Contacts of the helix formed by residues 23 - 53 (chain C) in PDB entry 1DPS
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 ASP 23 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 3.7 22.1 - - + +
21C VAL 3.6 0.6 + - - +
22C SER* 1.3 73.1 - - - +
24C SER* 1.3 58.1 + - - +
26C LYS* 3.6 13.7 + - - +
27C LYS* 2.9 39.1 + - + +
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Residues in contact with SER 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C SER* 4.0 8.7 - - - -
23C ASP* 1.3 80.9 - - - +
25C GLU* 1.3 61.7 + - - +
27C LYS* 3.8 7.2 - - - +
28C ALA* 3.2 22.7 + - - +
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Residues in contact with GLU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C VAL* 3.8 17.5 - - + +
22C SER* 3.0 19.2 + - - +
24C SER* 1.3 75.1 - - - +
26C LYS* 1.3 57.2 + - - +
28C ALA* 3.4 5.5 + - + +
29C THR* 2.8 46.5 + - - +
140C LYS* 3.8 29.9 - - + +
141C ASP* 3.7 24.3 + - + +
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Residues in contact with LYS 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 3.7 20.1 - - + +
15C LEU 5.3 2.4 + - - -
17C THR* 3.6 22.3 + - - +
19C ASN* 3.0 28.8 + - - -
20C ASP* 5.0 0.4 - - - +
21C VAL* 3.0 38.2 + - + +
22C SER 2.8 17.2 + - - +
23C ASP* 3.6 14.2 + - - +
25C GLU* 1.3 76.7 - - - +
27C LYS* 1.3 57.6 + - - +
29C THR* 3.8 4.2 - - - -
30C VAL* 2.9 36.6 + - - +
87C LEU* 3.3 34.9 + - + +
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Residues in contact with LYS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 4.0 26.2 - - + +
23C ASP* 2.9 23.5 + - + +
24C SER* 3.8 7.4 - - - +
26C LYS* 1.3 77.6 - - - +
28C ALA* 1.3 61.3 + - - +
30C VAL* 3.4 4.2 + - - +
31C GLU* 2.8 45.1 + - + +
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Residues in contact with ALA 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C SER 3.2 14.8 + - - +
25C GLU* 3.9 6.7 - - + +
27C LYS* 1.3 78.1 - - - +
29C THR* 1.3 62.5 + - - +
31C GLU* 3.6 7.1 + - - +
32C LEU* 3.1 25.8 + - - +
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Residues in contact with THR 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLU* 2.8 26.5 + - - +
26C LYS 3.8 0.2 - - - -
28C ALA* 1.3 74.9 - - - +
30C VAL* 1.3 59.4 + - - +
32C LEU* 3.3 8.7 + - + +
33C LEU* 2.9 37.9 + - + +
87C LEU* 3.4 26.4 - - + +
140C LYS 5.6 0.7 + - - -
141C ASP* 3.7 18.8 + - + +
144C THR* 3.1 36.8 - - + +
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 4.3 6.5 - - + -
26C LYS 2.9 23.0 + - - +
27C LYS* 3.8 5.4 - - - +
29C THR* 1.3 75.9 - - - +
31C GLU* 1.3 70.5 + - - +
33C LEU* 3.8 1.3 - - - +
34C ASN* 3.0 41.1 + - - +
84C ALA* 3.5 35.8 - - + +
87C LEU* 4.2 9.9 - - + -
89C GLY* 3.8 24.0 - - - +
90C VAL 4.6 3.4 - - - +
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Residues in contact with GLU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LYS* 2.8 42.4 + - + +
28C ALA* 4.0 6.3 - - - +
30C VAL* 1.3 84.6 - - - +
32C LEU* 1.3 63.5 + - - +
34C ASN* 3.4 6.8 + - - +
35C ARG* 3.2 27.4 + - - +
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ALA 3.1 19.3 + - - +
29C THR* 3.3 8.0 + - - +
31C GLU* 1.3 78.2 - - - +
