Contacts of the helix formed by residues 43 - 51 (chain B) in PDB entry 2PKG
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 43 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA 3.5 1.7 + - - -
42B LEU* 1.3 75.3 - - - +
44B VAL* 1.3 53.4 + - - -
45B GLU* 2.7 11.0 - - - -
46B ARG* 2.5 36.7 + - - +
47B THR* 2.6 19.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU 4.1 0.2 + - - -
43B GLY* 1.3 72.8 - - - +
45B GLU* 1.3 72.5 + - + +
47B THR* 3.7 8.6 - - - -
48B ARG* 3.3 26.8 + - - +
78B THR 4.9 2.5 - - - +
79B LEU* 5.0 3.4 - - - -
80B VAL* 3.8 26.1 - - - +
81B GLY* 4.2 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLY* 2.7 3.3 - - - -
44B VAL* 1.3 90.3 - - + +
46B ARG* 1.3 59.5 + - + +
48B ARG* 3.1 37.1 + - - +
49B SER* 3.2 22.9 + - - -
85B TYR* 5.1 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.3 57.8 + - + +
11B TYR* 4.0 10.3 - - - +
41B ALA 5.1 3.8 + - - -
42B LEU* 3.5 29.4 - - + +
43B GLY* 2.5 26.9 + - - +
45B GLU* 1.3 74.9 - - + +
47B THR* 1.3 69.6 + - - +
48B ARG 3.1 1.8 - - - -
49B SER* 2.6 26.7 + - - +
50B GLU 3.3 2.9 + - - -
51B LEU* 3.8 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 3.6 25.4 + - + -
42B LEU* 3.7 5.2 + - - +
43B GLY 2.6 27.3 + - - -
44B VAL* 3.7 6.6 - - - -
46B ARG* 1.3 71.9 - - - +
48B ARG* 1.3 57.5 + - - +
51B LEU* 2.7 58.3 + - + +
52B LEU* 3.3 7.2 + - + +
76B PHE* 4.4 9.9 - - + -
79B LEU 3.2 27.3 + - - +
80B VAL* 4.4 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.3 16.9 + - - +
45B GLU* 3.1 34.0 + - - +
47B THR* 1.3 77.4 - - - +
49B SER* 1.3 69.2 + - - +
52B LEU* 4.4 11.2 - - + +
53B PRO* 3.7 12.6 - - - +
80B VAL* 3.3 27.3 + - + -
85B TYR* 3.2 46.0 + - - -
88B CYS* 4.5 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.7 17.7 - - - +
45B GLU 3.2 17.7 + - - -
46B ARG* 2.6 29.5 + - - -
48B ARG* 1.3 79.9 - - - +
50B GLU* 1.3 74.5 + - - +
53B PRO* 3.3 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.3 32.1 + - + +
13B ILE* 3.1 39.3 - - - +
49B SER* 1.3 86.7 + - - +
51B LEU* 1.3 64.4 + - - +
52B LEU 3.6 0.7 - - - -
53B PRO* 3.8 10.3 - - + -
54B PHE* 3.2 22.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.6 2.8 - - + +
12B PRO* 6.4 0.2 - - + -
13B ILE* 5.3 3.6 - - + -
16B LEU* 5.2 6.7 - - + -
35B LEU* 3.9 28.7 - - + -
38B ILE* 4.8 12.8 - - + +
39B ALA* 4.4 17.7 - - + +
42B LEU* 5.2 7.9 - - + -
46B ARG 3.8 2.5 + - - +
47B THR* 2.7 47.3 + - + +
50B GLU* 1.3 77.1 - - - +
52B LEU* 1.3 65.2 + - + +
54B PHE* 3.1 20.4 - - + +
55B LEU* 3.1 28.3 + - + +
76B PHE* 4.7 8.1 - - + -
----------------------------------------------------------
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