Contacts of the helix formed by residues 45 - 71 (chain J) in PDB entry 1MFR
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 45 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 4.0 2.9 - - - -
146A ASP* 3.0 34.8 + - + -
150A ASN* 5.8 0.4 - - - -
37J PHE 4.6 1.8 - - - -
38J ASP* 3.4 44.0 + - - -
43J ALA* 3.3 15.5 + - + -
44J LEU* 1.3 68.6 - - - +
46J ASN* 1.3 65.3 + - - +
48J ALA* 3.5 6.9 - - - +
49J GLU* 3.1 30.0 + - - +
167J ASP* 3.6 3.2 + - - +
67X LYS* 5.2 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 46 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J HIS* 1.3 79.0 - - - +
47J VAL* 1.3 66.1 + - - +
49J GLU* 3.3 8.6 + - - +
50J PHE 3.0 17.7 + - - -
167J ASP* 3.0 45.2 + - - +
168J LYS* 4.4 11.3 - - - +
171J VAL* 3.2 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J PHE* 3.9 20.0 - - + -
44J LEU* 3.5 19.3 - - + +
46J ASN* 1.3 76.1 - - - +
48J ALA* 1.3 62.1 + - - +
50J PHE* 3.2 8.9 + - - +
51J PHE* 3.2 45.3 + - + -
92J THR* 4.1 26.5 - - + +
96J MET* 4.6 4.9 - - + -
163J GLU 5.8 0.2 - - - +
166J PHE* 4.3 13.0 - - + -
167J ASP* 3.1 22.8 + - + +
171J VAL* 4.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR* 3.2 39.8 - - + +
37J PHE* 3.7 24.8 - - + +
38J ASP* 4.1 4.5 - - + +
44J LEU 3.0 13.9 + - - +
45J HIS* 3.5 15.3 - - - +
46J ASN 3.2 0.2 - - - -
47J VAL* 1.3 78.3 - - - +
49J GLU* 1.3 58.4 + - - +
51J PHE* 3.4 1.7 + - - -
52J LYS 3.0 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR* 3.6 23.9 + - - -
45J HIS* 3.1 18.7 + - + +
46J ASN* 3.3 11.2 + - - +
48J ALA* 1.3 74.2 - - - +
50J PHE* 1.3 60.9 + - - +
52J LYS* 3.3 24.5 + - - +
53J GLU* 2.9 39.8 + - - +
67X LYS* 5.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J TYR* 5.9 0.4 - + - -
46J ASN 3.0 13.4 + - - +
47J VAL* 3.2 10.3 + - - +
49J GLU* 1.3 77.3 - - - +
51J PHE* 1.3 91.6 + + - +
53J GLU* 3.5 7.7 + - - +
54J HIS* 3.2 54.3 + + - -
96J MET* 4.0 19.7 - - + -
143J ARG* 3.9 17.9 - - - -
144J ILE* 4.5 12.1 - - + -
147J PHE* 3.7 29.6 - + - -
171J VAL* 3.7 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J TYR* 3.6 48.8 - + - +
33J MET* 3.8 29.6 - - + -
34J TYR 4.0 4.0 - - - +
37J PHE* 3.7 22.9 - + - -
47J VAL* 3.2 37.0 + - + -
48J ALA* 3.9 5.2 - - - +
50J PHE* 1.3 98.3 - + - +
52J LYS* 1.3 60.3 + - - +
54J HIS* 3.2 5.0 + - + +
55J SER* 2.9 24.1 + - - -
92J THR 5.7 0.2 - - - -
95J ALA* 4.1 12.1 - - + -
96J MET* 3.7 23.6 - - + -
99J ALA* 4.2 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 52 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR* 3.7 39.4 + - + +
48J ALA 3.0 17.8 + - - +
49J GLU* 3.6 34.3 + - - +
50J PHE 3.3 0.2 - - - -
51J PHE* 1.3 75.9 - - - +
53J GLU* 1.3 63.6 + - + +
55J SER* 3.2 20.8 + - - +
56J HIS* 3.3 29.7 + - + +
63X GLU* 3.7 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J GLU* 2.9 26.2 + - + +
50J PHE* 3.6 8.8 - - + +
52J LYS* 1.3 78.5 - - + +
54J HIS* 1.3 62.1 - - + +
56J HIS* 3.3 10.0 + - - +
57J GLU* 3.1 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 54 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J TYR* 3.9 24.4 - + + -
50J PHE* 3.2 40.5 + + - +
51J PHE* 3.4 10.3 - - - +
53J GLU* 1.3 82.0 - - + +
55J SER* 1.3 64.2 + - - +
57J GLU* 3.6 17.1 + - - +
