Contacts of the helix formed by residues 49 - 57 (chain B) in PDB entry 2PG4
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 49 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR 3.7 1.0 + - - -
48B MSE 1.3 79.3 - - - +
50B LEU* 1.3 58.5 + - - +
52B ASP* 3.4 3.8 + - - +
53B ARG* 3.0 46.8 + - - +
56B ARG* 4.9 1.0 + - - -
98B EDO 2.9 20.4 + - - -
99B EDO 4.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 5.1 1.3 - - + -
12B HIS* 3.6 44.4 - - + +
16B ILE* 4.0 24.7 - - + -
41B VAL* 4.3 7.9 - - + -
45B THR* 3.3 28.6 + - + +
46B PHE* 4.1 6.7 - - + -
49B GLY* 1.3 72.4 - - - +
51B LYS* 1.3 68.3 + - - +
53B ARG* 3.1 17.3 + - + +
54B LEU* 3.0 48.4 + - + +
95B CL 3.7 11.7 - - + -
99B EDO 4.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.5 2.0 - - + -
46B PHE* 3.1 49.8 + - + +
47B PHE* 4.0 18.6 - - - -
50B LEU* 1.3 77.7 - - - +
52B ASP* 1.3 76.0 + - - +
54B LEU* 3.1 8.6 + - - +
55B ILE* 3.1 33.3 + - + +
60B VAL* 4.4 1.0 - - - +
62B GLU* 2.9 34.3 + - - +
72B LEU* 4.0 22.2 - - + -
98B EDO 3.5 22.8 + - - -
100B PEG 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLY* 3.9 3.6 - - - +
50B LEU 3.2 0.6 - - - -
51B LYS* 1.3 99.2 + - - +
53B ARG* 1.3 59.8 + - - +
55B ILE* 3.8 16.1 - - - +
56B ARG* 3.0 47.2 + - + +
98B EDO 3.2 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLU* 3.9 19.6 - - - +
7B ARG 5.7 2.5 - - - -
8B LEU* 3.8 16.0 - - + +
12B HIS* 4.1 3.6 + - - -
49B GLY* 3.0 25.2 + - - +
50B LEU* 3.1 17.0 + - - +
52B ASP* 1.3 75.6 - - - +
54B LEU* 1.3 61.1 + - - +
56B ARG* 3.5 27.5 + - - +
57B ALA* 3.0 29.3 + - - +
95B CL 3.1 31.4 - - - +
99B EDO 3.0 46.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.9 24.9 - - + -
12B HIS* 5.4 0.4 - - + +
13B LEU* 4.0 16.4 - - + -
16B ILE* 3.7 36.1 - - + -
17B LEU* 4.6 6.3 - - + -
46B PHE* 5.3 0.9 - - + -
50B LEU* 3.0 39.3 + - + +
51B LYS* 3.5 11.0 - - - +
53B ARG* 1.3 77.0 - - - +
55B ILE* 1.3 58.3 - - - +
57B ALA* 3.6 4.4 + - - -
58B GLY 3.5 2.4 + - - -
59B LEU* 3.0 35.3 + - + +
60B VAL* 3.5 21.6 + - + -
72B LEU* 5.0 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LYS* 3.1 20.4 + - + +
52B ASP* 3.8 27.6 - - - +
54B LEU* 1.3 75.4 - - - +
56B ARG* 1.3 59.9 + - + +
58B GLY* 2.8 22.9 + - - -
60B VAL* 3.6 29.9 - - + +
61B LYS* 5.2 4.0 - - + -
62B GLU* 3.8 35.9 - - + +
72B LEU* 4.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASP* 5.3 0.3 - - - +
4B GLU* 4.1 30.4 + - + +
49B GLY 4.9 0.8 + - - -
52B ASP* 3.0 40.7 + - + +
53B ARG* 3.5 28.6 - - - +
55B ILE* 1.3 79.1 - - + +
57B ALA* 1.3 57.8 + - - +
58B GLY 3.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASP* 4.2 4.8 - - - +
4B GLU* 3.9 11.2 - - + +
5B THR* 3.7 33.4 + - - +
8B LEU* 4.6 2.7 - - + -
53B ARG 3.0 17.9 + - - +
54B LEU* 4.0 5.4 - - - +
55B ILE 3.2 0.4 - - - -
56B ARG* 1.3 75.4 - - - +
58B GLY* 1.3 61.3 + - - +
59B LEU* 3.3 11.9 + - + +
77B LYS* 3.0 27.2 + - - -
----------------------------------------------------------
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