Contacts of the helix formed by residues 22 - 54 (chain J) in PDB entry 1F33
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 SER 22 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J ASP 3.6 3.6 + - - -
21J VAL* 1.3 74.6 - - - +
23J ASP* 1.3 65.9 + - - +
24J SER* 3.6 10.3 - - - -
25J GLU* 3.0 32.2 + - - +
26J LYS 2.8 20.6 + - - -
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Residues in contact with ASP 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J THR* 4.7 7.3 + - - +
14J LEU* 3.5 28.8 - - + +
21J VAL 4.2 4.2 - - - +
22J SER* 1.3 73.1 - - - +
24J SER* 1.3 56.8 + - - +
26J LYS* 3.7 6.5 + - - +
27J LYS* 2.8 40.9 + - + +
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Residues in contact with SER 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J SER* 2.9 12.2 - - - -
23J ASP* 1.3 79.4 - - - +
25J GLU* 1.3 60.0 + - - +
27J LYS* 3.4 5.7 + - - +
28J ALA* 3.0 27.3 + - - +
140J LYS* 4.2 12.2 + - - -
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Residues in contact with GLU 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J VAL* 3.7 19.2 - - + +
22J SER* 3.0 18.6 + - - +
24J SER* 1.3 77.7 - - - +
26J LYS* 1.3 58.4 + - - +
28J ALA* 4.2 7.0 - - - -
29J THR* 2.6 44.7 + - - +
140J LYS* 3.1 44.3 - - + +
141J ASP* 3.4 15.6 + - - +
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Residues in contact with LYS 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J LEU* 3.9 20.8 - - + +
15J LEU 5.1 2.4 + - - -
17J THR* 3.3 24.0 + - - +
19J ASN* 2.8 31.2 + - - -
21J VAL* 2.9 37.5 + - + +
22J SER 2.8 20.5 + - - +
23J ASP* 3.7 10.1 + - - +
25J GLU* 1.3 71.5 - - - +
27J LYS* 1.3 57.5 + - - +
29J THR* 3.8 2.3 - - - -
30J VAL* 2.8 38.0 + - - +
87J LEU* 3.1 36.8 - - + +
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Residues in contact with LYS 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J THR* 3.5 20.7 + - - -
13J ASN* 2.9 39.0 - - + +
14J LEU* 3.5 29.1 - - + +
23J ASP* 2.8 31.1 + - + +
24J SER* 3.5 5.4 - - - +
26J LYS* 1.3 78.0 - - - +
28J ALA* 1.3 61.3 + - - +
30J VAL* 3.6 4.4 + - - +
31J GLU* 3.2 23.9 + - - +
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Residues in contact with ALA 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J SER 3.0 13.1 + - - +
25J GLU 3.6 3.6 - - - +
27J LYS* 1.3 77.4 - - - +
29J THR* 1.3 66.3 + - - +
31J GLU* 3.2 10.8 + - - +
32J LEU* 3.0 21.5 + - - +
140J LYS* 3.8 30.1 - - + +
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Residues in contact with THR 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J VAL* 5.7 0.2 - - - +
25J GLU* 2.6 31.3 + - - +
28J ALA* 1.3 69.4 - - - +
30J VAL* 1.3 61.0 + - - +
32J LEU* 2.9 9.2 + - + +
33J LEU* 2.8 37.5 + - + +
87J LEU* 3.3 24.4 - - + +
140J LYS* 5.3 4.2 + - - +
141J ASP* 3.8 18.1 + - - +
144J THR* 3.1 36.8 - - + +