58J GLU* 3.2 32.2 + - - +
103J GLU* 3.6 17.5 + - - -
140J ASP* 3.7 26.7 - - + -
143J ARG* 3.1 27.1 + - - -
144J ILE* 4.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J SER* 2.9 47.1 + - - +
30J TYR* 3.7 14.1 - - - +
31J SER* 3.8 14.8 - - - -
51J PHE 2.9 9.4 + - - -
52J LYS* 3.2 16.6 + - - +
53J GLU 3.3 0.4 - - - -
54J HIS* 1.3 74.9 - - - +
56J HIS* 1.3 75.0 + - - +
58J GLU 3.4 0.9 + - - -
59J ARG* 3.1 12.0 + - - +
63X GLU* 4.5 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 56 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J LYS* 3.4 28.9 + - + +
53J GLU* 3.3 12.3 + - - +
54J HIS 3.2 0.2 - - - -
55J SER* 1.3 90.6 + - - +
57J GLU* 1.3 56.4 + - - +
59J ARG* 3.5 7.8 + - + +
60J GLU* 3.1 26.0 + - - +
59X ARG* 6.0 3.1 - - + +
63X GLU* 3.0 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J GLU* 3.1 21.6 + - - +
54J HIS* 3.6 25.3 + - - +
55J SER 3.2 0.2 - - - -
56J HIS* 1.3 75.4 - - - +
58J GLU* 1.3 64.0 + - + +
60J GLU* 3.2 6.9 + - - +
61J HIS* 3.0 46.0 + - + +
140J ASP* 4.1 18.0 - - - +
143J ARG* 5.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J GLU* 2.7 30.9 - - - +
26J ALA* 4.2 9.0 - - + -
27J SER* 3.8 13.0 - - - +
30J TYR* 4.0 17.5 - - + -
54J HIS* 3.2 21.0 + - - +
57J GLU* 1.3 80.1 - - - +
59J ARG* 1.3 58.3 + - - +
61J HIS* 3.1 11.1 + - - +
62J ALA* 3.0 25.8 + - - +
103J GLU* 3.4 14.9 - - - +
106J VAL* 5.7 0.7 - - - -
176J MG 2.0 31.9 - - - -
177J MG 2.6 24.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J LEU* 4.9 11.7 - - + -
27J SER* 3.6 14.3 + - - +
55J SER 3.1 17.7 + - - +
56J HIS* 3.6 10.3 - - + +
57J GLU 3.1 0.2 - - - -
58J GLU* 1.3 73.6 - - - +
60J GLU* 1.3 63.3 + - - +
62J ALA* 3.2 8.7 + - - +
63J GLU* 3.1 36.8 + - + +
56X HIS* 6.1 2.0 - - + +
59X ARG* 5.7 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J HIS 3.1 15.1 + - - +
57J GLU* 3.2 10.7 + - - +
59J ARG* 1.3 75.5 - - - +
61J HIS* 1.3 59.9 + - + +
63J GLU* 3.5 11.6 + - - +
64J LYS* 3.1 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 61 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J GLU* 3.4 15.2 + - - +
57J GLU* 3.0 30.9 + - + +
58J GLU* 3.1 18.4 + - - +
59J ARG 3.2 0.4 - - - -
60J GLU* 1.3 78.4 - - + +
62J ALA* 1.3 63.1 + - - +
64J LYS* 3.4 18.2 + - - +
65J PHE* 3.3 12.9 + - - -
132J GLU 4.6 6.9 + - - -
133J TYR* 3.0 39.8 + + + -
136J GLU* 5.1 13.5 - - + +
137J GLN* 5.1 1.3 - - - -
140J ASP* 5.6 0.2 - - - -
176J MG 2.7 24.9 - - - -
177J MG 4.3 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J LEU* 3.7 16.2 - - + +
23J GLU* 3.8 10.3 - - + +
24J LEU* 3.7 34.3 - - + -
58J GLU 3.0 11.9 + - - +
59J ARG 3.2 8.9 + - - +
61J HIS* 1.3 75.1 - - - +
63J GLU* 1.3 63.9 + - + +
65J PHE* 3.3 8.6 + - - +
66J MET* 3.1 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J LEU* 6.4 0.4 - - + -
59J ARG* 3.1 25.0 + - + +
60J GLU* 3.8 12.5 - - - +
62J ALA* 1.3 75.3 - - + +
64J LYS* 1.3 64.3 + - - +
66J MET* 3.2 25.1 + - + +
67J LYS* 3.1 23.9 + - - +
31X SER* 4.8 5.8 + - - +
34X TYR* 5.1 10.3 - - + -
52X LYS* 3.7 20.0 + - - +
55X SER* 4.4 4.5 + - - -
56X HIS* 3.1 35.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60J GLU* 3.1 19.6 + - - +
61J HIS* 3.6 17.4 + - - +
