Contacts of the helix formed by residues 48 - 76 (chain J) in PDB entry 2FFX
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 LEU 48 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J PHE* 3.1 31.1 + - + +
46J VAL* 3.6 12.1 - - + +
47J ALA* 1.3 80.1 - - - +
49J GLU* 1.3 65.6 + - - +
50J GLY 3.3 2.7 - - - -
51J VAL* 3.1 15.6 + - + +
52J SER 2.9 17.7 + - - -
96J THR* 3.3 13.2 - - - +
167J GLU* 3.2 39.7 - - + +
168J TYR* 4.8 11.4 - - + -
171J GLU* 4.0 26.9 - - + +
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Residues in contact with GLU 49 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J PHE 5.0 0.4 - - - -
47J ALA 3.8 2.6 + - - -
48J LEU* 1.3 72.7 - - - +
50J GLY* 1.3 57.5 + - - +
52J SER* 3.2 7.4 + - - -
53J HIS* 2.8 33.0 + - + +
171J GLU* 3.5 9.3 + - - +
172J ARG* 4.5 11.6 + - - +
177J HIS* 4.5 20.2 - - + +
204J CD 2.4 30.4 - - - -
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Residues in contact with GLY 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J GLU* 1.3 73.4 - - - +
51J VAL* 1.3 56.2 + - - +
53J HIS* 3.8 2.3 + - - +
54J PHE* 3.0 27.0 + - - +
171J GLU* 2.8 26.5 + - - -
175J LEU* 3.7 18.0 - - - +
176J LYS 3.4 22.4 + - - +
177J HIS* 4.3 3.5 - - - +
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Residues in contact with VAL 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J PHE* 3.5 27.4 - - + -
48J LEU* 3.1 23.8 + - + +
50J GLY* 1.3 72.4 - - - +
52J SER* 1.3 66.6 + - - +
54J PHE* 3.2 5.0 + - + +
55J PHE* 3.1 47.1 + - + -
96J THR* 3.8 26.5 - - + +
100J MET* 5.8 1.3 - - + -
170J PHE* 5.6 0.2 - - + -
171J GLU* 4.0 9.4 - - + +
175J LEU* 3.5 22.9 - - + -
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Residues in contact with SER 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J GLY* 2.7 30.9 + - - -
41J PHE* 3.8 17.4 - - - +
42J ASP* 3.9 11.5 + - - +
48J LEU 2.9 12.3 + - - -
49J GLU* 3.5 12.8 - - - -
51J VAL* 1.3 78.1 - - - +
53J HIS* 1.3 56.6 - - - +
55J PHE 3.4 0.3 + - - -
56J ARG* 2.9 44.2 + - - +
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Residues in contact with HIS 53 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J GLU* 2.8 20.0 + - + +
50J GLY 3.8 4.0 + - - +
52J SER* 1.3 74.7 - - - +
54J PHE* 1.3 67.1 + - - +
56J ARG* 3.9 7.4 - - + +
57J GLU* 3.0 57.3 + - + +
176J LYS* 3.4 56.6 + - + +
177J HIS* 5.7 2.2 - - - -
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Residues in contact with PHE 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J GLY 3.0 16.2 + - - +
51J VAL* 3.2 11.6 + - - +
53J HIS* 1.3 80.4 + - - +
55J PHE* 1.3 81.6 + + - +
57J GLU* 3.4 5.8 + - - +
58J LEU* 3.2 48.5 + - + +
100J MET* 3.7 27.4 - - + -
144J LEU* 5.0 6.5 - - + -
147J LYS* 4.9 6.7 - - + -
148J MET* 4.4 12.1 - - + -
151J HIS* 4.0 28.3 - + - -
175J LEU* 4.2 19.1 - - + -
176J LYS* 6.1 3.1 - - - +
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Residues in contact with PHE 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR* 3.4 31.6 - + + +