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Residues in contact with VAL 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J LEU* 4.9 3.6 - - + -
26J LYS 2.8 27.7 + - - +
27J LYS* 3.8 5.8 - - - +
29J THR* 1.3 71.8 - - - +
31J GLU* 1.3 58.6 + - - +
33J LEU* 3.9 1.5 - - - +
34J ASN* 3.0 47.5 + - - +
84J ALA* 3.6 34.0 - - + +
87J LEU* 4.1 10.1 - - + +
89J GLY* 3.7 27.6 - - - +
90J VAL 4.2 2.9 - - - +
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Residues in contact with GLU 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J LYS 3.2 11.1 + - - +
28J ALA* 3.4 11.7 - - - +
29J THR 3.1 0.6 - - - -
30J VAL* 1.3 80.7 - - - +
32J LEU* 1.3 64.7 + - - +
34J ASN* 3.7 4.6 + - - +
35J ARG* 3.2 27.5 + - - +
101J LYS* 6.2 1.6 - - - +
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Residues in contact with LEU 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J ALA 3.0 12.8 + - - +
29J THR* 2.9 12.0 + - - +
31J GLU* 1.3 75.5 - - - +
33J LEU* 1.3 65.2 + - + +
35J ARG* 3.3 39.5 - - - +
36J GLN* 3.2 20.7 + - + +
135J ALA* 3.9 31.0 - - + +
138J GLU* 3.6 19.5 - - - +
139J ALA* 4.0 23.3 - - + +
144J THR* 5.0 5.4 - - + -
148J LEU* 4.2 11.7 - - + -
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Residues in contact with LEU 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J THR* 2.8 36.1 + - + +
30J VAL 3.9 3.1 - - - +
32J LEU* 1.3 70.1 - - - +
34J ASN* 1.3 60.3 + - - +
35J ARG 3.0 1.3 - - - -
36J GLN* 2.8 23.8 + - - +
37J VAL* 2.8 17.0 + - - +
80J MET* 3.6 34.9 - - + +
83J ARG* 3.5 20.0 - - + +
84J ALA* 3.4 37.5 - - + +
144J THR* 3.6 22.2 - - + -
147J ILE* 5.2 2.7 - - + -
148J LEU* 4.6 9.9 - - + -
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Residues in contact with ASN 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J VAL* 3.0 38.3 + - - +
31J GLU* 4.1 4.9 - - - +
33J LEU* 1.3 76.1 - - - +
35J ARG* 1.3 61.7 + - - +
37J VAL* 3.7 8.5 - - - +
38J ILE* 3.1 33.6 + - + +
84J ALA* 4.5 4.8 - - - +
90J VAL 3.0 22.0 + - - -
91J ALA* 3.3 6.0 - - - +
92J LEU* 2.6 50.5 + - + +
101J LYS* 6.1 2.2 - - - +
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Residues in contact with ARG 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J GLU* 3.2 18.0 + - - +
32J LEU* 3.3 37.3 - - - +
33J LEU 3.0 0.4 - - - -
34J ASN* 1.3 79.4 - - - +
36J GLN* 1.3 70.4 + - - +
38J ILE* 3.6 8.8 + - - +
39J GLN* 3.3 23.0 + - - +
101J LYS* 6.2 1.3 - - - +
131J ASP* 2.8 40.8 + - - -
135J ALA* 4.3 4.2 - - - +
138J GLU* 3.8 14.3 + - - -
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Residues in contact with GLN 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J LEU* 3.2 17.0 + - + +
33J LEU* 2.8 8.7 + - - +
35J ARG* 1.3 82.4 + - - +
37J VAL* 1.3 54.8 + - - +
39J GLN* 2.9 27.1 + - - +
40J PHE* 2.7 59.3 + - - -
80J MET* 3.6 19.7 - - - -
131J ASP* 3.7 10.2 - - - +
132J VAL* 3.6 20.3 - - - +
