Contacts of the helix formed by residues 469 - 481 (chain D) in PDB entry 4OIR
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 ASP 469 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467D GLU 3.3 5.0 + - - +
468D LEU* 1.3 73.1 - - - +
470D LEU* 1.3 68.6 + - - +
471D GLU* 3.8 12.9 - - - +
472D ALA* 3.5 26.1 + - + +
473D LEU* 3.4 17.8 + - - +
508D ARG* 5.8 0.2 - - - +
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Residues in contact with LEU 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D LEU* 5.0 9.9 - - + -
468D LEU* 3.9 11.9 + - + +
469D ASP* 1.3 74.4 + - - +
471D GLU* 1.3 70.3 + - - +
473D LEU* 3.0 9.3 + - + +
474D GLU* 2.9 21.5 + - - +
499D VAL* 3.9 18.6 - - + +
502D PHE* 4.4 11.9 - - + +
503D LEU* 3.6 50.0 - - + +
507D ASN 5.3 1.3 - - - +
508D ARG* 3.7 25.9 - - - +
509D PRO* 4.3 20.9 - - + -
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Residues in contact with GLU 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469D ASP* 3.6 14.7 - - - +
470D LEU* 1.3 79.8 + - - +
472D ALA* 1.3 56.1 + - - +
474D GLU* 3.2 16.5 + - - +
475D LYS* 2.9 52.6 + - + +
503D LEU* 3.9 19.4 - - + +
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Residues in contact with ALA 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469D ASP* 3.5 29.7 + - + +
470D LEU 3.2 0.4 - - - -
471D GLU* 1.3 79.3 - - - +
473D LEU* 1.3 56.5 + - - +
475D LYS* 3.4 8.0 + - - +
476D GLU* 2.9 37.6 + - + +
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Residues in contact with LEU 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D LEU* 3.9 14.6 - - + +
468D LEU* 4.5 22.2 - - + -
469D ASP 3.4 8.8 + - - +
470D LEU* 3.0 11.9 + - + +
472D ALA* 1.3 76.2 - - - +
474D GLU* 1.3 61.7 + - - +
476D GLU* 4.3 9.9 - - + -
477D LEU* 2.9 52.0 + - + +
495D ARG* 3.3 32.8 - - - +
499D VAL* 4.0 21.1 - - + -
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Residues in contact with GLU 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D LEU 2.9 12.1 + - - +
471D GLU* 3.3 18.3 - - - +
473D LEU* 1.3 77.8 - - - +
475D LYS* 1.3 67.6 + - - +
477D LEU* 3.3 2.6 + - - +
478D LEU* 2.9 43.1 + - + +
496D LEU* 3.8 25.8 - - + +
499D VAL* 4.3 3.3 - - + +
500D ARG* 3.5 24.3 + - + +
503D LEU* 3.9 23.1 - - + +
1388D ARG* 3.6 16.3 + - - -
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Residues in contact with LYS 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D GLU* 2.9 40.2 + - + +
472D ALA* 3.8 6.3 - - - +
474D GLU* 1.3 85.0 + - + +
476D GLU* 1.3 60.8 + - + +
478D LEU* 3.1 17.2 + - + +
479D GLU* 2.9 37.6 + - + +
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Residues in contact with GLU 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D ALA* 2.9 25.7 + - + +
473D LEU* 3.7 14.4 - - + +
475D LYS* 1.3 76.2 - - + +
477D LEU* 1.3 60.6 + - + +
479D GLU* 3.2 14.3 + - - +
480D GLU* 2.9 25.9 + - - +
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Residues in contact with LEU 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473D LEU* 2.9 42.1 + - + +
474D GLU 3.8 3.6 - - - +
476D GLU* 1.3 75.3 - - + +
478D LEU* 1.3 59.2 - - - +
480D GLU* 3.1 13.0 + - + +
481D MET* 2.9 32.2 + - - +
492D ALA* 3.9 27.2 - - + +
495D ARG* 3.8 44.4 - - + +
496D LEU* 4.0 19.5 - - + +
499D VAL* 4.0 9.4 - - + -
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Residues in contact with LEU 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474D GLU* 2.9 31.5 + - + +
475D LYS* 3.1 21.7 + - + +
477D LEU* 1.3 73.7 - - - +
479D GLU* 1.3 71.8 + - - +
481D MET* 3.1 22.4 + - + +
482D LYS* 3.8 10.4 + - - +
496D LEU* 3.8 12.8 - - + -
500D ARG* 3.4 30.7 - - - +
1390D LEU* 4.4 7.0 - - + -
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Residues in contact with GLU 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475D LYS* 2.9 24.4 + - + +
476D GLU* 3.4 14.8 - - - +
478D LEU* 1.3 80.1 - - - +
480D GLU* 1.3 61.6 + - - +
481D MET 3.3 0.5 + - - -
482D LYS* 3.2 45.7 + - - +
483D HIS* 4.2 3.1 + - - +
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Residues in contact with GLU 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476D GLU 2.9 14.1 + - - +
477D LEU* 3.1 23.7 + - + +
479D GLU* 1.3 78.3 - - - +
481D MET* 1.3 58.4 + - - +
482D LYS 3.2 0.9 + - - -
483D HIS* 3.4 22.7 - - - +
488D ARG* 2.9 53.8 + - - +
489D ARG* 4.5 5.4 - - - -
492D ALA* 3.6 20.1 - - + +
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Residues in contact with MET 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477D LEU 2.9 18.0 + - - +
478D LEU* 3.1 18.5 + - + +
480D GLU* 1.3 78.4 - - - +
482D LYS* 1.3 60.0 + - + +
483D HIS 3.3 0.7 - - - -
489D ARG* 3.2 50.1 - - + +
492D ALA* 3.7 3.4 - - + -
493D ARG* 3.6 16.8 - - + -
496D LEU* 4.6 11.7 - - + -
1390D LEU* 4.2 14.6 - - + -
1391D GLU* 3.9 49.2 - - + +
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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