Contacts of the helix formed by residues 437 - 450 (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 LEU 437 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388E PRO* 3.8 29.0 - - + +
389E ALA* 5.3 0.6 + - - -
391E THR* 3.7 31.9 - - + -
392E GLU* 4.0 18.4 - - + +
427E CYS* 3.7 32.3 - - + +
431E ARG* 4.1 27.6 - - + +
435E ARG 3.4 3.4 + - - +
436E ASP* 1.3 73.2 + - - +
438E ALA* 1.3 58.1 + - - +
441E GLY* 3.0 28.2 + - - +
444E ILE* 3.8 21.8 - - + -
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Residues in contact with ALA 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389E ALA* 6.5 0.4 - - - +
392E GLU* 4.6 23.9 - - + +
436E ASP* 3.0 13.2 + - - +
437E LEU* 1.3 80.5 - - - +
439E ARG* 1.3 61.9 + - + +
441E GLY* 4.5 1.0 + - - -
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Residues in contact with ARG 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436E ASP* 2.8 46.1 + - + +
438E ALA* 1.3 81.3 - - + +
440E GLU* 1.3 84.2 + - + +
441E GLY 3.5 0.7 + - - -
442E ASN 5.3 0.5 + - - -
443E THR* 5.4 0.5 + - - -
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Residues in contact with GLU 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435E ARG* 3.2 37.7 + - - +
436E ASP 2.6 38.5 + - - +
439E ARG* 1.3 95.8 + - + +
441E GLY* 1.3 63.1 + - - -
442E ASN 3.4 2.2 - - - -
443E THR* 3.0 15.9 + - - +
444E ILE* 2.9 34.5 + - + +
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Residues in contact with GLY 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388E PRO* 3.6 25.3 - - - +
437E LEU 3.0 22.4 + - - -
438E ALA 4.5 1.2 + - - -
439E ARG 3.5 2.4 - - - -
440E GLU* 1.3 75.8 - - - +
442E ASN* 1.3 62.1 + - - +
444E ILE* 3.2 7.0 + - - +
445E ILE* 3.2 26.2 + - - +
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Residues in contact with ASN 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385E TRP* 3.8 32.0 - - + +
388E PRO* 5.7 0.2 - - - +
439E ARG 5.3 0.8 + - - -
440E GLU 3.4 0.6 - - - -
441E GLY* 1.3 74.0 - - - +
443E THR* 1.3 57.2 + - - +
445E ILE* 3.4 2.1 + - - +
446E ARG* 3.0 61.6 + - - +
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Residues in contact with THR 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435E ARG* 4.4 5.6 - - - +
439E ARG 5.4 0.5 + - - -
440E GLU* 3.0 20.0 + - - +
442E ASN* 1.3 76.1 - - - +
444E ILE* 1.3 59.6 + - - +
446E ARG* 3.3 14.9 + - + +
447E GLU* 2.9 55.9 + - + +
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Residues in contact with ILE 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426E ALA* 3.8 33.3 - - + +
427E CYS* 4.2 12.6 - - - +
430E ALA* 3.5 21.1 - - + -
435E ARG* 3.8 30.7 - - + +
437E LEU* 3.8 21.3 - - + -
440E GLU* 2.9 33.6 + - + +
441E GLY* 3.6 7.2 - - - +
443E THR* 1.3 77.2 - - - +
445E ILE* 1.3 62.8 + - - +
447E GLU* 3.5 10.5 + - - +
448E ALA* 3.3 20.6 + - - +
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Residues in contact with ILE 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384E VAL 4.0 18.6 - - - +
385E TRP* 3.9 21.8 - - + +
387E MET* 4.5 0.2 - - + -
388E PRO* 3.9 12.8 - - + -
423E ALA* 4.1 24.0 - - + +
426E ALA* 5.5 1.3 - - + -
427E CYS* 4.2 21.5 - - - -
441E GLY 3.2 14.0 + - - +
442E ASN* 3.8 6.3 - - - +
444E ILE* 1.3 77.7 - - + +
446E ARG* 1.3 63.0 + - - +
448E ALA* 3.1 8.4 + - - +
449E THR* 3.1 19.9 + - - +
455E LEU* 4.4 7.0 - - + -
459E CYS* 3.4 31.0 - - - -
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Residues in contact with ARG 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385E TRP* 4.0 11.2 - - + -
442E ASN* 3.0 62.2 + - - +
443E THR* 3.7 13.9 + - - +
445E ILE* 1.3 71.6 - - - +
447E GLU* 1.3 67.6 + - + +
449E THR* 2.6 28.1 + - - +
450E LYS* 3.6 16.2 + - - +
463E LYS* 3.5 28.6 - - - +
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Residues in contact with GLU 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435E ARG* 2.5 45.0 + - - -
443E THR* 2.9 33.7 + - + +
444E ILE* 3.6 6.4 - - - +
446E ARG* 1.3 76.5 - - + +
448E ALA* 1.3 63.1 + - - +
450E LYS* 3.1 26.9 + - - +
451E TRP* 3.7 8.7 - - - -
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Residues in contact with ALA 448 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422E VAL* 4.4 1.6 - - + -
426E ALA* 4.0 21.8 - - + -
444E ILE 3.3 9.0 + - - +
445E ILE* 3.1 9.7 + - - +
447E GLU* 1.3 76.3 - - - +
449E THR* 1.3 64.5 + - - +
450E LYS 3.1 3.1 + - - -
451E TRP* 3.2 26.8 + - + +
452E SER* 3.0 23.0 + - - -
455E LEU* 3.5 18.8 - - + -
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Residues in contact with THR 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385E TRP* 5.8 1.1 - - + -
445E ILE* 3.1 16.7 + - + +
446E ARG* 2.6 22.6 + - - +
448E ALA* 1.3 74.8 - - - +
450E LYS* 1.3 70.2 + - - +
451E TRP 3.3 0.5 + - - -
452E SER 3.6 20.4 + - - +
453E PRO* 5.1 0.3 - - - +
455E LEU* 3.9 9.6 - - + -
456E ALA* 3.9 25.3 - - - +
459E CYS* 3.7 29.8 - - + -
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Residues in contact with LYS 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446E ARG* 3.6 19.7 - - - +
447E GLU* 3.3 19.3 - - - +
448E ALA 3.1 1.0 - - - -
449E THR* 1.3 83.9 + - - +
451E TRP* 1.3 60.9 + - + +
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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