135J ALA* 3.6 20.7 - - - +
148J LEU* 3.9 18.2 - - + -
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Residues in contact with VAL 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I TRP* 4.5 7.0 - - + -
33J LEU 2.8 22.3 + - - +
34J ASN* 3.4 15.5 + - - +
36J GLN* 1.3 72.1 - - - +
38J ILE* 1.3 57.7 + - - +
40J PHE* 3.7 1.6 - - - +
41J ILE* 2.8 53.6 + - + +
77J LEU* 4.0 16.8 - - + +
80J MET* 4.0 11.9 - - + -
81J ALA* 3.8 32.3 - - + +
84J ALA* 6.2 0.2 - - + -
91J ALA* 5.8 0.2 - - + -
92J LEU 3.5 22.2 - - - +
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Residues in contact with ILE 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J ASN* 3.1 20.1 + - + +
35J ARG* 3.8 7.9 - - - +
37J VAL* 1.3 75.8 - - - +
39J GLN* 1.3 63.5 + - - +
41J ILE 3.5 0.2 + - - -
42J ASP* 3.1 23.9 + - - +
92J LEU* 4.0 18.2 - - + +
97J VAL* 3.6 23.8 - - + -
98J ILE* 3.5 38.7 - - + +
101J LYS* 3.6 29.8 - - + +
102J THR* 4.0 23.8 - - - +
103J PRO* 5.0 1.3 - - + -
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Residues in contact with GLN 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J ARG* 3.3 11.8 + - - +
36J GLN* 2.9 33.7 + - - +
38J ILE* 1.3 80.9 - - - +
40J PHE* 1.3 57.4 + - + +
42J ASP* 3.4 4.7 + - - +
43J LEU* 3.0 28.6 + - - +
103J PRO* 3.3 38.6 - - + +
104J LEU* 4.0 3.4 - - + +
127J ILE* 4.3 6.5 - - - +
128J VAL* 3.4 38.1 - - + +
131J ASP* 3.0 34.9 + - - +
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Residues in contact with PHE 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J GLN* 2.7 50.0 + - - +
37J VAL 3.8 3.1 - - - +
39J GLN* 1.3 71.0 - - - +
41J ILE* 1.3 66.1 + - - +
43J LEU* 3.1 7.2 + - + +
44J SER* 2.9 25.5 + - - -
73J LEU* 3.8 31.3 - - + +
76J HIS* 4.0 18.6 - + + -
77J LEU* 4.1 15.7 - - + -
80J MET* 3.6 19.3 - - + -
128J VAL* 3.7 17.9 - - + -
132J VAL* 4.3 9.2 - - + -
151J ALA* 3.9 13.9 - - + -
155J LEU* 3.2 34.1 - - + -
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Residues in contact with ILE 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I LEU* 3.6 28.9 - - + -
52I TRP* 4.3 11.7 - - + -
37J VAL* 2.8 35.3 + - + +
40J PHE* 1.3 72.5 - - - +
42J ASP* 1.3 61.4 + - - +
44J SER* 2.6 21.6 + - - +
45J LEU* 3.1 18.1 + - + +
77J LEU* 3.2 25.8 - - + -
93J GLY* 3.6 34.3 - - - +
98J ILE* 3.9 20.0 - - + -
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Residues in contact with ASP 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I THR* 2.9 37.6 + - - +
96I GLN* 4.8 1.6 - - - +
38J ILE 3.1 18.8 + - - +
39J GLN 3.8 3.6 - - - +
41J ILE* 1.3 75.6 - - - +
43J LEU* 1.3 59.7 + - - +
45J LEU* 3.2 5.9 + - - +
46J ILE* 2.9 42.3 + - - +
98J ILE* 3.8 8.7 - - + +
102J THR* 2.6 31.0 + - - +
104J LEU* 3.4 20.4 - - + +
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Residues in contact with LEU 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39J GLN 3.0 17.8 + - - +
