Contacts of the helix formed by residues 453 - 462 (chain H) in PDB entry 1RBO
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 PRO 453 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411H TRP* 3.7 22.3 - - + -
449H THR 5.1 0.4 - - - +
451H TRP 3.4 11.4 - - - +
452H SER* 1.3 83.6 - - - +
454H GLU* 1.3 66.6 + - - +
456H ALA* 3.3 8.1 + - + +
457H ALA* 3.0 31.4 + - - +
2I GLN* 3.9 25.4 - - - +
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Residues in contact with GLU 454 (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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409H HIS* 2.9 25.4 + - - -
411H TRP* 3.9 14.0 - - + -
415H PRO* 3.7 38.3 - - + +
418H VAL* 3.9 21.4 - - + +
419H ALA* 3.6 4.6 - - - +
452H SER* 3.8 5.4 + - - +
453H PRO* 1.3 93.6 - - - +
455H LEU* 1.3 61.4 + - - +
458H ALA 3.3 6.8 + - - -
2I GLN* 3.5 23.6 - - - +
4I TRP* 3.9 30.9 - - + -
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Residues in contact with LEU 455 (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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384H VAL* 3.8 24.0 - - + -
419H ALA* 3.6 28.0 - - - +
422H VAL* 4.2 11.7 - - + -
423H ALA* 4.0 11.4 - - + -
445H ILE* 3.8 18.2 - - + +
448H ALA* 3.5 31.9 - - + -
449H THR* 3.9 11.0 - - + +
452H SER* 3.1 20.6 + - - +
454H GLU* 1.3 75.3 - - - +
456H ALA* 1.3 68.2 + - - +
458H ALA* 3.1 1.7 + - - +
459H CYS* 2.9 31.2 + - - -
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Residues in contact with ALA 456 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449H THR* 3.9 30.3 - - - +
452H SER 2.9 15.6 + - - +
453H PRO* 3.6 8.7 - - + +
455H LEU* 1.3 77.6 - - - +
457H ALA* 1.3 61.9 + - - +
459H CYS* 3.3 2.5 + - - +
460H GLU* 3.2 34.5 + - + +
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Residues in contact with ALA 457 (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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409H HIS* 4.0 9.9 - - + -
410H PRO* 4.1 8.1 - - + +
411H TRP* 4.0 30.1 - - + +
453H PRO 3.0 16.7 + - - +
454H GLU 3.9 4.3 - - - +
456H ALA* 1.3 78.3 - - - +
458H ALA* 1.3 61.0 + - - +
460H GLU* 3.5 16.2 + - - +
461H VAL* 3.4 25.6 + - - +
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Residues in contact with ALA 458 (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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384H VAL* 4.1 12.1 - - + +
409H HIS* 3.6 25.7 + - + -
410H PRO* 5.0 0.7 - - - -
419H ALA* 3.9 12.6 - - + -
454H GLU 3.3 5.9 + - - +
455H LEU 3.1 9.2 + - - +
457H ALA* 1.3 75.0 - - - +
459H CYS* 1.3 67.0 + - - +
461H VAL* 3.2 12.9 + - - +
462H TRP* 3.3 37.4 + - + +
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Residues in contact with CYS 459 (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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384H VAL* 4.1 7.6 - - - -
385H TRP* 3.0 41.7 + - + +
445H ILE* 3.4 32.5 - - - -
449H THR* 3.7 16.6 - - + -
455H LEU* 2.9 29.5 + - - +
456H ALA* 3.7 4.9 - - - +
458H ALA* 1.3 76.0 - - - +
460H GLU* 1.3 62.4 + - + +
463H LYS* 3.1 16.0 + - - +
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Residues in contact with GLU 460 (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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456H ALA* 3.2 23.8 + - - +
457H ALA* 3.7 16.6 + - - +
458H ALA 3.3 0.2 - - - -
459H CYS* 1.3 76.9 - - - +
461H VAL* 1.3 65.5 + - + +
463H LYS* 3.9 12.1 + - - +
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Residues in contact with VAL 461 (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 GLY 4.9 4.7 - - - +
410H PRO* 3.8 26.5 - - + -
457H ALA 3.4 15.9 - - - +
458H ALA 3.2 7.0 + - - +
460H GLU* 1.3 82.0 - - + +
462H TRP* 1.3 88.9 + - + +
463H LYS 3.9 0.2 + - - -
464H GLU 5.2 0.7 + - - -
465H ILE* 4.6 4.7 - - - +
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Residues in contact with TRP 462 (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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383H HIS* 3.5 52.1 - + + +
384H VAL* 4.5 6.3 - - + -
385H TRP* 3.9 5.6 - - + -
404H GLY 3.7 11.2 - - - -
405H GLY* 3.6 30.7 - - - -
408H GLY* 3.5 36.8 - - - -
409H HIS* 3.8 8.1 - + - -
458H ALA* 3.3 42.1 + - + +
461H VAL* 1.3 95.1 - - + +
463H LYS* 1.3 65.5 + - - +
464H GLU 3.2 2.7 - - - -
465H ILE* 3.0 31.0 + - + +
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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