Contacts of the helix formed by residues 485 - 497 (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 ALA 485 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310H ALA* 4.1 5.9 - - - +
313H LEU* 4.2 8.1 - - + -
314H ALA* 3.7 31.4 - - - +
317H HIS* 4.1 15.8 + - + +
401H ILE* 3.5 24.3 - - + +
404H MET* 5.3 2.7 - - + -
484H THR* 1.3 73.2 + - - +
486H LEU* 1.3 58.7 + - - +
488H ILE* 3.3 8.9 + - - +
489H LYS* 2.9 26.9 + - - +
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Residues in contact with LEU 486 (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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314H ALA* 4.0 7.5 - - + +
318H MET* 4.2 26.9 - - + -
484H THR* 3.1 11.9 - - + +
485H ALA* 1.3 76.2 - - - +
487H ARG* 1.3 60.8 + - - +
489H LYS* 2.9 23.3 + - + +
490H LYS* 2.8 61.5 + - + +
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Residues in contact with ARG 487 (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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483H LEU* 4.1 22.4 - - + -
484H THR* 2.9 31.0 - - + +
486H LEU* 1.3 76.1 - - - +
488H ILE* 1.3 61.2 + - - +
490H LYS* 3.0 40.0 + - - +
491H THR* 2.8 43.4 + - + +
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Residues in contact with ILE 488 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310H ALA* 3.9 8.7 - - + -
401H ILE* 4.4 9.2 - - + -
404H MET* 4.4 15.0 - - - -
408H PHE* 3.6 27.8 - - + -
470H ILE* 3.9 12.1 - - + -
474H CYS* 3.6 31.2 - - - -
483H LEU* 3.8 22.4 - - + -
484H THR 3.0 15.9 + - - +
485H ALA* 3.7 6.3 - - - +
487H ARG* 1.3 75.4 - - - +
489H LYS* 1.3 64.0 + - - +
491H THR* 4.1 6.4 - - - +
492H LEU* 3.0 37.2 + - + +
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Residues in contact with LYS 489 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307H LEU* 4.1 8.0 - - + +
310H ALA* 4.1 9.9 - - + +
311H SER* 3.4 35.7 - - - +
314H ALA* 4.8 4.0 - - + -
485H ALA 2.9 12.6 + - - +
486H LEU* 2.9 31.4 + - + +
488H ILE* 1.3 78.8 - - - +
490H LYS* 1.3 60.5 + - - +
492H LEU* 3.6 4.3 - - - +
493H SER* 2.9 50.2 + - - +
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Residues in contact with LYS 490 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486H LEU* 2.8 49.0 + - + +
487H ARG* 3.0 45.0 + - - +
489H LYS* 1.3 80.0 - - - +
491H THR* 1.3 66.8 + - + +
492H LEU 3.0 1.1 - - - -
493H SER* 2.8 18.5 + - - -
494H GLN* 3.0 13.6 + - - +
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Residues in contact with THR 491 (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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466H VAL* 3.9 20.6 - - - +
470H ILE* 3.9 13.7 - - + +
483H LEU* 5.4 4.0 - - + -
487H ARG* 2.8 39.0 + - + +
488H ILE* 4.1 5.2 - - - -
490H LYS* 1.3 74.7 - - + +
492H LEU* 1.3 56.3 + - - +
494H GLN* 3.5 9.6 + - - +
495H LEU* 3.1 26.3 + - - +
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Residues in contact with LEU 492 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303H ILE* 4.2 9.4 - - + +
306H ALA* 3.8 38.6 - - + +
307H LEU* 3.9 17.2 - - + +
310H ALA* 4.6 0.7 - - + -
408H PHE* 3.9 4.7 - - + -
466H VAL* 4.5 1.1 - - + -
467H MET* 4.2 14.6 - - - -
470H ILE* 3.4 24.0 - - + -
488H ILE* 3.0 37.1 + - + +
489H LYS* 3.6 4.5 - - - +
491H THR* 1.3 79.0 + - - +
493H SER* 1.3 59.2 + - - +
495H LEU* 3.5 20.6 + - + +
496H SER* 2.9 28.2 + - - -
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Residues in contact with SER 493 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307H LEU* 4.3 11.5 - - - +
489H LYS* 2.9 38.5 + - - +
490H LYS* 2.8 12.2 + - - -
492H LEU* 1.3 75.4 - - - +
494H GLN* 1.3 64.5 + - - +
496H SER* 3.2 7.9 + - - -
497H GLN* 3.1 36.3 + - - +
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Residues in contact with GLN 494 (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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490H LYS 3.0 10.6 + - - +
491H THR* 3.7 11.7 - - - +
493H SER* 1.3 76.4 - - - +
495H LEU* 1.3 63.5 + - - +
497H GLN* 3.1 19.8 + - - +
498H GLN* 3.1 61.6 + - - +
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Residues in contact with LEU 495 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303H ILE* 4.0 25.4 - - + -
462H GLU* 4.0 18.2 - - - +
463H ALA* 4.1 17.3 - - - +
466H VAL* 3.9 38.1 - - + -
467H MET* 5.3 1.8 - - + -
491H THR 3.1 17.4 + - - +
492H LEU* 3.6 14.8 - - + +
493H SER 3.2 0.2 - - - -
494H GLN* 1.3 78.8 - - - +
496H SER* 1.3 62.0 + - - +
498H GLN* 3.1 20.4 + - - +
499H GLU* 3.0 35.0 + - - +
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Residues in contact with SER 496 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303H ILE* 3.9 24.0 - - - +
307H LEU* 4.3 13.5 - - - +
492H LEU 2.9 17.7 + - - -
493H SER* 3.2 9.6 + - - -
495H LEU* 1.3 77.2 - - - +
497H GLN* 1.3 60.8 + - - +
498H GLN 3.4 0.2 - - - -
499H GLU* 3.8 2.7 + - - +
500H GLY 3.5 26.0 + - - -
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Residues in contact with GLN 497 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493H SER* 3.1 22.0 + - - +
494H GLN* 3.1 13.1 + - - +
496H SER* 1.3 76.1 - - - +
498H GLN* 1.3 58.7 + - + +
499H GLU 3.1 8.2 + - - -
500H GLY* 3.8 7.9 + - - +
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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