40J PHE* 3.1 6.9 + - + +
42J ASP* 1.3 75.9 - - - +
44J SER* 1.3 52.4 + - - +
46J ILE* 3.4 7.8 + - + +
47J THR* 2.7 37.1 + - - -
73J LEU* 4.1 10.5 - - + -
104J LEU* 3.9 11.5 - - + +
124J ARG* 3.8 28.7 - - + -
125J TYR* 3.5 46.7 - - + -
128J VAL* 3.9 11.4 - - + -
155J LEU* 3.8 29.2 - - + -
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Residues in contact with SER 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J PHE 2.9 12.8 + - - -
41J ILE* 2.6 25.9 + - - +
43J LEU* 1.3 75.6 - - - +
45J LEU* 1.3 67.9 + - - +
47J THR* 3.3 5.6 + - - -
48J LYS* 3.3 24.1 + - - +
70J ARG* 4.1 16.5 - - - +
73J LEU* 3.9 25.5 - - - +
74J ILE* 4.7 13.2 - - - +
77J LEU* 4.7 2.2 - - - +
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Residues in contact with LEU 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I ILE* 3.5 32.5 - - + -
45I LEU* 4.6 19.5 - - + -
93I GLY 3.8 20.1 - - - +
94I THR* 5.0 0.7 - - - -
95I THR* 4.1 32.5 - - - +
98I ILE* 5.3 1.8 - - + -
41J ILE* 3.1 25.4 + - + +
42J ASP* 3.2 11.4 + - - +
44J SER* 1.3 83.9 + - - +
46J ILE* 1.3 63.2 + - + +
48J LYS* 3.3 8.8 + - - +
49J GLN* 3.1 19.9 + - - +
52J TRP* 5.3 0.5 - - - -
98J ILE* 5.2 2.2 - - + -
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Residues in contact with ILE 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I THR* 5.2 6.3 - - + -
96I GLN* 5.8 2.9 - - - +
42J ASP* 2.9 33.9 + - - +
43J LEU* 3.6 7.6 - - + +
45J LEU* 1.3 75.2 - - + +
47J THR* 1.3 64.8 + - - +
49J GLN* 3.0 18.3 + - - +
50J ALA* 3.0 13.0 + - - +
104J LEU* 3.7 31.9 - - + -
105J LYS 4.8 2.0 - - - +
106J SER* 6.2 0.2 - - - -
107J TYR* 3.3 42.6 - - + +
121J LEU* 3.9 10.8 - - + -
124J ARG* 4.2 23.1 - - + +
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Residues in contact with THR 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J LEU 2.7 25.5 + - - -
44J SER* 3.5 8.7 - - - -
45J LEU 3.3 0.2 - - - -
46J ILE* 1.3 77.0 - - - +
48J LYS* 1.3 57.6 + - + +
50J ALA* 3.5 2.9 + - - +
51J HIS* 2.9 28.5 + - + +
66J LEU* 3.4 44.7 - - + +
70J ARG* 4.5 9.2 - - + +
73J LEU* 3.8 2.9 - - - +
121J LEU* 4.2 9.0 - - - -
125J TYR* 2.6 33.0 + - + +
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Residues in contact with LYS 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I ASP* 2.7 26.2 + - - +
82I GLU* 5.5 1.0 + - - -
44J SER 3.3 9.6 + - - +
45J LEU* 3.6 10.3 - - - +
46J ILE 3.2 0.6 - - - -
47J THR* 1.3 79.0 - - - +
49J GLN* 1.3 59.0 + - - +
51J HIS* 3.1 34.3 + - + +
52J TRP* 2.8 65.6 + - + +
67J ASP* 2.8 23.0 + - - +
70J ARG* 2.9 48.0 - - + +
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Residues in contact with GLN 49 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90I VAL* 5.2 0.8 - - - +
91I ALA 2.5 24.8 + - - +
92I LEU* 3.2 2.8 - - - -
93I GLY* 3.0 20.6 + - - +
94I THR* 3.3 36.1 - - + +
