Contacts of the helix formed by residues 462 - 474 (chain H) in PDB entry 1B6C
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 GLU 462 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460H SER 3.4 5.5 + - - -
461H CYS* 1.3 71.8 - - - +
463H ALA* 1.3 63.0 + - - +
465H ARG* 3.1 36.3 + - - +
466H VAL* 3.0 33.2 + - + +
495H LEU* 4.0 11.0 - - + +
498H GLN* 3.7 25.4 + - - +
499H GLU* 4.7 6.4 - - - +
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Residues in contact with ALA 463 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299H VAL* 3.5 32.3 - - + -
302H MET* 4.0 11.0 - - + -
303H ILE* 4.5 0.7 - - + -
461H CYS* 3.2 10.0 + - - -
462H GLU* 1.3 78.2 - - - +
464H LEU* 1.3 62.2 + - - +
466H VAL* 3.4 3.3 + - - +
467H MET* 3.2 25.5 + - - +
495H LEU* 4.1 13.0 - - + +
499H GLU* 3.6 20.6 + - - +
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Residues in contact with LEU 464 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299H VAL* 4.8 0.2 - - + -
302H MET* 3.6 29.4 - - + -
412H ALA* 4.0 20.2 - - + +
415H CYS* 4.1 17.3 - - + -
417H ILE* 3.9 15.9 - - + -
457H ARG* 5.5 4.0 - - - +
458H TRP* 3.5 41.4 - - + +
461H CYS* 3.2 30.0 + - + +
463H ALA* 1.3 77.0 - - + +
465H ARG* 1.3 56.4 + - - +
467H MET* 3.5 3.4 - - + +
468H ALA* 2.7 36.4 + - - +
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Residues in contact with ARG 465 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458H TRP 3.2 14.5 + - - +
459H GLN* 3.2 43.8 + - - +
460H SER 3.4 15.4 + - - -
461H CYS 3.1 9.7 + - - +
462H GLU* 3.1 50.6 + - - +
464H LEU* 1.3 78.3 - - - +
466H VAL* 1.3 59.4 + - - +
468H ALA* 3.8 5.4 - - - +
469H LYS* 3.0 29.3 + - + +
472H ARG* 4.7 1.3 + - - +
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Residues in contact with VAL 466 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462H GLU* 3.0 24.9 + - + +
463H ALA 3.8 4.7 - - - +
465H ARG* 1.3 77.0 - - + +
467H MET* 1.3 62.5 + - - +
469H LYS* 3.2 8.1 + - + +
470H ILE* 2.9 42.4 + - + +
491H THR* 3.9 22.7 - - - +
492H LEU* 4.5 2.2 - - + -
495H LEU* 3.9 33.4 - - + -
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Residues in contact with MET 467 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302H MET* 3.8 37.5 - - + -
303H ILE* 5.7 2.7 - - - -
306H ALA* 3.8 23.8 - - + -
408H PHE* 3.7 48.9 - - + +
411H ILE* 5.1 1.8 - - + -
412H ALA* 4.8 9.4 - - + +
463H ALA 3.2 14.5 + - - +
464H LEU* 3.5 9.6 - - - +
466H VAL* 1.3 78.3 - - - +
468H ALA* 1.3 51.3 + - - +
470H ILE* 3.0 7.9 + - - +
471H MET* 2.8 40.1 + - - +
492H LEU* 4.2 18.6 - - - -
495H LEU* 5.3 3.6 - - + -
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Residues in contact with ALA 468 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454H ILE* 3.8 23.6 - - + +
458H TRP* 4.2 7.0 - - + -
459H GLN* 4.1 5.8 - - - +
464H LEU 2.7 21.7 + - - +
465H ARG* 3.8 4.5 - - - +
467H MET* 1.3 72.0 - - - +
469H LYS* 1.3 64.2 + - - +
471H MET* 3.3 14.8 + - - +
472H ARG* 3.1 44.3 + - - +
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Residues in contact with LYS 469 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465H ARG* 3.0 19.9 + - + +
466H VAL* 3.6 7.0 - - - +
468H ALA* 1.3 77.8 - - - +
470H ILE* 1.3 57.6 + - + +
472H ARG* 3.5 24.4 + - - +
473H GLU* 2.6 66.3 + - + +
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Residues in contact with ILE 470 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408H PHE* 3.8 23.8 - - + -
466H VAL* 2.9 23.2 + - + +
467H MET* 3.0 10.1 + - - +
469H LYS* 1.3 74.8 - - + +
471H MET* 1.3 66.8 + - - +
473H GLU* 3.1 9.6 + - - +
474H CYS* 3.0 24.6 + - - -
483H LEU* 4.2 9.6 - - + -
488H ILE* 3.9 35.2 - - + -
491H THR* 3.9 19.3 - - + +
492H LEU* 3.4 33.0 - - + -
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Residues in contact with MET 471 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405H GLY* 4.0 14.6 - - - +
408H PHE* 4.2 13.0 - - + +
409H TRP* 3.0 50.9 - - + -
412H ALA* 4.8 2.5 - - - -
454H ILE* 4.1 6.1 - - + -
458H TRP* 3.7 23.1 - - + -
467H MET* 2.8 25.3 + - - +
468H ALA* 3.5 11.7 - - - +
470H ILE* 1.3 72.5 - - - +
472H ARG* 1.3 58.2 + - - +
474H CYS* 2.9 22.5 + - - +
475H TRP* 3.0 46.9 + - + -
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Residues in contact with ARG 472 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454H ILE* 3.7 24.6 - - + +
459H GLN* 3.1 32.5 + - - +
465H ARG* 4.7 1.0 + - - +
468H ALA* 3.1 30.5 + - - +
469H LYS* 3.5 32.7 - - - +
470H ILE 3.3 0.2 - - - -
471H MET* 1.3 79.0 - - - +
473H GLU* 1.3 58.3 + - + +
475H TRP* 3.1 24.1 + - + +
476H TYR* 3.7 23.1 + - + +
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Residues in contact with GLU 473 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469H LYS* 2.6 58.0 + - + +
470H ILE 3.1 1.5 + - - +
472H ARG* 1.3 76.0 - - - +
474H CYS* 1.3 58.3 + - - +
476H TYR* 2.8 38.8 + - + -
481H ALA 5.4 0.2 - - - +
482H ARG* 3.1 29.1 - - - +
483H LEU* 3.1 46.5 + - + +
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Residues in contact with CYS 474 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401H ILE* 3.4 41.3 - - - +
402H TYR* 3.4 11.3 - - - +
405H GLY* 3.8 21.5 - - - -
408H PHE* 5.8 0.4 - - - -
470H ILE* 3.0 21.3 + - - -
471H MET 2.9 11.2 + - - +
473H GLU* 1.3 81.0 - - - +
475H TRP* 1.3 61.1 + - + +
476H TYR 3.6 0.9 - - - -
482H ARG* 3.2 23.6 + - - -
483H LEU* 5.0 1.3 - - - -
488H ILE* 3.6 22.4 - - - -
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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