Contacts of the helix formed by residues 347 - 350 (chain P) in PDB entry 1ZD2
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 347 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326P GLN* 4.5 2.4 + - - -
342P MET 3.8 1.9 - - - +
343P ALA 3.0 23.8 - - - +
344P LEU 4.3 4.3 - - - +
345P PHE* 3.4 7.9 - - - +
346P TYR* 1.3 90.2 - - - +
348P GLU* 1.3 63.4 + - + +
349P ARG 3.2 0.2 + - - -
350P VAL* 3.1 25.1 - - + +
485P ILE* 4.5 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 348 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325P SER 4.1 1.9 - - - +
326P GLN* 3.3 26.5 + - - +
346P TYR* 4.4 2.0 - - - +
347P PRO* 1.3 80.4 - - + +
349P ARG* 1.3 72.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 349 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316P VAL* 3.8 23.0 + - + +
319P LEU* 3.9 16.4 - - + +
320P ASP* 2.4 45.0 + - - +
324P LEU 3.5 13.2 + - - -
325P SER* 2.5 47.2 + - - +
326P GLN* 2.9 23.5 - - - -
327P ALA 3.0 7.3 + - - +
329P PHE* 3.9 5.5 - - + -
342P MET* 5.6 1.3 - - + -
346P TYR* 2.7 33.6 + - + +
348P GLU* 1.3 91.8 - - + +
350P VAL* 1.3 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 350 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326P GLN* 4.1 4.9 + - - -
327P ALA 3.4 6.1 - - - +
329P PHE* 4.0 15.7 - - + +
342P MET* 3.3 45.5 - - + +
343P ALA* 4.0 1.8 - - + +
346P TYR 3.6 5.4 - - - +
347P PRO 3.1 15.1 + - - +
349P ARG* 1.3 78.0 - - - +
351P ARG* 1.3 64.5 + - - +
352P ALA 2.9 35.7 - - - +
353P VAL* 4.0 8.7 - - + +
485P ILE* 3.8 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