Contacts of the helix formed by residues 45 - 60 (chain F) in PDB entry 2CNW
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 45 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F LEU 4.5 1.4 + - - -
40F LEU* 3.4 12.7 + - - +
43F ASP* 3.2 4.0 - - - +
44F VAL* 1.3 80.3 - - - +
46F LEU* 1.3 60.2 + - - -
47F SER 3.8 0.9 - - - -
48F ALA 4.5 0.4 - - - -
49F THR* 2.5 34.8 + - - -
234F GLN* 3.3 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ARG* 3.4 33.0 - - - +
36C ARG* 3.3 61.7 - - + +
39C MET* 4.9 6.1 - - + -
40C ASP* 3.7 22.3 + - + +
40F LEU* 4.0 23.1 - - + -
45F GLY* 1.3 71.1 - - - +
47F SER* 1.3 61.9 + - - +
49F THR* 3.0 4.3 + - - -
50F GLU* 2.8 43.4 + - - +
234F GLN* 4.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 47 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ARG* 5.6 0.4 - - - +
46F LEU* 1.3 78.6 + - - +
48F ALA* 1.3 59.8 + - - +
50F GLU* 3.9 16.1 - - - +
51F GLU* 3.1 24.3 + - - +
268F PRO* 5.8 0.7 - - - +
271F ARG* 3.4 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F VAL* 3.6 31.2 - - + +
45F GLY 4.2 0.8 + - - -
46F LEU 3.2 0.6 - - - -
47F SER* 1.3 80.7 + - - +
49F THR* 1.3 57.9 + - - +
51F GLU* 3.8 3.6 - - - +
52F ILE* 3.0 37.4 + - + +
75F MET* 4.4 0.4 - - - +
267F ILE* 4.1 15.3 - - + -
268F PRO* 4.3 5.6 - - + -
271F ARG* 4.0 25.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 49 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ARG* 6.1 2.2 - - - +
36F GLU* 4.1 17.9 - - + +
39F LEU* 3.8 20.2 - - + +
40F LEU* 3.6 19.3 - - + +
44F VAL* 3.7 13.5 - - - +
45F GLY 2.5 24.4 + - - -
46F LEU* 3.0 4.8 + - - -
48F ALA* 1.3 76.1 - - - +
50F GLU* 1.3 64.5 + - - +
52F ILE* 3.5 7.2 + - - +
53F LEU* 3.0 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ARG* 4.1 6.8 + - - -
36C ARG* 3.0 40.6 + - - +
46F LEU* 2.8 33.8 + - - +
47F SER* 3.9 13.0 + - - +
49F THR* 1.3 69.6 - - - +
51F GLU* 1.3 58.2 + - - +
53F LEU* 3.2 7.6 + - - +
54F GLN* 2.8 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F SER 3.1 16.3 + - - +
48F ALA* 3.8 5.6 - - - +
50F GLU* 1.3 78.8 - - - +
52F ILE* 1.3 64.8 + - - +
54F GLN* 3.5 5.0 + - - +
55F GLU* 3.1 52.5 + - + +
71F LYS* 3.1 29.5 + - - -
75F MET* 3.3 16.4 - - + +
271F ARG* 5.1 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F LEU* 4.8 12.3 - - + -
39F LEU* 4.1 24.7 - - + -
44F VAL* 4.7 3.8 - - + -
48F ALA 3.0 25.7 + - - +
49F THR 3.9 3.6 - - - +
50F GLU 3.2 0.2 - - - -
51F GLU* 1.3 80.2 - - - +
53F LEU* 1.3 64.4 + - - +
55F GLU* 3.1 14.2 + - - +
56F VAL* 3.1 21.8 + - + +
68F VAL* 5.1 5.6 - - + -
71F LYS* 4.1 13.2 - - + +
72F LEU* 3.4 32.1 - - + -
75F MET* 3.8 26.7 - - + -
267F ILE* 4.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LEU* 3.9 40.9 - - + +
35F LEU* 3.7 29.8 - - + -
36F GLU* 3.5 44.0 - - + +
39F LEU* 5.4 1.3 - - + -
49F THR* 3.0 31.3 + - + +
50F GLU* 3.9 4.9 - - - +
52F ILE* 1.3 76.5 - - + +
54F GLN* 1.3 56.8 + - - +
56F VAL* 3.3 6.5 - - - +
57F ARG* 3.0 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F GLU* 2.8 25.9 + - + +
51F GLU* 3.9 6.1 - - - +
53F LEU* 1.3 73.3 - - - +
55F GLU* 1.3 62.1 + - + +
57F ARG* 3.0 47.2 + - - +
58F ALA* 3.4 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F GLU* 3.1 45.0 + - + +
52F ILE* 3.1 6.4 + - - +
54F GLN* 1.3 80.7 - - + +
56F VAL* 1.3 63.0 + - + +
58F ALA* 3.5 5.8 + - - +
59F SER* 2.9 25.6 + - - -
71F LYS* 3.1 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LEU* 4.2 13.7 - - + -
35F LEU* 4.6 13.7 - - + -
52F ILE* 3.1 18.3 + - + +
53F LEU* 3.3 20.0 - - - +
55F GLU* 1.3 75.7 - - + +
57F ARG* 1.3 61.8 + - - +
58F ALA 3.2 1.8 - - - -
59F SER* 3.3 20.3 + - - -
60F GLY 4.7 1.0 + - - -
64F LEU* 4.8 20.0 - - + +
67F ALA* 4.9 12.1 - - + +
68F VAL* 4.0 30.1 - - + +
71F LYS* 5.6 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F GLU* 5.7 6.1 - - - +
32F LEU* 4.8 17.5 - - + -
53F LEU* 3.0 19.8 + - - +
54F GLN* 3.0 57.6 - - - +
56F VAL* 1.3 77.8 - - - +
58F ALA* 1.3 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F GLN 3.4 15.5 + - - +
55F GLU* 3.7 6.7 - - - +
56F VAL 3.2 0.2 - - - -
57F ARG* 1.3 78.6 - - - +
59F SER* 1.3 68.1 + - - +
60F GLY* 3.4 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F GLU 2.9 15.3 + - - -
56F VAL* 3.3 25.1 + - - -
58F ALA* 1.3 79.7 - - - +
60F GLY* 1.3 61.9 + - - +
61F ARG* 3.2 32.7 + - - +
64F LEU* 6.0 2.7 - - - -
67F ALA* 4.7 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F VAL 4.7 1.4 + - - -
57F ARG 5.5 0.2 + - - -
58F ALA 3.4 3.1 + - - -
59F SER* 1.3 77.8 - - - +
61F ARG* 1.3 64.3 + - - +
62F LYS* 4.0 14.3 - - - +
----------------------------------------------------------
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