Contacts of the helix formed by residues 58 - 71 (chain E) in PDB entry 2WJZ
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 LYS 58 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E ASP* 4.4 2.5 - - - -
53E THR* 3.7 37.8 - - - +
54E ALA 3.5 20.9 + - - -
59E ARG* 1.3 60.7 + - - +
60E LYS 3.3 2.5 - - - +
61E THR* 3.7 8.3 + - - -
62E MET* 3.0 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E LYS* 1.3 76.8 - - - +
60E LYS* 1.3 61.7 + - - +
62E MET* 4.4 4.3 - - - +
63E LEU* 3.6 32.0 + - - +
85E ASP* 4.5 4.9 + - - -
87E GLU* 4.3 3.6 - - - +
88E THR* 3.5 40.8 + - + +
91E GLU* 2.6 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E LYS 3.3 1.4 - - - +
59E ARG* 1.3 78.1 - - - +
61E THR* 1.3 59.2 + - - +
63E LEU* 3.4 9.7 + - - +
64E GLU* 3.0 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E ASP* 4.0 9.6 + - - +
15E GLY* 3.7 25.5 - - - +
51E ASP* 4.3 4.3 - - - +
53E THR* 3.7 35.4 - - - +
58E LYS* 3.3 14.3 + - - +
60E LYS* 1.3 77.5 - - - +
62E MET* 1.3 57.4 + - - +
64E GLU* 3.2 9.7 - - + +
65E LEU* 2.9 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E ASP* 3.3 37.9 - - + +
58E LYS* 3.0 18.4 + - - +
59E ARG* 4.4 4.9 - - - +
61E THR* 1.3 74.0 - - - +
63E LEU* 1.3 60.1 + - - +
65E LEU* 3.3 7.3 + - - +
66E VAL* 2.9 34.4 + - + +
79E VAL* 4.8 10.9 - - + +
80E GLY 4.2 11.7 - - - +
81E GLY 3.4 25.8 - - - +
82E GLY 5.3 3.1 - - - +
83E ILE* 3.9 14.1 - - + -
88E THR* 5.5 3.6 - - + -
92E LEU* 3.6 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E ARG* 3.6 20.5 + - - +
60E LYS* 3.4 10.5 + - - +
61E THR 3.3 0.4 - - - -
62E MET* 1.3 74.2 - - - +
64E GLU* 1.3 65.2 + - - +
66E VAL* 4.5 1.1 - - - +
67E GLU* 3.1 26.3 + - - +
91E GLU* 3.2 50.5 - - + +
92E LEU* 3.6 21.8 - - + -
95E ARG* 3.7 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E LYS 3.0 13.7 + - - +
61E THR* 3.2 15.0 - - + +
63E LEU* 1.3 78.5 - - - +
65E LEU* 1.3 62.5 + - - +
67E GLU* 3.8 6.0 - - - +
68E LYS* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E VAL* 5.7 9.0 - - + -
15E GLY* 5.4 11.0 - - - -
32E PRO* 6.2 5.4 - - + -
33E VAL* 5.4 0.6 - - - +
49E PHE* 6.2 5.2 - - + -
51E ASP* 6.1 0.9 - - - +
61E THR* 2.9 14.2 + - + +
62E MET* 3.5 12.1 - - - +
64E GLU* 1.3 78.0 - - - +
66E VAL* 1.3 58.5 + - + +
68E LYS* 3.3 4.0 + - - +
69E VAL* 2.9 39.4 + - + +
79E VAL* 5.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E MET 2.9 24.6 + - - +
63E LEU 4.1 3.8 - - - +
64E GLU 3.3 0.2 - - - -
65E LEU* 1.3 72.9 - - - +
67E GLU* 1.3 58.0 + - - +
69E VAL* 3.9 4.8 - - - +
70E ALA* 2.9 29.6 + - - +
77E PHE* 4.1 4.4 - - + -
79E VAL* 3.5 34.8 - - + -
92E LEU* 3.5 28.3 - - + +
95E ARG* 3.7 14.1 - - + -
96E GLY 4.0 1.3 - - - -
97E ALA* 3.4 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E LEU 3.1 18.6 + - - +
64E GLU* 3.8 5.4 - - - +
65E LEU 3.3 0.2 - - - -
66E VAL* 1.3 76.6 - - - +
68E LYS* 1.3 62.1 + - - +
70E ALA* 4.3 1.7 - - - +
71E GLU* 3.3 26.2 + - - +
95E ARG* 3.8 43.3 + - + +
18F ARG* 5.6 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E VAL* 3.7 32.9 - - + +
64E GLU 3.1 16.6 + - - +
65E LEU* 3.9 4.3 - - - +
67E GLU* 1.3 78.2 - - - +
69E VAL* 1.3 61.7 + - - +
71E GLU* 3.7 24.5 + - - +
72E GLN 3.7 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E PRO* 5.3 2.9 - - + -
33E VAL* 4.6 21.5 - - + +
49E PHE* 3.8 31.4 - - + -
65E LEU* 2.9 26.4 + - + +
66E VAL 3.9 2.9 - - - +
68E LYS* 1.3 73.9 - - - +
70E ALA* 1.3 62.8 + - - +
71E GLU 3.1 1.1 - - - -
72E GLN 3.1 1.6 + - - -
73E ILE* 2.9 60.8 + - + +
77E PHE* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E VAL 2.9 18.3 + - - +
67E GLU 4.3 2.0 - - - +
69E VAL* 1.3 78.3 - - - +
71E GLU* 1.3 60.3 + - - +
72E GLN 3.3 0.5 + - - -
73E ILE* 3.9 12.1 - - - +
77E PHE* 4.0 3.1 - - + -
95E ARG 4.2 2.0 - - - +
96E GLY* 3.8 33.7 - - - +
15F ASN* 4.1 7.3 - - - +
18F ARG* 3.3 27.7 - - - +
22F ARG* 3.7 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E GLU* 3.3 19.2 + - - +
68E LYS* 3.7 14.3 - - - +
69E VAL 3.1 0.2 - - - -
70E ALA* 1.3 80.0 - - - +
72E GLN* 1.3 73.5 + - + +
18F ARG* 3.7 19.6 - - + +
22F ARG* 4.0 12.1 + - - +
----------------------------------------------------------
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