Contacts of the helix formed by residues 418 - 422 (chain E) in PDB entry 1D00
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 ASN 418 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C ILE* 4.0 10.6 - - - +
357C LYS* 4.9 3.5 - - - +
491C PHE* 3.4 27.9 - - + -
385E ARG 4.7 0.6 + - - -
386E TYR* 3.2 58.9 - - + +
387E GLY 4.9 3.6 + - - +
416E GLY 3.2 0.6 - - - -
417E PRO* 1.3 93.7 - - - +
419E ASP* 1.3 67.0 + - - +
420E ALA 3.1 3.4 - - - -
421E LEU* 2.9 21.3 + - + +
422E LEU* 3.3 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 419 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387E GLY 5.0 1.0 - - - +
388E TYR* 5.2 0.2 - - - -
389E LYS 5.1 2.1 + - - -
414E MET 3.9 1.0 - - - +
415E LYS* 3.5 13.1 - - + +
416E GLY* 2.9 44.3 + - - +
417E PRO 3.5 1.2 + - - -
418E ASN* 1.3 76.6 - - - +
420E ALA* 1.3 61.4 + - - +
421E LEU 3.2 0.7 + - - -
422E LEU* 3.2 19.8 + - - +
424E TRP* 3.0 41.7 + - + +
458E ARG* 3.7 23.4 + - - +
459E PRO* 3.6 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 420 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C GLN* 3.1 46.3 - - + +
486C ARG* 5.0 5.2 + - - -
491C PHE* 4.1 15.2 - - + -
417E PRO 5.3 0.2 + - - -
418E ASN 2.9 1.4 + - - -
419E ASP* 1.3 78.0 - - - +
421E LEU* 1.3 61.3 + - - +
422E LEU 4.6 2.9 - - - +
458E ARG* 3.7 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C ILE* 4.4 12.8 - - + -
435C LEU* 4.0 29.2 - - + -
436C ASP 5.0 1.1 - - - +
437C GLN* 4.2 20.9 - - + -
442C HIS* 6.4 0.4 - - + -
491C PHE* 3.5 49.4 - - + -
418E ASN* 2.9 19.6 + - + +
420E ALA* 1.3 81.2 - - - +
422E LEU* 1.3 69.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 422 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386E TYR 3.9 15.9 - - - +
387E GLY* 3.7 31.0 - - - +
388E TYR* 3.7 34.3 - - + +
418E ASN* 3.3 17.3 - - + +
419E ASP* 3.2 26.9 + - - +
420E ALA 4.6 2.8 - - - +
421E LEU* 1.3 91.5 - - + +
423E ARG* 1.3 60.9 + - - +
424E TRP* 3.1 24.9 + - + +
----------------------------------------------------------
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