37J LEU* 3.7 19.1 - - + -
38J GLY* 3.7 18.8 - - - +
41J PHE* 3.9 17.7 - + - -
51J VAL* 3.1 43.9 + - + +
54J PHE* 1.3 97.6 - + - +
56J ARG* 1.3 65.0 + - - +
57J GLU 3.2 0.2 - - - -
58J LEU* 3.1 3.9 + - + +
59J ALA 3.0 18.2 + - - -
96J THR 5.5 0.2 - - - -
99J ALA* 3.9 26.0 - - + -
100J MET* 4.2 8.3 - - + -
103J ALA* 3.7 24.9 - - + -
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Residues in contact with ARG 56 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR 4.7 1.8 - - - +
35J LEU* 5.5 4.6 - - + +
38J GLY* 3.7 15.7 - - - -
39J PHE* 3.7 42.1 - - + +
42J ASP* 6.2 1.8 - - - -
52J SER* 2.9 38.6 + - - +
53J HIS* 3.9 7.9 - - + +
55J PHE* 1.3 75.9 - - - +
57J GLU* 1.3 66.0 + - - +
59J ALA* 3.3 17.2 + - - +
60J GLU* 3.3 12.0 + - - +
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Residues in contact with GLU 57 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J HIS* 3.0 55.8 + - + +
54J PHE* 3.6 7.0 - - - +
55J PHE 3.2 0.2 - - - -
56J ARG* 1.3 81.4 - - - +
58J LEU* 1.3 57.9 + - + +
60J GLU* 3.2 11.8 + - - +
61J GLU* 3.0 33.8 + - + +
176J LYS* 4.5 7.8 + - - +
205J CD 2.6 30.0 - - - -
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Residues in contact with LEU 58 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR* 3.7 30.3 - - + -
54J PHE* 3.2 36.0 + - + +
55J PHE* 3.1 10.8 + - + +
57J GLU* 1.3 76.1 - - + +
59J ALA* 1.3 65.5 + - - +
61J GLU* 3.1 16.4 + - + +
62J LYS* 2.9 29.5 + - - +
107J GLU* 5.2 0.2 - - - +
144J LEU* 3.8 32.8 - - + -
148J MET* 3.6 27.1 - - + -
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Residues in contact with ALA 59 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J SER* 2.9 36.6 + - - +
34J TYR* 3.6 22.2 - - + +
35J LEU* 4.0 14.1 - - + +
55J PHE 3.0 7.8 + - - +
56J ARG* 3.4 13.0 - - - +
57J GLU 3.2 0.4 - - - -
58J LEU* 1.3 76.7 - - - +
60J GLU* 1.3 62.1 + - - +
62J LYS 3.4 0.5 + - - -
63J ARG* 3.1 12.8 + - - +
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Residues in contact with GLU 60 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J ARG 3.3 8.5 + - - +
57J GLU* 3.2 13.4 + - - +
58J LEU 3.2 0.4 - - - -
59J ALA* 1.3 77.7 - - - +
61J GLU* 1.3 70.4 + - - +
63J ARG* 3.2 28.3 + - - +
64J GLU* 3.1 42.9 + - - +
205J CD 2.5 29.6 - - - -
206J CD 4.1 3.5 - - - -
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Residues in contact with GLU 61 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J TYR* 5.4 0.2 - - - -
57J GLU* 3.0 23.4 + - + +
58J LEU* 3.1 24.0 + - + +
60J GLU* 1.3 82.7 - - - +
62J LYS* 1.3 68.2 - - + +
64J GLU* 3.4 9.4 + - - +
65J GLY* 3.1 17.0 + - - -
140J GLU* 5.5 1.9 - - - +
144J LEU* 6.3 0.4 - - + -
206J CD 2.5 25.8 - - - -
207J CD 2.5 28.3 - - - -
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Residues in contact with LYS 62 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J TYR* 3.5 23.0 - - + +
30J ALA* 4.1 6.5 - - + -
31J SER* 3.8 21.8 - - - +
34J TYR* 3.9 19.7 - - + -
58J LEU* 2.9 21.4 + - - +
