEU* 5.8 0.7 - - + -
462A MET* 3.7 19.7 - - + -
465A THR* 3.1 30.6 + - + +
466A ASN* 3.7 10.5 - - - +
468A CYS* 1.3 75.8 - - - +
470A ALA* 1.3 68.3 + - - +
472A SER* 3.3 1.5 + - - +
473A GLN* 2.9 37.4 + - + +
505A GLN* 3.2 22.4 - - - +
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Residues in contact with ALA 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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466A ASN 3.0 17.0 + - - +
467A ALA* 3.7 8.1 - - - +
469A ILE* 1.3 78.5 - - - +
471A LEU* 1.3 59.3 + - - +
473A GLN* 3.8 3.3 - - - +
474A ARG* 3.0 39.0 + - - +
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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
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467A ALA 3.1 14.1 + - - +
468A CYS* 3.9 0.7 - - - +
469A ILE 3.1 0.6 - - - -
470A ALA* 1.3 79.1 - - - +
472A SER* 1.3 65.9 + - - +
474A ARG* 3.2 33.7 + - - +
475A TRP* 3.1 32.9 + - + +
486A PHE* 4.6 0.2 - - + -
490A ASP* 4.2 11.9 - - + +
491A LEU* 4.0 23.1 - - + -
494A LEU* 4.3 13.9 - - + -
502A PHE* 3.6 27.6 - - + -
524A TYR* 3.7 24.0 - - - +
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Residues in contact with SER 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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468A CYS 2.9 17.0 + - - -
469A ILE* 3.3 4.2 + - - -
471A LEU* 1.3 73.3 - - - +
473A GLN* 1.3 62.2 + - - +
475A TRP* 3.2 2.8 + - - +
476A ILE* 2.8 41.3 + - - +
502A PHE* 3.5 14.5 - - - -
505A GLN* 2.9 36.4 + - - +
506A THR* 3.4 21.1 - - - -
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Residues in contact with GLN 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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469A ILE* 2.9 32.9 + - + +
470A ALA* 3.8 4.0 - - - +
472A SER* 1.3 80.5 + - - +
474A ARG* 1.3 62.7 + - + +
476A ILE* 3.6 22.9 - - - +
477A THR* 2.8 48.0 + - + +
509A ARG* 3.6 17.3 + - - +
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Residues in contact with ARG 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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470A ALA* 3.0 26.3 + - - +
471A LEU* 3.5 22.9 - - - +
472A SER 3.2 0.4 - - - -
473A GLN* 1.3 77.9 - - - +
475A TRP* 1.3 58.6 + - - +
477A THR* 3.7 4.9 + - - -
478A ALA* 2.9 29.5 + - - +
482A ASP* 5.5 0.5 - - - +
485A SER* 4.6 8.7 + - - -
486A PHE* 3.5 44.7 - - + +
490A ASP* 3.9 17.8 + - - +
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Residues in contact with TRP 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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471A LEU* 3.1 23.2 + - + +
472A SER* 3.7 7.9 - - - +
474A ARG* 1.3 76.7 - - - +
476A ILE* 1.3 66.2 + - - +
477A THR 3.2 0.7 + - - -
478A ALA* 3.3 13.6 + - - +
483A LEU* 4.2 6.3 - - + -
486A PHE* 3.4 53.4 - + + -
502A PHE* 3.6 17.9 - + + -
506A THR* 5.0 2.5 - - + -
512A LEU* 4.1 11.8 - - + +
516A HIS* 3.3 48.7 - + + -
519A ARG* 3.9 9.2 - - + -
520A MET* 3.4 47.6 - - + -
523A VAL* 4.0 1.3 - - + -
524A TYR* 2.9 38.6 + + - -
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Residues in contact with ILE 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A SER* 2.8 33.4 + - - +
473A GLN* 3.6 21.5 - - - +
475A TRP* 1.3 73.2 - - - +
477A THR* 1.3 66.3 + - + +
478A ALA 3.9 1.0 + - - +
505A GLN* 4.2 12.1 - - + +
506A THR* 4.5 14.8 - - + -
509A ARG* 3.7 61.9 - - + +
512A LEU* 4.6 11.8 - - + +
516A HIS* 5.9 0.3 - - - -
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Residues in contact with THR 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A GLN* 2.8 41.3 + - + +
474A ARG* 3.7 5.5 + - - -
476A ILE* 1.3 85.7 - - + +
478A ALA* 1.3 68.2 + - - +
479A LYS* 3.6 11.8 + - - +
482A ASP* 4.5 1.4 - - - +
509A ARG* 5.8 2.0 - - - +
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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