Contacts of the helix formed by residues 574 - 579 (chain D) in PDB entry 5DO7
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 GLY 574 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453D PHE* 4.2 11.2 - - - -
570D PHE 3.0 13.3 + - - -
571D TYR 3.6 10.9 - - - +
572D LEU 2.8 20.8 + - - +
573D ALA* 1.3 76.5 - - - +
575D GLY* 1.3 69.0 + - - +
576D PHE 3.8 0.7 - - - -
577D MET 4.3 0.2 + - - -
578D ILE* 3.9 5.0 + - - +
580D LEU 5.5 0.2 + - - -
596D LEU* 4.8 0.4 - - - -
597D ARG* 3.6 23.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 575 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C GLN* 4.8 0.7 - - - -
453D PHE* 4.6 1.2 - - - -
573D ALA 3.6 2.1 + - - -
574D GLY* 1.3 70.0 - - - +
576D PHE* 1.3 53.8 + - - +
578D ILE 2.8 12.8 + - - -
579D ASN* 2.8 31.5 + - - -
580D LEU* 4.6 20.4 - - - -
597D ARG* 4.1 9.6 - - - +
600D PHE* 4.0 21.5 - - - -
635D LEU* 6.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 576 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C GLN* 3.4 24.8 + - - +
420C VAL* 5.6 8.3 - - + +
548C PHE 5.4 2.7 - - - -
549C LEU* 3.9 29.6 - - + -
446D MET 3.4 24.5 - - - -
447D ASP* 5.5 0.7 - - - -
449D ALA* 3.9 9.2 - - + -
450D ALA* 3.2 40.8 - - + -
453D PHE* 3.9 33.6 - + + -
574D GLY 3.8 0.2 - - - -
575D GLY* 1.3 72.2 - - - +
577D MET* 1.3 70.8 + - + +
600D PHE* 3.9 17.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 577 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C GLN* 3.4 14.7 - - - +
420C VAL* 4.7 3.9 - - - +
421C GLY* 3.5 44.0 - - - +
424C TYR* 3.6 16.2 - - + -
425C GLN* 3.5 25.4 - - + +
549C LEU* 4.7 11.9 - - - -
453D PHE* 3.7 24.9 - - + -
571D TYR* 3.5 40.8 - - + +
572D LEU* 5.0 4.9 - - + +
574D GLY 4.3 1.1 + - - +
575D GLY 2.8 3.4 + - - -
576D PHE* 1.3 85.8 - - + +
578D ILE* 1.3 70.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 578 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C PHE* 5.4 7.0 - - + -
404C VAL* 4.0 26.2 - - + -
417C GLN* 4.4 4.0 - - - -
418C ASP* 2.9 27.1 - - - +
421C GLY* 4.9 9.9 - - - -
572D LEU* 2.8 46.0 - - + +
573D ALA* 4.9 1.1 - - - +
574D GLY 3.9 3.6 - - - +
575D GLY 2.8 10.7 + - - -
577D MET* 1.3 85.6 - - + +
579D ASN* 1.3 70.9 + - - +
580D LEU* 5.6 0.2 - - - -
582D SER 4.7 2.1 - - - +
583D LEU* 3.6 39.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 579 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C LYS* 2.8 35.9 + - - +
417C GLN* 3.5 37.5 + - + +
418C ASP* 3.9 7.2 - - - +
599C MET* 4.1 7.7 - - - +
575D GLY 2.8 15.7 + - - -
578D ILE* 1.3 88.1 - - - +
580D LEU* 1.3 89.9 + - - +
581D SER* 4.3 1.0 + - - -
582D SER* 3.7 20.5 + - - -
583D LEU* 4.5 0.9 - - - +
----------------------------------------------------------
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