Contacts of the helix formed by residues 56 - 74 (chain E) in PDB entry 3F5O
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 HIS 56 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E HIS 3.0 18.4 + - - +
49E THR 4.0 4.3 - - - -
50E ASN* 3.8 8.9 - - - +
54E THR 3.2 1.6 + - - -
55E LEU* 1.3 72.8 - - - +
57E GLY* 1.3 62.9 + - - +
58E GLY* 2.8 34.7 + - - -
59E LEU* 3.0 19.2 + - + +
60E THR* 3.0 12.2 + - - -
151E CL 3.7 13.0 - - + +
21F PHE* 3.7 33.1 - + + +
22F GLU* 3.0 42.3 + - - -
62F THR* 3.9 9.8 - - + +
65F ASP* 3.9 6.0 + - - -
66F ASN* 3.1 25.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E LEU 3.4 2.4 + - - -
56E HIS* 1.3 71.0 - - - +
58E GLY* 1.3 55.3 + - - +
60E THR* 3.4 2.8 - - - -
61E ALA* 3.0 18.4 + - - +
90E TYR* 2.8 42.8 + - - -
151E CL 3.1 16.0 - - - +
65F ASP* 3.6 12.1 - - - -
83F SER* 5.2 0.7 - - - -
86F MET* 5.2 0.2 - - - -
150F COA 4.1 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E HIS* 2.8 15.2 - - - -
57E GLY* 1.3 74.1 - - - +
59E LEU* 1.3 60.5 + - - +
61E ALA* 3.4 8.6 + - - +
62E THR* 2.9 30.5 + - - -
21F PHE* 4.0 0.7 - - - -
58F GLY 3.9 0.7 - - - +
61F ALA 4.8 1.3 - - - -
62F THR* 3.3 33.6 + - - -
65F ASP* 3.4 4.6 + - - -
86F MET* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E VAL* 4.2 6.1 - - + +
25E LEU* 3.6 29.8 - - + -
42E MET* 4.4 3.6 - - + -
48E HIS* 3.4 54.3 - - + +
55E LEU* 3.7 11.7 - - + -
56E HIS* 3.0 11.6 + - + +
58E GLY* 1.3 74.5 - - - +
60E THR* 1.3 54.9 + - - +
62E THR* 3.1 6.6 + - - -
63E LEU* 2.8 37.8 + - + +
21F PHE* 3.7 38.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E LEU* 3.2 26.0 + - - +
56E HIS 3.0 9.5 + - - -
57E GLY* 3.4 11.0 - - - -
59E LEU* 1.3 77.3 - - - +
61E ALA* 1.3 56.0 + - - +
63E LEU* 3.2 12.8 + - - +
64E VAL* 2.9 29.0 + - + +
88E ILE* 4.0 8.3 - - + -
90E TYR* 3.7 23.2 - - + -
120E LEU* 4.0 14.8 - - + +
129E ILE* 5.4 2.1 - - + +
130E ALA* 3.8 22.7 - - + -
150F COA 5.8 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E GLY 3.0 14.0 + - - +
58E GLY* 3.5 10.1 - - - +
59E LEU 3.2 0.2 - - - -
60E THR* 1.3 76.8 - - - +
62E THR* 1.3 57.1 + - - +
64E VAL* 3.2 3.2 + - - +
65E ASP* 2.9 30.2 + - - +
86E MET* 3.7 6.3 - - + +
88E ILE* 3.7 29.2 - - + -
90E TYR* 4.5 0.2 + - - -
58F GLY* 4.9 0.7 - - - -
61F ALA* 3.6 29.4 - - + -
86F MET* 4.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E PHE* 3.6 14.2 - - + +
22E GLU* 6.4 0.2 - - - -
24E VAL* 3.9 25.1 - - + -
25E LEU* 4.2 12.6 - - + -
58E GLY 2.9 16.5 + - - -
59E LEU* 3.1 13.8 + - - -
61E ALA* 1.3 73.9 - - - +
63E LEU* 1.3 54.2 + - - +
65E ASP* 3.6 2.5 - - - +
66E ASN* 2.8 36.3 + - - +
21F PHE* 4.7 0.5 - - - -
56F HIS* 4.1 14.8 - - + +
58F GLY* 3.2 25.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
25E LEU* 3.5 30.1 - - + -
28E ILE* 3.9 19.5 - - + -
42E MET* 4.3 15.0 - - + -
55E LEU* 4.6 2.7 - - + -
59E LEU* 2.8 27.2 + - + +
60E THR* 3.5 9.9 - - - +
62E THR* 1.3 70.7 - - - +
64E VAL* 1.3 66.6 + - - +
67E ILE* 2.9 36.9 + - + +
100E ILE* 4.2 14.4 - - + -
102E ILE* 4.0 25.4 - - + -
120E LEU* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E THR 2.9 19.8 + - - +
61E ALA* 3.2 8.5 + - - +
63E LEU* 1.3 77.5 - - - +
65E ASP* 1.3 55.4 + - - +
68E SER* 2.7 33.8 + - - -
86E MET* 3.7 24.0 - - + -
87E ASN 4.8 0.2 - - - +
88E ILE* 4.4 12.8 - - + -
118E VAL* 3.6 26.2 - - + +
120E LEU* 4.0 20.6 - - + -
132E GLY* 4.3 26.2 - - - +
134E HIS* 4.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ALA 2.9 16.1 + - - +
62E THR* 3.6 7.4 - - - +
64E VAL* 1.3 76.7 - - - +
66E ASN* 1.3 66.9 + - - +
