Contacts of the helix formed by residues 453 - 462 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411L TRP* 3.7 21.5 - - + -
449L THR 5.1 0.4 - - - +
451L TRP 3.4 11.0 - - - +
452L SER* 1.3 84.0 - - - +
454L GLU* 1.3 66.6 + - - +
456L ALA* 3.3 7.9 + - + +
457L ALA* 3.0 31.4 + - - +
2S GLN* 3.9 25.6 - - - +
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Residues in contact with GLU 454 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409L HIS* 2.9 25.9 + - - -
411L TRP* 3.9 15.1 - - + -
415L PRO* 3.7 38.3 - - + +
418L VAL* 3.9 20.0 - - + +
419L ALA* 3.6 4.5 - - - +
452L SER* 3.8 5.8 + - - +
453L PRO* 1.3 92.7 - - - +
455L LEU* 1.3 61.5 + - - +
457L ALA 3.5 0.2 + - - -
458L ALA 3.3 6.8 + - - -
2S GLN* 3.5 22.9 - - - +
3S VAL 6.0 0.2 - - - -
4S TRP* 3.9 29.1 - - + -
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Residues in contact with LEU 455 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384L VAL* 3.8 23.3 - - + -
419L ALA* 3.6 28.0 - - - +
422L VAL* 4.2 10.5 - - + -
423L ALA* 4.0 11.2 - - + -
445L ILE* 3.8 17.7 - - + +
448L ALA* 3.5 33.2 - - + -
449L THR* 3.9 9.6 - - + +
452L SER* 3.1 20.4 + - - +
454L GLU* 1.3 75.3 - - - +
456L ALA* 1.3 67.9 + - - +
458L ALA* 3.1 2.1 + - - +
459L CYS* 2.9 31.3 + - - -
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Residues in contact with ALA 456 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449L THR* 3.9 31.1 - - - +
452L SER 2.9 15.8 + - - +
453L PRO* 3.3 9.4 + - + +
455L LEU* 1.3 76.8 - - - +
457L ALA* 1.3 62.6 + - - +
459L CYS* 3.3 2.5 + - - +
460L GLU* 3.2 34.0 + - + +
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Residues in contact with ALA 457 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409L HIS* 4.0 10.3 - - + -
410L PRO* 4.1 7.4 - - + +
411L TRP* 4.0 29.6 - - + +
453L PRO 3.0 17.1 + - - +
454L GLU 3.9 4.7 - - - +
455L LEU 3.2 0.2 - - - -
456L ALA* 1.3 76.3 - - - +
458L ALA* 1.3 61.8 + - - +
460L GLU* 3.5 15.9 + - - +
461L VAL* 3.4 25.8 + - - +
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Residues in contact with ALA 458 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384L VAL* 4.1 12.8 - - + -
409L HIS* 3.6 26.2 + - + -
410L PRO* 5.0 0.4 - - - -
419L ALA* 3.9 12.6 - - + -
454L GLU 3.3 5.5 + - - +
455L LEU 3.1 7.9 + - - +
457L ALA* 1.3 77.2 - - - +
459L CYS* 1.3 65.7 + - - +
461L VAL* 3.2 12.7 + - - +
462L TRP* 3.3 38.1 + - + +
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Residues in contact with CYS 459 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384L VAL* 4.1 7.2 - - - -
385L TRP* 3.0 41.9 + - + +
445L ILE* 3.4 33.2 - - - -
449L THR* 3.7 16.8 - - + -
455L LEU* 2.9 28.2 + - - +
456L ALA 3.7 4.7 - - - +
458L ALA* 1.3 77.6 - - - +
460L GLU* 1.3 61.6 + - - +
463L LYS* 3.1 15.9 + - - +
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Residues in contact with GLU 460 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456L ALA* 3.2 23.5 + - + +
457L ALA* 3.7 17.4 + - - +
458L ALA 3.3 0.2 - - - -
459L CYS* 1.3 75.8 - - + +
461L VAL* 1.3 64.9 + - + +
463L LYS* 3.9 12.5 + - - +
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Residues in contact with VAL 461 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408L GLY 4.9 4.3 - - - +
410L PRO* 3.8 26.0 - - + -
457L ALA 3.4 16.4 - - - +
458L ALA 3.2 7.0 + - - +
460L GLU* 1.3 81.3 - - + +
462L TRP* 1.3 87.5 + - + +
463L LYS 3.9 0.5 + - - -
464L GLU 5.2 0.5 + - - -
465L ILE* 4.6 5.0 - - - +
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Residues in contact with TRP 462 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383L HIS* 3.5 53.1 - + + +
384L VAL* 4.5 7.0 - - + -
385L TRP* 3.9 6.1 - - + -
404L GLY 3.7 11.0 - - - -
405L GLY* 3.6 30.5 - - - -
408L GLY* 3.5 37.0 - - - -
409L HIS* 3.8 8.1 - + - -
458L ALA* 3.3 43.0 + - + +
461L VAL* 1.3 96.3 - - + +
463L LYS* 1.3 66.7 + - - +
464L GLU 3.2 2.9 - - - -
465L ILE* 3.0 31.2 + - + +
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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