Contacts of the helix formed by residues 106 - 111 (chain C) in PDB entry 1PZY
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 ALA 106 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 4.5 5.6 - - + +
32C HIS* 3.8 20.0 - - + -
33C THR* 4.2 14.5 + - - +
104C TRP 3.0 0.8 + - - -
105C LYS* 1.3 77.4 - - - +
107C TYR* 1.3 65.1 + - - +
109C PRO* 3.7 0.9 - - - -
110C MET* 3.0 27.0 + - + +
111C CYS* 3.7 3.3 + - - -
360D PHE* 3.2 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ILE* 4.1 9.4 - - + +
25C GLU* 2.7 38.6 + - + -
29C VAL* 3.7 29.4 - - + +
101C ILE* 3.4 48.7 - - + +
102C ASP* 4.2 9.6 - - - +
104C TRP* 2.9 16.8 + - + +
106C ALA* 1.3 77.0 - - - +
108C LYS* 1.3 64.9 + - + +
111C CYS* 2.9 49.0 + - + -
112C SER* 3.5 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ASP* 4.9 14.6 + - - +
104C TRP 4.7 0.2 + - - -
105C LYS 4.3 0.8 + - - +
107C TYR* 1.3 85.1 - - + +
109C PRO* 1.3 67.9 - - + +
112C SER* 2.8 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C LYS 3.1 24.0 - - - +
106C ALA* 3.6 9.0 - - - +
108C LYS* 1.3 97.6 - - + +
110C MET* 1.3 65.8 + - - +
112C SER* 5.1 1.1 - - - -
113C GLU* 6.1 1.6 - - - +
360D PHE* 4.1 22.7 - - + +
363D ILE* 3.8 23.1 - - + +
364D ALA* 4.7 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C CYS* 3.3 10.2 - - - -
32C HIS* 3.4 50.6 + - + +
106C ALA 3.0 15.8 + - - +
109C PRO* 1.3 81.3 - - + +
111C CYS* 1.3 59.9 + - - +
112C SER 3.8 1.5 + - - -
113C GLU* 4.6 6.1 - - - +
118C TRP* 4.9 0.5 + - - -
286D TYR* 3.9 18.4 - - + -
288D GLN* 4.1 27.2 + - + +
319D ASP* 4.3 12.1 - - + +
360D PHE* 4.2 14.8 - - + -
363D ILE* 3.3 28.9 - - + -
406D NAG 4.5 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLU* 4.4 3.7 - - - +
28C CYS* 2.0 51.1 - - + -
29C VAL* 3.3 24.9 - - + -
32C HIS* 4.4 0.4 - - - -
106C ALA 4.0 8.5 - - - -
107C TYR* 2.9 39.8 + - + +
110C MET* 1.3 81.8 - - - +
112C SER* 1.3 55.4 + - - +
113C GLU 3.4 4.7 - - - -
115C LEU* 3.3 23.1 - - + +
----------------------------------------------------------
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