Contacts of the helix formed by residues 453 - 462 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411E TRP* 3.7 22.5 - - + -
449E THR 5.1 0.4 - - - +
451E TRP 3.4 11.0 - - - +
452E SER* 1.3 84.8 - - - +
454E GLU* 1.3 66.7 + - - +
456E ALA* 3.3 8.1 + - + +
457E ALA* 3.0 30.3 + - - +
2F GLN* 3.9 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 454 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409E HIS* 2.9 25.4 + - - -
411E TRP* 3.9 14.7 - - + -
415E PRO* 3.7 37.5 - - + +
418E VAL* 3.9 20.1 - - + +
419E ALA* 3.6 4.8 - - - +
452E SER* 3.8 5.9 + - - +
453E PRO* 1.3 94.0 - - - +
455E LEU* 1.3 61.4 + - - +
458E ALA 3.3 6.6 + - - -
2F GLN* 3.5 23.2 - - - +
3F VAL 6.0 0.2 - - - -
4F TRP* 3.9 29.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 455 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384E VAL* 3.8 23.6 - - + -
419E ALA* 3.6 27.9 - - - +
422E VAL* 4.2 11.2 - - + -
423E ALA* 4.0 11.9 - - + -
445E ILE* 3.8 17.7 - - + +
448E ALA* 3.5 31.6 - - + -
449E THR* 3.9 11.2 - - + +
452E SER* 3.1 20.0 + - - +
454E GLU* 1.3 75.8 - - - +
456E ALA* 1.3 67.6 + - - +
458E ALA* 3.1 2.3 + - - +
459E CYS* 2.9 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 456 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449E THR* 3.9 29.8 - - - +
452E SER 2.9 16.3 + - - +
453E PRO* 3.6 8.7 - - + +
455E LEU* 1.3 77.2 - - - +
457E ALA* 1.3 62.6 + - - +
459E CYS* 3.3 3.0 + - - +
460E GLU* 3.2 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 457 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409E HIS* 4.0 10.1 - - + -
410E PRO* 4.1 7.6 - - + +
411E TRP* 4.0 29.6 - - + +
453E PRO 3.0 17.2 + - - +
454E GLU 3.9 4.3 - - - +
456E ALA* 1.3 77.1 - - - +
458E ALA* 1.3 61.1 + - - +
460E GLU* 3.5 15.7 + - - +
461E VAL* 3.4 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 458 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384E VAL* 4.1 12.1 - - + +
409E HIS* 3.6 25.3 + - + -
410E PRO* 5.0 0.7 - - - -
419E ALA* 3.9 11.9 - - + -
454E GLU 3.3 5.7 + - - +
455E LEU 3.1 8.8 + - - +
457E ALA* 1.3 76.6 - - - +
459E CYS* 1.3 66.0 + - - +
461E VAL* 3.2 12.6 + - - +
462E TRP* 3.3 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 459 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384E VAL* 4.1 7.9 - - - -
385E TRP* 3.0 41.7 + - + +
445E ILE* 3.4 33.0 - - - -
449E THR* 3.7 16.4 - - + -
455E LEU* 2.9 28.9 + - - +
456E ALA* 3.7 5.2 - - - +
458E ALA* 1.3 76.7 - - - +
460E GLU* 1.3 62.0 + - - +
463E LYS* 3.1 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 460 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456E ALA* 3.2 23.2 + - + +
457E ALA* 3.7 17.0 + - - +
458E ALA 3.3 0.4 - - - -
459E CYS* 1.3 76.4 - - - +
461E VAL* 1.3 64.7 + - + +
463E LYS* 3.9 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 461 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408E GLY 4.9 4.5 - - - +
410E PRO* 3.8 27.4 - - + -
457E ALA 3.4 15.7 - - - +
458E ALA* 3.2 6.6 + - - +
460E GLU* 1.3 80.5 - - + +
462E TRP* 1.3 89.1 + - + +
463E LYS 3.9 0.2 + - - -
464E GLU 5.2 0.9 + - - -
465E ILE* 4.6 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 462 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383E HIS* 3.5 52.9 - + + +
384E VAL* 4.5 6.7 - - + -
385E TRP* 3.9 5.6 - - + -
404E GLY 3.7 11.4 - - - -
405E GLY* 3.6 31.4 - - - -
408E GLY* 3.5 36.3 - - - -
409E HIS* 3.8 8.3 - + - -
458E ALA* 3.3 42.9 + - + +
461E VAL* 1.3 95.6 - - + +
463E LYS* 1.3 65.6 + - - +
464E GLU 3.2 2.7 - - - -
465E ILE* 3.0 30.1 + - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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