33C LEU* 1.3 66.8 + - + +
35C ARG* 3.3 14.9 + - - +
36C GLN* 3.3 22.3 + - + +
135C ALA* 4.5 13.0 - - + +
138C GLU* 4.5 9.4 - - + +
139C ALA* 4.0 32.8 - - + +
144C THR* 4.3 10.3 - - + -
148C LEU* 3.7 31.2 - - + -
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C THR* 2.9 35.1 + - + +
30C VAL 4.0 3.1 - - - +
32C LEU* 1.3 70.5 - - + +
34C ASN* 1.3 60.0 + - - +
36C GLN* 3.1 5.8 + - - +
37C VAL* 2.8 33.2 + - - +
80C MET* 3.7 39.5 - - + +
83C ARG* 3.7 20.4 - - + -
84C ALA* 3.7 35.4 - - + +
144C THR* 3.8 23.8 - - + +
147C ILE* 5.0 3.6 - - + -
148C LEU* 4.5 10.8 - - + -
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Residues in contact with ASN 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 3.0 32.6 + - - +
31C GLU* 3.9 7.5 + - - +
33C LEU* 1.3 72.7 - - - +
35C ARG* 1.3 65.9 + - - +
37C VAL* 3.8 8.9 - - - +
38C ILE* 3.0 32.5 + - + +
84C ALA* 5.0 4.4 - - - +
90C VAL 3.0 22.0 + - - -
91C ALA* 3.5 7.7 - - - +
92C LEU* 3.0 47.0 + - + +
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLU 3.2 16.4 + - - +
32C LEU* 3.4 15.6 + - - +
33C LEU 3.2 0.2 - - - -
34C ASN* 1.3 77.4 - - - +
36C GLN* 1.3 73.5 + - - +
38C ILE* 3.4 10.6 + - + +
39C GLN* 3.3 33.5 + - - +
103C PRO* 5.6 4.6 - - - +
131C ASP* 2.8 44.7 + - - -
135C ALA* 5.0 5.1 - - - +
138C GLU* 5.8 1.6 + - - -
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Residues in contact with GLN 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.3 15.3 + - + +
33C LEU* 3.1 8.4 + - - +
35C ARG* 1.3 91.3 - - - +
37C VAL* 1.3 65.6 + - - +
39C GLN* 2.8 21.4 + - - +
40C PHE* 2.9 45.4 + - - -
80C MET* 3.7 19.1 - - + -
131C ASP* 2.9 25.3 + - - -
132C VAL* 3.4 15.0 - - - +
135C ALA* 3.8 15.9 - - - +
148C LEU* 3.9 21.3 - - + -
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Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TRP* 4.4 10.3 - - + -
33C LEU 2.8 25.9 + - - +
34C ASN* 3.3 11.9 + - - +
36C GLN* 1.3 71.1 - - - +
38C ILE* 1.3 63.3 + - - +
40C PHE* 4.0 2.1 - - - +
41C ILE* 3.0 51.2 + - + +
77C LEU* 3.9 21.1 - - + +
80C MET* 3.9 27.4 - - + -
81C ALA* 3.9 12.8 - - + +
91C ALA* 5.8 0.4 - - + -
92C LEU 3.8 15.9 - - - +
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Residues in contact with ILE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ASN* 3.0 27.0 + - + +
35C ARG* 3.6 9.9 - - + +
36C GLN 3.2 0.4 - - - -
37C VAL* 1.3 77.7 - - - +
39C GLN* 1.3 57.8 + - - +
41C ILE* 3.5 2.6 + - - +
42C ASP* 3.1 26.3 + - - +
92C LEU* 4.1 12.3 - - + +
97C VAL* 3.8 19.5 - - + -
98C ILE* 4.0 22.5 - - + +
101C LYS* 3.6 35.9 - - + +
102C THR* 3.9 32.5 - - - +
103C PRO* 4.8 2.0 - - + -
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Residues in contact with GLN 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ARG* 3.3 14.0 + - - +
36C GLN* 2.8 36.0 + - - +
38C ILE* 1.3 79.1 - - - +
40C PHE* 1.3 65.0 + - + +
42C ASP* 3.8 5.8 - - - +
43C LEU* 2.9 28.9 + - - +
103C PRO* 3.4 36.7 - - + +
104C LEU* 4.0 4.0 - - + +
127C ILE* 4.7 2.8 - - - +
128C VAL* 4.1 30.9 + - + +
131C ASP* 2.9 33.6 + - - +
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Residues in contact with PHE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLN* 2.9 48.0 + - - +