68E SER* 2.9 15.7 + - - -
69E THR* 2.9 25.1 + - - -
83E SER* 3.5 10.6 + - - -
86E MET* 3.9 11.7 - - + +
134E HIS* 3.0 27.0 - - - -
136E LYS* 4.8 1.4 + - - -
149E UOC 5.0 2.3 - - - +
56F HIS* 4.0 3.8 + - - -
57F GLY* 3.6 11.4 + - - -
58F GLY 3.4 22.4 + - - +
90F TYR* 4.8 0.2 + - - -
151F CL 4.2 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E GLU* 2.8 24.1 + - - +
25E LEU* 3.4 30.4 - - + +
62E THR* 2.8 21.2 + - - +
65E ASP* 1.3 79.1 - - - +
67E ILE* 1.3 60.3 + - - +
69E THR* 3.2 1.9 + - - -
70E MET* 2.9 29.7 + - + +
149E UOC 3.1 30.8 - - + +
56F HIS* 3.1 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E LEU* 4.4 8.1 - - + -
28E ILE* 3.8 18.6 - - + -
38E VAL* 3.9 24.5 - - + +
40E CYS* 3.9 12.3 - - + -
63E LEU* 2.9 29.6 + - + +
64E VAL 4.8 0.2 - - - +
66E ASN* 1.3 76.6 - - - +
68E SER* 1.3 61.9 + - - +
70E MET* 3.2 30.9 + - + +
71E ALA 3.1 17.3 + - - -
102E ILE* 3.7 30.5 - - + +
104E ALA* 3.4 20.1 - - + +
118E VAL* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E VAL 2.7 24.3 + - - -
65E ASP 2.9 2.9 + - - -
67E ILE* 1.3 75.3 - - - +
69E THR* 1.3 62.9 + - - +
71E ALA* 3.2 6.0 + - - +
72E LEU* 3.1 24.9 + - - +
104E ALA* 3.6 11.5 - - - +
105E HIS 5.7 0.4 - - - -
116E THR* 3.1 32.1 + - - -
117E SER 5.2 0.2 - - - -
118E VAL* 3.6 11.0 - - - -
134E HIS* 2.8 24.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E ASP* 2.9 17.4 + - - -
66E ASN* 3.2 10.2 + - - -
68E SER* 1.3 78.4 + - - +
70E MET* 1.3 63.4 + - - +
72E LEU* 3.1 11.7 + - - +
73E LEU* 2.9 21.9 + - + +
80E PRO* 3.7 23.6 - - + +
136E LYS* 2.9 36.5 + - - +
149E UOC 3.6 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LEU* 4.2 14.3 - - + +
12E ILE* 3.8 31.6 - - + -
25E LEU* 5.2 1.1 - - + -
28E ILE* 3.8 16.2 - - + -
38E VAL* 3.8 15.5 - - + -
40E CYS* 4.3 7.6 - - - -
66E ASN* 2.9 20.6 + - + +
67E ILE* 3.2 40.6 + - + +
69E THR* 1.3 74.7 - - - +
71E ALA* 1.3 63.3 + - - +
73E LEU* 3.1 22.5 + - + +
74E CYS* 3.1 16.8 + - - -
149E UOC 3.7 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E GLY* 3.7 12.6 - - - +
38E VAL* 3.6 14.7 - - + +
67E ILE 3.1 12.2 + - - +
68E SER* 3.2 9.8 + - - +
70E MET* 1.3 74.1 - - - +
72E LEU* 1.3 62.1 + - - +
74E CYS* 3.1 15.3 + - - +
75E THR* 3.4 13.9 - - - +
104E ALA* 3.9 27.6 - - + +
105E HIS* 4.3 1.1 - - - -
106E VAL* 3.8 17.0 - - + +
116E THR* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E SER 3.1 14.7 + - - +
69E THR* 3.1 8.9 + - - +
71E ALA* 1.3 72.5 - - - +
73E LEU* 1.3 61.6 + - - +
74E CYS 3.1 1.8 - - - -
75E THR* 2.6 26.9 + - - -
78E GLY* 3.6 7.6 - - - -
79E ALA 3.7 17.2 + - - +
80E PRO* 3.9 9.0 - - + +
106E VAL* 3.8 23.1 - - + -
109E GLN* 4.3 14.1 - - - +
114E ALA* 3.6 33.9 - - + -
116E THR* 3.9 14.6 - - - +
136E LYS* 3.7 32.1 - - + -
138E LEU* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LEU* 4.7 14.1 - - + -
11E VAL* 5.3 9.9 - - + -
15E MET* 6.1 0.9 - - - -
69E THR* 2.9 18.3 + - + +
70E MET* 3.1 17.2 + - - +
72E LEU* 1.3 76.3 - - - +
74E CYS* 1.3 60.5 + - - +
75E THR 3.1 7.6 + - - +
78E GLY* 3.6 30.3 - - - +
80E PRO* 3.8 25.4 - - + -
149E UOC 4.5 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E MET* 3.9 26.1 - - - +
8E LEU* 3.9 18.2 - - - -
33E ALA* 3.9 27.6 - - - -
34E ALA 3.6 15.5 - - - +
35E PRO* 3.1 10.0 - - - +
36E GLY 2.9 16.3 + - - -
38E VAL* 4.0 3.1 - - + -
70E MET 3.1 16.0 + - - +
71E ALA* 3.1 13.2 + - - +
72E LEU 3.1 1.4 - - - -
73E LEU* 1.3 75.8 - - - +
75E THR* 1.3 59.6 + - - +
----------------------------------------------------------
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