62J ALA 3.3 0.4 - - - -
63J GLU* 1.3 77.1 - - - +
65J PHE* 1.3 58.6 + - - +
67J LYS* 3.5 8.1 + - - +
68J TYR* 2.9 26.5 + - - +
128J PHE* 3.7 10.1 - - + -
132J GLU* 2.9 53.1 + - + +
133J TYR* 3.2 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J VAL* 3.9 30.2 - - + +
19J MET* 3.4 33.0 - - + -
20J LEU* 4.2 18.6 - - + +
23J GLU* 4.1 15.0 - - + -
61J HIS 3.3 17.1 + - - -
62J ALA 3.3 8.9 + - - +
63J GLU 3.2 0.2 - - - -
64J LYS* 1.3 79.3 - - - +
66J MET* 1.3 65.3 + - - +
68J TYR* 3.5 3.1 - - + +
69J GLN* 3.0 24.8 + - - +
110J LEU* 4.0 10.5 - - + -
113J LEU* 4.5 7.6 - - + -
125J LEU* 5.3 0.2 - - + -
128J PHE* 3.5 24.7 - + - -
129J LEU* 4.0 11.7 - - + -
133J TYR* 3.4 31.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 66 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J LEU* 3.8 29.8 - - + +
24J LEU* 5.1 7.6 - - + -
62J ALA* 3.1 21.1 + - + +
63J GLU* 3.2 23.5 + - + +
65J PHE* 1.3 75.8 - - - +
67J LYS* 1.3 62.9 + - - +
69J GLN* 3.4 4.9 - - - +
70J ASN* 3.3 26.3 + - - -
76J VAL* 3.9 21.0 - - + +
78J LEU* 4.7 7.4 - - + -
28X TYR* 5.5 0.2 - - + -
31X SER* 3.3 40.8 - - - +
34X TYR* 4.6 14.8 - - + -
35X ALA* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J GLU 3.1 10.0 + - - +
64J LYS* 3.6 10.8 - - - +
66J MET* 1.3 78.8 - - - +
68J TYR* 1.3 56.8 + - - +
70J ASN* 3.5 3.1 + - - +
71J LYS* 3.0 45.1 + - + +
142Q LYS* 6.0 0.6 - - - +
34X TYR* 3.3 30.1 - - - +
38X ASP* 3.2 32.9 + - - +
45X HIS* 5.1 4.8 + - - -
49X GLU* 5.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 68 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J TYR* 3.9 18.4 - + - -
16J VAL* 4.6 7.4 - - + -
64J LYS 2.9 18.8 + - - +
65J PHE* 3.5 7.0 - - - +
67J LYS* 1.3 74.9 - - - +
69J GLN* 1.3 68.2 + - - +
71J LYS* 3.1 17.4 + - + +
72J ARG* 2.8 52.6 + - + +
124J HIS* 2.8 41.7 + + - -
125J LEU* 3.2 36.3 - - + -
128J PHE* 3.6 43.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J TYR* 3.0 36.0 + - - -
13J GLU* 3.2 28.1 + - - +
16J VAL* 3.5 14.2 - - + +
17J ASN* 3.4 18.6 + - - -
20J LEU* 5.8 0.8 - - + +
65J PHE 3.0 15.5 + - - +
66J MET 3.4 6.1 - - - +
68J TYR* 1.3 82.7 - - - +
70J ASN* 1.3 60.9 + - - +
72J ARG* 3.2 5.1 + - - +
73J GLY 3.1 3.6 + - - -
74J GLY* 2.9 42.9 + - - -
75J ARG 4.0 6.7 - - - -
76J VAL* 3.7 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 70 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J VAL* 4.5 0.5 - - - +
66J MET 3.3 12.3 + - - +
67J LYS 3.9 2.9 - - - +
68J TYR 3.3 0.2 - - - -
69J GLN* 1.3 76.4 - - - +
71J LYS* 1.3 65.2 + - - +
73J GLY* 3.2 10.7 + - - -
74J GLY 3.9 11.8 - - - +
75J ARG* 4.0 2.3 + - - +
76J VAL* 4.6 9.2 + - - +
142Q LYS* 3.3 17.4 - - - +
34X TYR* 6.3 0.2 - - - -
35X ALA* 3.0 30.5 + - - +
38X ASP* 3.2 39.0 + - - +
39X ARG* 3.3 28.7 - - - +
40X ASP* 4.9 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J VAL* 3.4 17.7 - - - +
67J LYS* 3.0 30.0 + - + +
68J TYR* 3.1 22.1 + - + +
70J ASN* 1.3 76.5 - - - +
72J ARG* 1.3 63.5 + - + +
128J PHE* 6.2 2.4 - - - -
135Q GLU* 2.8 36.9 + - - +
138Q VAL* 4.3 25.5 - - + +
139Q LYS* 4.6 10.7 - - - +
142Q LYS* 4.1 27.2 - - + +
----------------------------------------------------------
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