37C VAL 4.0 0.2 - - - +
39C GLN* 1.3 73.7 - - + +
41C ILE* 1.3 62.1 + - - +
43C LEU* 3.4 5.8 + - - +
44C SER* 2.9 29.6 + - - -
73C LEU* 4.0 30.5 - - + +
76C HIS* 3.9 19.3 - - + -
77C LEU* 3.8 20.1 - - + +
80C MET* 3.9 15.7 - - + -
128C VAL* 3.6 19.1 - - + -
132C VAL* 4.3 8.5 - - + -
151C ALA* 3.9 16.6 - - + -
155C LEU* 3.7 33.4 - - + -
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Residues in contact with ILE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 3.7 22.7 - - + -
52A TRP* 4.4 6.3 - - + -
37C VAL* 3.0 39.5 + - + +
38C ILE 3.8 0.4 - - - +
40C PHE* 1.3 73.7 - - - +
42C ASP* 1.3 63.3 + - - +
44C SER* 2.8 22.0 + - - +
45C LEU* 3.0 16.8 + - + +
77C LEU* 3.5 27.6 - - + -
93C GLY* 3.8 28.7 - - - +
98C ILE* 3.2 26.9 - - + -
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Residues in contact with ASP 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 2.7 31.8 + - - -
96A GLN* 4.8 4.0 + - - +
38C ILE 3.1 17.2 + - - +
39C GLN* 3.9 4.0 - - - +
40C PHE 3.3 0.2 - - - -
41C ILE* 1.3 78.4 - - - +
43C LEU* 1.3 61.4 + - - +
45C LEU* 3.1 6.2 + - - +
46C ILE* 3.0 39.1 + - - +
98C ILE* 3.8 8.1 - - + -
102C THR* 2.6 39.5 + - - +
104C LEU* 3.7 16.2 - - + +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLN 2.9 19.8 + - - +
40C PHE* 3.8 5.2 - - - +
41C ILE 3.3 0.2 - - - -
42C ASP* 1.3 76.0 - - - +
44C SER* 1.3 54.4 + - - +
46C ILE* 3.7 7.6 - - + +
47C THR* 2.6 37.9 + - - -
73C LEU* 4.1 12.8 - - + -
104C LEU* 3.9 14.2 - - + +
124C ARG* 3.9 25.6 - - + +
125C TYR* 3.6 42.0 - - + -
128C VAL* 3.9 16.2 - - + -
155C LEU* 3.8 28.7 - - + -
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Residues in contact with SER 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C PHE 2.9 15.9 + - - -
41C ILE* 2.8 21.3 + - - +
43C LEU* 1.3 77.7 - - - +
45C LEU* 1.3 65.2 + - - +
47C THR* 3.5 5.1 + - - -
48C LYS* 3.4 17.8 + - - +
70C ARG* 3.8 25.3 + - - +
73C LEU* 3.8 19.5 - - - +
74C ILE* 4.2 20.7 - - - +
77C LEU* 4.8 0.4 - - - +
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 3.9 24.9 - - + -
45A LEU* 4.7 15.0 - - + -
93A GLY 3.8 19.6 - - - +
94A THR* 4.9 4.0 - - - -
95A THR* 3.2 33.7 - - - +
98A ILE* 4.6 7.2 - - + -
41C ILE* 3.0 31.6 + - + +
42C ASP* 3.1 8.7 + - - +
44C SER* 1.3 79.6 - - - +
46C ILE* 1.3 60.0 + - + +
48C LYS* 3.3 7.8 + - + +
49C GLN* 3.0 27.4 + - - +
52C TRP* 5.4 0.3 - - - -
98C ILE* 5.2 0.9 - - + -
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Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 5.1 6.5 - - + -
95A THR 6.3 0.2 - - - +
42C ASP* 3.0 32.5 + - - +
43C LEU* 3.7 11.0 - - + +
45C LEU* 1.3 74.1 - - + +
47C THR* 1.3 66.0 + - - +
49C GLN* 3.3 8.5 + - - +
50C ALA* 3.0 23.4 + - - +
104C LEU* 3.8 27.8 - - + +
105C LYS 4.7 2.7 - - - +
107C TYR* 3.5 41.6 - - + +
121C LEU* 3.9 11.9 - - + -
124C ARG* 3.9 22.0 - - + +
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Residues in contact with THR 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU 2.6 23.5 + - - -
44C SER* 3.6 9.2 - - - -
45C LEU 3.3 0.2 - - - -
46C ILE* 1.3 78.4 - - - +
48C LYS* 1.3 56.3 + - - +