59J ALA 3.9 0.2 - - - +
61J GLU* 1.3 79.9 - - - +
63J ARG* 1.3 66.4 + - - +
65J GLY* 3.0 9.0 + - - -
66J TYR* 3.0 18.8 + - - -
107J GLU* 2.7 43.5 + - - -
110J LEU* 3.6 18.6 - - + +
141J GLU* 2.9 17.6 + - - -
144J LEU* 4.0 9.8 - - - +
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Residues in contact with ARG 63 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J SER* 4.2 2.9 + - - +
59J ALA 3.1 13.7 + - - +
60J GLU* 3.4 39.0 + - - +
61J GLU 3.2 0.2 - - - -
62J LYS* 1.3 77.8 - - - +
64J GLU* 1.3 70.7 + - - +
66J TYR* 3.3 35.6 + - + +
67J GLU* 2.7 77.2 + - - +
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Residues in contact with GLU 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60J GLU* 3.1 33.2 + - - +
61J GLU* 3.4 13.3 - - - +
63J ARG* 1.3 89.7 + - - +
65J GLY* 1.3 57.2 + - - +
67J GLU* 3.9 10.4 - - - +
68J ARG* 3.0 48.4 + - - +
206J CD 2.5 30.8 - - - -
207J CD 3.8 10.7 - - - -
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Residues in contact with GLY 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J TYR* 4.0 10.3 - - - -
61J GLU 3.1 11.0 + - - -
62J LYS 3.0 8.9 + - - -
64J GLU* 1.3 77.7 - - - +
66J TYR* 1.3 60.2 + - - +
68J ARG* 3.2 15.1 + - - -
69J LEU* 3.1 25.8 + - - +
137J PHE* 3.5 16.4 - - - -
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Residues in contact with TYR 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J VAL* 4.1 17.4 - - + +
27J TYR* 3.8 15.7 - - + -
28J LEU* 3.4 49.4 - - + +
31J SER* 4.2 10.9 + - - -
62J LYS 3.0 22.4 + - - -
63J ARG* 3.4 39.4 - - + +
65J GLY* 1.3 72.3 - - - +
67J GLU* 1.3 76.7 + - + +
69J LEU* 3.7 10.2 - - - +
70J LEU* 2.9 44.9 + - + +
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Residues in contact with GLU 67 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J ARG* 2.7 61.7 + - - +
64J GLU* 3.9 9.5 - - - +
66J TYR* 1.3 91.5 - - + +
68J ARG* 1.3 58.2 + - - +
70J LEU* 3.4 9.4 + - + +
71J LYS* 3.0 28.6 + - - +
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Residues in contact with ARG 68 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64J GLU* 3.0 38.3 + - - +
65J GLY* 3.6 8.3 - - - +
67J GLU* 1.3 75.8 - - - +
69J LEU* 1.3 63.5 + - - +
71J LYS* 3.3 11.5 + - + +
72J MET* 3.0 23.6 + - - +
132J PHE* 3.7 12.2 - - + -
136J HIS* 3.2 55.4 + - + +
137J PHE* 3.4 25.9 - - + -
140J GLU* 6.0 0.4 + - - -
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Residues in contact with LEU 69 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J VAL* 4.0 19.6 - - + +
23J LEU* 3.8 41.5 - - + -
24J VAL* 3.7 20.2 - - + +
27J TYR* 4.2 12.8 - - + -
65J GLY 3.1 19.3 + - - +
66J TYR* 3.7 14.4 - - - +
68J ARG* 1.3 76.2 - - - +
70J LEU* 1.3 58.5 + - - +
72J MET* 3.3 6.1 + - + +
73J GLN* 2.9 28.6 + - - +
117J LEU* 5.0 1.8 - - + -
132J PHE* 3.7 26.2 - - + -
133J LEU* 4.9 3.1 - - + -
137J PHE* 3.8 12.3 - - + -
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Residues in contact with LEU 70 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J ASN* 5.1 3.4 - - - +
