Contacts of the helix formed by residues 64 - 73 (chain E) in PDB entry 2Q6W
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 GLN 64 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E SER 3.6 15.2 + - - +
61E TRP* 3.2 26.1 + - - +
63E SER* 1.3 77.3 + - - +
65E LYS* 1.3 49.9 + - - +
66E ASP* 3.2 7.0 - - + -
67E LEU* 2.7 49.4 + - + +
68E LEU 3.5 1.7 + - - -
31F LEU* 5.1 10.3 - - - +
32F PRO* 6.4 0.2 - - - +
35F SER* 5.5 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ASN 3.0 27.8 - - - +
63E SER* 3.1 13.6 + - - +
64E GLN* 1.3 68.8 - - - +
66E ASP* 1.3 61.0 + - - +
67E LEU 3.2 0.2 - - - -
68E LEU* 3.7 22.5 + - + +
69E GLU* 3.3 19.6 + - - +
72E ARG* 5.0 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E GLN* 4.6 4.0 - - + +
65E LYS* 1.3 76.9 - - - +
67E LEU* 1.4 57.3 + - - +
69E GLU* 3.0 26.7 + - - +
70E GLN* 3.4 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E TYR* 5.7 1.8 - - + -
61E TRP* 4.4 8.7 - - + +
64E GLN* 2.7 47.1 + - + +
66E ASP* 1.4 70.6 - - - +
68E LEU* 1.3 60.0 + - + +
70E GLN* 3.3 12.0 - - - +
71E LYS* 3.0 30.2 + - - +
31F LEU* 5.0 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E PHE* 4.2 4.9 - - + -
45E GLY 4.4 0.2 - - - +
46E GLU* 3.9 15.5 - - + +
47E TYR* 3.7 22.7 - - + -
61E TRP 4.1 10.8 - - - +
62E ASN* 3.3 49.4 - - - +
64E GLN 3.5 2.0 + - - -
65E LYS* 3.7 17.7 + - + +
66E ASP 3.4 0.2 - - - -
67E LEU* 1.3 74.2 - - - +
69E GLU* 1.3 51.3 + - - +
70E GLN 2.7 7.2 + - - -
71E LYS* 3.0 2.8 + - - +
72E ARG* 2.6 75.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E LYS 3.3 11.6 + - - +
66E ASP* 3.0 23.5 + - - +
68E LEU* 1.3 73.7 - - - +
70E GLN* 1.3 56.2 + - + +
72E ARG* 3.5 12.9 - - - +
73E GLY* 3.3 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ASP 3.5 11.6 + - - +
67E LEU* 3.3 16.1 - - - +
68E LEU 2.7 0.2 + - - -
69E GLU* 1.3 79.0 - - - +
71E LYS* 1.3 69.3 + - + +
72E ARG 3.1 0.7 - - - -
73E GLY* 3.1 10.6 + - - -
74E ARG* 2.8 47.1 + - - +
77E ASN* 4.3 5.5 + - - +
29F GLU* 5.6 2.3 - - - +
31F LEU* 4.9 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E TYR* 2.9 21.2 + - + +
28E ASP* 2.8 21.4 + - + +
40E PHE* 3.2 38.7 - - + -
42E SER* 5.3 0.7 - - - -
47E TYR* 3.2 31.2 - - + +
67E LEU 3.0 14.0 + - - +
68E LEU* 3.0 3.6 + - - +
70E GLN* 1.3 83.2 - - + +
72E ARG* 1.3 61.5 + - - +
74E ARG* 3.2 29.4 + - + +
75E VAL 4.7 0.3 + - - -
28F ASP* 2.7 28.8 + - - +
29F GLU 3.3 12.9 + - - -
31F LEU* 3.8 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E PHE* 3.8 9.2 - - + -
42E SER* 5.5 4.2 - - - +
45E GLY* 2.7 33.2 + - - +
46E GLU* 4.6 2.6 - - - +
65E LYS* 5.0 12.7 + - - +
68E LEU* 2.6 58.8 + - - +
69E GLU* 3.5 11.6 - - - +
71E LYS* 1.3 72.3 - - - +
73E GLY* 1.3 59.2 + - - +
74E ARG 3.6 0.3 + - - -
75E VAL* 4.4 10.0 + - - +
76E ASP* 5.6 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E GLU 3.3 9.5 + - - -
70E GLN 3.1 4.7 + - - -
71E LYS 3.1 1.2 - - - -
72E ARG* 1.3 74.7 - - - +
74E ARG* 1.3 58.4 + - - +
75E VAL* 3.1 3.6 - - - -
76E ASP* 2.8 29.6 + - - +
77E ASN* 3.0 27.1 + - - -
----------------------------------------------------------
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