45J LEU 3.1 9.8 + - - +
46J ILE* 3.0 13.4 + - - +
48J LYS* 1.3 78.9 - - - +
50J ALA* 1.3 62.2 + - - +
52J TRP* 4.0 6.0 - - - -
53J ASN* 2.9 47.1 + - - +
107J TYR* 4.3 16.5 - - + -
108J PRO 4.4 3.8 + - - -
109J LEU* 4.0 20.4 - - - +
117J HIS* 5.4 1.4 - - - -
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Residues in contact with ALA 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J ILE 3.0 3.1 + - - +
47J THR 3.8 2.5 - - - +
49J GLN* 1.3 76.3 - - - +
51J HIS* 1.3 67.5 + - - +
53J ASN 3.3 1.7 + - - -
54J MET* 3.2 31.8 + - + +
107J TYR* 3.4 23.0 - - + +
117J HIS* 3.4 17.6 - - + +
121J LEU* 3.6 36.3 - - + -
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Residues in contact with HIS 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I GLU* 4.7 5.1 + - - -
47J THR* 2.9 21.0 + - + +
48J LYS* 3.1 33.6 + - + +
50J ALA* 1.3 78.4 - - - +
52J TRP* 1.3 90.7 + + - +
54J MET* 3.5 11.3 + - - +
59J PHE* 4.6 0.7 - - - -
63J HIS* 2.7 80.1 + + - -
64J GLU* 5.0 0.2 - - - -
66J LEU* 4.0 17.4 - - + +
67J ASP* 3.9 21.8 + - + -
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Residues in contact with TRP 52 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I VAL* 4.5 3.4 - - + -
41I ILE* 4.3 10.8 - - + -
77I LEU* 3.5 21.3 - - + -
78I ASP* 3.3 32.1 + - - +
81I ALA* 3.3 25.7 - - + +
82I GLU* 4.3 15.9 + - + +
85I VAL* 3.5 25.2 - - + +
91I ALA* 3.8 24.7 - - + -
93I GLY* 4.2 23.6 - - - -
45J LEU 5.3 0.7 - - - -
48J LYS* 2.8 51.2 + - + +
49J GLN* 4.0 7.0 - - - -
51J HIS* 1.3 95.9 - + - +
53J ASN* 1.3 65.4 + - - +
54J MET 3.8 2.6 + - - +
59J PHE* 5.5 0.2 - - - -
63J HIS* 4.7 4.0 - + - -
160K TRP* 3.8 11.4 - - + -
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Residues in contact with ASN 53 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I VAL* 3.4 14.6 - - - +
89I GLY 4.3 0.9 - - - +
90I VAL* 3.4 15.0 - - + +
91I ALA 2.9 46.0 + - - +
49J GLN* 2.9 33.9 + - - +
50J ALA 3.3 2.8 + - - -
52J TRP* 1.3 82.5 - - - +
54J MET* 1.3 61.6 + - - +
55J ARG* 4.8 1.9 - - - +
111J ILE 4.6 1.3 - - - +
112J HIS* 3.1 33.8 + - + +
117J HIS* 3.3 18.7 + - + +
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Residues in contact with MET 54 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I VAL* 6.0 0.3 - - - +
50J ALA* 3.2 18.7 + - + +
51J HIS 3.5 11.4 - - - +
52J TRP 3.6 2.9 - - - +
53J ASN* 1.3 78.5 - - - +
55J ARG* 1.3 68.4 + - - +
59J PHE* 3.4 31.8 - - + +
62J VAL* 3.4 29.8 - - + -
63J HIS* 4.1 13.0 - - - +
66J LEU* 3.3 29.4 - - + -
112J HIS 3.2 5.6 - - - +
114J VAL* 4.3 17.3 - - + +
117J HIS* 3.7 28.9 - - + -
118J LEU* 5.0 0.7 - - + -
121J LEU* 4.6 2.0 - - + -
160K TRP* 5.2 1.7 + - - -
164K SER* 4.4 0.9 + - - -
----------------------------------------------------------
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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