24J VAL* 3.7 25.6 - - + -
66J TYR* 2.9 37.8 + - + +
67J GLU* 3.6 8.3 - - + +
68J ARG 3.3 0.2 - - - -
69J LEU* 1.3 77.0 - - - +
71J LYS* 1.3 64.5 + - - +
73J GLN* 3.3 7.9 + - + +
74J ASN* 3.2 26.2 + - - +
80J ALA* 4.0 19.0 - - + +
82J PHE* 3.9 36.1 - - + -
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Residues in contact with LYS 71 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J GLU 3.0 17.2 + - - +
68J ARG* 3.6 11.9 - - + +
69J LEU 3.3 0.2 - - - -
70J LEU* 1.3 76.3 - - - +
72J MET* 1.3 58.9 + - - +
74J ASN* 3.3 8.5 + - - +
75J GLN* 3.0 58.4 + - + +
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Residues in contact with MET 72 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J TYR* 4.0 11.4 - - - -
20J VAL* 3.9 25.8 - - + -
68J ARG 3.0 17.1 + - - +
69J LEU* 3.6 5.2 - - + +
70J LEU 3.3 0.2 - - - -
71J LYS* 1.3 75.6 - - - +
73J GLN* 1.3 67.1 + - - +
75J GLN* 3.1 15.9 + - + +
76J ARG* 3.0 39.3 + - + +
128J HIS* 4.7 10.3 - - + +
129J LEU* 3.7 28.9 - - + -
132J PHE* 3.6 43.7 - - + -
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Residues in contact with GLN 73 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J TYR* 2.7 39.4 + - - -
17J GLU* 3.2 23.7 + - - +
20J VAL* 3.8 11.8 - - + +
21J ASN* 3.1 29.2 + - - +
69J LEU 2.9 14.4 + - - +
70J LEU* 3.4 15.9 - - + +
72J MET* 1.3 83.8 - - - +
74J ASN* 1.3 60.8 + - - +
76J ARG* 3.4 2.1 + - - +
77J GLY 3.3 2.4 + - - -
78J GLY* 2.8 45.8 + - - +
79J ARG 3.9 2.0 + - - +
80J ALA* 4.0 15.7 - - + +
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Residues in contact with ASN 74 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J ILE* 3.6 10.6 - - - +
70J LEU 3.2 12.2 + - - +
71J LYS* 3.7 9.3 - - - +
72J MET 3.2 0.2 - - - -
73J GLN* 1.3 80.7 - - - +
75J GLN* 1.3 65.6 + - + +
77J GLY* 3.1 10.0 + - - -
78J GLY 3.7 14.4 - - - +
79J ARG* 3.8 11.6 + - - +
80J ALA* 5.0 7.7 + - - +
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Residues in contact with GLN 75 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J ILE* 3.4 17.0 - - - +
71J LYS* 3.0 47.5 + - + +
72J MET* 3.1 25.8 + - + +
74J ASN* 1.3 76.2 - - - +
76J ARG* 1.3 63.8 + - + +
128J HIS* 5.1 8.2 - - + -
132J PHE* 5.6 1.9 - - - -
----------------------------------------------------------
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Residues in contact with ARG 76 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J ILE* 4.2 4.8 - - - +
9J ARG* 3.6 24.1 - - - +
10J GLN 3.1 21.7 + - - +
11J ASN* 3.0 31.5 + - - +
12J TYR* 3.5 40.4 - - + +
72J MET* 3.0 36.0 + - + +
73J GLN 3.9 0.4 - - - +
75J GLN* 1.3 79.9 - - + +
77J GLY* 1.3 60.3 + - - +
78J GLY 3.3 0.4 + - - -
126J ASP* 3.2 30.7 + - - -
128J HIS* 3.7 35.6 + - - +
129J LEU* 4.1 4.2 - - - +
----------------------------------------------------------
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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