50C ALA* 3.5 2.9 + - - +
51C HIS* 3.1 27.9 + - - +
66C LEU* 3.3 42.4 - - + +
70C ARG* 4.4 9.9 - - + +
73C LEU* 4.0 2.5 - - - +
121C LEU* 4.2 8.5 - - - -
125C TYR* 2.8 35.7 + - - +
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Residues in contact with LYS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASP* 3.0 32.7 + - - +
82A GLU* 5.5 1.0 + - - -
44C SER 3.4 3.9 + - - +
45C LEU* 3.3 9.5 + - + +
46C ILE 3.3 0.4 - - - -
47C THR* 1.3 75.4 - - - +
49C GLN* 1.3 67.4 + - - +
51C HIS* 3.1 33.4 + - + +
52C TRP* 2.9 51.5 + - + -
67C ASP* 2.8 28.3 + - - +
70C ARG* 3.3 51.1 - - + +
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Residues in contact with GLN 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 4.4 6.3 - - - +
91A ALA 3.1 21.2 + - - +
92A LEU* 3.8 0.4 - - - +
93A GLY* 2.8 31.5 + - - -
94A THR* 3.6 24.9 - - + +
45C LEU 3.0 14.9 + - - +
46C ILE* 3.4 13.9 - - - +
48C LYS* 1.3 76.9 - - - +
50C ALA* 1.3 61.2 + - - +
52C TRP* 4.0 7.6 - - - -
53C ASN* 2.9 41.2 + - - +
107C TYR* 3.7 20.2 - - + -
108C PRO 4.9 1.2 + - - -
109C LEU* 3.7 21.1 - - + +
117C HIS* 4.5 0.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE 3.0 16.2 + - - +
47C THR 3.8 2.2 - - - +
49C GLN* 1.3 75.2 - - - +
51C HIS* 1.3 65.1 + - - +
53C ASN 3.2 11.4 + - - -
54C MET* 3.3 21.6 + - + +
107C TYR* 3.5 22.9 - - + +
117C HIS* 3.6 17.0 + - + -
121C LEU* 3.6 25.4 - - + -
----------------------------------------------------------
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Residues in contact with HIS 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 4.6 6.5 + - - -
47C THR 3.1 18.8 + - - +
48C LYS* 3.1 37.9 + - + +
50C ALA* 1.3 75.8 - - - +
52C TRP* 1.3 83.7 + + - +
53C ASN 3.5 0.2 + - - -
54C MET* 3.5 15.4 - - - +
59C PHE* 4.4 0.7 - - - -
63C HIS* 2.8 76.1 + + - +
66C LEU* 4.0 20.8 - - + +
67C ASP* 3.9 15.7 + - + +
----------------------------------------------------------
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Residues in contact with TRP 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 4.6 3.8 - - + -
41A ILE* 4.5 9.4 - - + -
77A LEU* 4.0 18.4 - - + -
78A ASP* 3.3 31.1 + - - +
81A ALA* 3.3 28.9 - - + +
82A GLU* 4.3 16.1 + - + +
85A VAL* 3.7 26.2 - - + +
91A ALA* 3.7 25.4 - - + -
93A GLY* 4.3 22.7 - - - -
45C LEU 5.4 0.2 - - - -
48C LYS* 2.9 54.7 + - + +
49C GLN* 4.0 8.3 - - - -
51C HIS* 1.3 94.8 + + - +
53C ASN* 1.3 67.0 + - - +
54C MET 3.6 3.5 + - - +
63C HIS* 4.7 3.1 - + - -
160E TRP* 3.9 10.0 + - - -
----------------------------------------------------------
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Residues in contact with ASN 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 3.5 8.8 - - - +
89A GLY 4.2 0.7 - - - +
90A VAL* 3.4 16.8 - - + +
91A ALA 3.0 46.4 + - - +
49C GLN* 2.9 34.2 + - - +
50C ALA 3.2 2.8 + - - -
52C TRP* 1.3 83.6 - - - +
54C MET* 1.3 59.3 + - - +
55C ARG* 5.0 1.6 + - - +
111C ILE 4.6 2.0 - - - +
112C HIS* 3.0 32.3 + - + +
117C HIS* 3.4 20.4 - - + +
----------------------------------------------------------
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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