Contacts of the helix formed by residues 124 - 129 (chain D) in PDB entry 2PGW
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 124 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D GLY 4.7 0.9 - - - +
123D LEU* 1.3 89.9 - - + +
125D VAL* 1.3 65.8 + - - +
126D HIS* 3.3 28.9 - - + +
127D GLN* 3.0 40.8 + - - +
128D LEU* 3.8 3.2 + - - +
312D HIS* 3.8 9.4 - - + -
352D ARG* 3.6 27.4 - - + +
353D LYS 3.3 23.3 - - - +
355D GLY 3.4 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D TRP* 3.7 35.2 - - + +
123D LEU 3.6 0.6 + - - -
124D PRO* 1.3 71.3 - - - +
126D HIS* 1.3 62.0 + - - +
128D LEU* 2.9 21.8 + - + +
129D LEU* 3.3 29.8 + - + +
278D ILE* 4.3 15.5 - - + -
312D HIS* 3.9 22.3 + - + -
355D GLY* 2.9 31.6 + - - -
356D LEU* 3.6 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D PRO* 3.5 11.4 - - + +
125D VAL* 1.3 77.3 - - - +
127D GLN* 1.3 74.8 + - + +
128D LEU 3.1 0.2 - - - -
129D LEU* 3.2 17.6 + - - +
130D GLY 3.4 0.5 + - - -
131D GLY* 2.9 23.8 + - - +
132D ALA* 3.7 20.7 + - + +
312D HIS* 3.1 52.2 + + - +
315D LEU* 3.3 26.7 - - + +
316D ALA* 4.3 4.9 - - + +
350D ALA* 5.0 0.4 - - + -
351D PHE 3.2 18.6 + - - -
352D ARG* 3.2 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D LEU* 4.1 12.5 - - + +
124D PRO* 3.0 33.8 + - + +
126D HIS* 1.3 94.4 - - + +
128D LEU* 1.3 62.1 + - - +
130D GLY 4.3 2.8 + - - -
131D GLY* 4.7 0.7 - - - -
352D ARG* 3.6 27.2 + - - +
75H SER* 3.9 13.3 + - - -
77H HIS* 3.5 43.5 - - + +
78H ASP* 2.9 31.0 + - - +
117H GLN* 3.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D TRP* 4.1 26.2 - - + +
117D GLN* 3.9 15.9 - - + +
118D GLY* 3.6 31.6 - - - +
121D ALA* 4.5 10.5 - - + -
123D LEU* 3.8 31.2 - - + -
124D PRO 4.1 7.0 - - - +
125D VAL* 2.9 17.3 + - - +
127D GLN* 1.3 78.7 - - - +
129D LEU* 1.3 65.0 + - - +
130D GLY 3.5 1.5 + - - -
77H HIS* 5.8 0.7 - - + -
114H TRP* 4.4 11.0 - - - -
117H GLN* 5.3 1.6 - - - -
128H LEU* 3.9 22.4 - - + +
129H LEU* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D TRP* 4.3 27.4 - - + -
125D VAL* 3.3 32.8 - - + +
126D HIS* 3.2 9.1 + - - +
128D LEU* 1.3 84.9 - - + +
130D GLY* 1.3 56.2 + - - +
131D GLY 3.6 1.7 - - - +
133D HIS* 6.1 0.5 - - - -
278D ILE* 3.7 20.6 - - + -
279D GLN* 5.4 4.0 - - + +
282D MSE 4.2 25.8 - - + +
312D HIS 4.6 4.7 - - - +
316D ALA* 3.8 31.5 - - + +
114H TRP* 4.7 1.3 - - - -
279H GLN* 2.9 21.0 + - - -
----------------------------------------------------------
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