Contacts of the helix formed by residues 25 - 52 (chain C) in PDB entry 3KXC
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 GLY 25 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLN* 1.3 79.9 - - - +
26C GLU* 1.3 61.3 + - - -
27C VAL* 3.2 3.7 + - - -
28C GLU 3.3 1.4 + - - -
29C ASN* 2.9 35.2 + - - +
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLY* 1.3 71.0 - - - -
27C VAL* 1.3 67.5 + - + +
29C ASN* 3.8 8.0 - - - +
30C GLY* 2.9 25.3 + - - -
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Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLY 3.2 1.0 - - - -
26C GLU* 1.3 82.2 - - + +
28C GLU* 1.3 61.2 + - - +
30C GLY* 3.1 4.6 + - - -
31C ARG* 2.9 48.0 + - + +
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Residues in contact with GLU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 3.4 47.8 + - + +
25C GLY 3.3 1.6 + - - -
27C VAL* 1.3 78.1 - - - +
29C ASN* 1.3 63.7 + - - +
31C ARG* 3.1 28.7 + - - +
32C CYS* 2.9 24.3 + - - +
35C LYS* 4.0 20.0 + - - -
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Residues in contact with ASN 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 2.8 30.3 - - - +
25C GLY 2.9 30.7 + - - +
26C GLU* 3.8 7.9 - - - +
28C GLU* 1.3 74.3 - - - +
30C GLY* 1.3 62.2 + - - +
32C CYS* 3.1 8.2 + - - +
33C ILE* 3.1 26.5 + - - +
117C LYS* 4.4 19.4 + - - -
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Residues in contact with GLY 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLU 2.9 16.2 + - - -
27C VAL* 3.1 4.9 + - - -
29C ASN* 1.3 74.3 - - - +
31C ARG* 1.3 61.3 + - - +
33C ILE* 3.2 10.4 + - - +
34C THR* 3.0 26.4 + - - -
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Residues in contact with ARG 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 2.9 31.9 + - + +
28C GLU* 3.3 34.5 + - - +
30C GLY* 1.3 75.2 - - - +
32C CYS* 1.3 57.7 + - - +
34C THR* 3.4 8.2 + - - -
35C LYS* 2.9 47.3 + - - +
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Residues in contact with CYS 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C MET 5.3 4.7 - - - -
15C VAL 5.1 4.7 - - - -
17C GLY* 5.9 6.1 - - - -
24C GLN* 4.8 9.4 - - - +
28C GLU* 2.9 15.1 + - - +
29C ASN* 3.1 14.6 + - - +
31C ARG* 1.3 74.1 - - - +
33C ILE* 1.3 59.9 - - - +
35C LYS* 3.2 12.9 + - - +
36C LEU* 2.9 43.8 + - - +
117C LYS* 4.6 18.2 - - - -
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Residues in contact with ILE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ASN* 3.1 15.1 + - + +
30C GLY* 3.2 11.0 + - - +
32C CYS* 1.3 75.6 - - - +
34C THR* 1.3 59.7 + - - +
36C LEU* 3.2 13.9 + - + +
37C GLU* 2.9 28.8 + - + +
116C SER* 5.2 6.3 - - - +
117C LYS* 3.6 45.1 - - + +
120C ALA* 4.0 15.1 - - + +
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Residues in contact with THR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLY 3.0 15.5 + - - -
31C ARG* 3.6 11.4 - - - -
33C ILE* 1.3 77.7 - - - +
35C LYS* 1.3 57.3 + - + +
37C GLU* 3.5 5.5 + - - +
38C ASN* 2.9 54.7 + - - +
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Residues in contact with LYS 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLN* 3.6 31.6 - - + +
33A ASP* 3.4 34.4 + - - +
28C GLU* 4.0 18.4 + - - -
31C ARG* 2.9 34.6 + - - +
32C CYS* 3.2 10.7 + - - +
34C THR* 1.3 72.8 - - + +
36C LEU* 1.3 67.8 + - + +
38C ASN* 3.4 6.0 + - - +
39C MET* 3.0 34.4 + - + +
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C HIS* 5.6 0.2 - - + -
14C MET* 4.2 27.4 - - + +
15C VAL* 4.0 22.7 - - + -
32C CYS* 2.9 28.0 + - - +
33C ILE* 3.5 20.6 - - + +
35C LYS* 1.3 77.0 - - - +
37C GLU* 1.3 62.8 + - - +
39C MET* 3.4 19.8 + - + +
40C GLY 3.1 17.8 + - - -
117C LYS* 3.8 25.6 - - + +
120C ALA* 3.9 7.9 - - + -
121C PHE* 3.5 25.2 - - + +
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Residues in contact with GLU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE* 2.9 17.0 + - + +
34C THR* 3.8 6.5 - - - +
36C LEU* 1.3 77.4 - - - +
38C ASN* 1.3 57.8 + - - +
40C GLY 3.1 2.4 + - - -
41C PHE 2.8 30.5 + - - -
120C ALA* 3.6 24.8 + - + +
121C PHE* 4.4 0.2 - - - +
123C CYS* 3.9 9.7 - - + +
124C GLY* 3.3 21.2 + - - +
127C ARG* 2.7 50.5 + - - +
139C VAL 5.0 5.5 + - - +
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Residues in contact with ASN 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN* 5.2 5.8 - - - +
34C THR* 2.9 40.9 + - - +
35C LYS* 3.8 6.4 - - - +
37C GLU* 1.3 90.8 + - - +
39C MET* 1.3 60.3 + - - +
41C PHE* 3.3 8.1 + - - +
42C ARG* 3.1 27.4 + - - +
127C ARG* 3.7 8.8 - - - +
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Residues in contact with MET 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.9 25.6 - - + +
26A LEU* 3.8 32.1 - - + -
29A GLN* 3.9 20.9 - - + +
14C MET* 4.3 18.8 - - + +
35C LYS* 3.0 30.2 + - + +
36C LEU* 3.7 30.5 - - + +
38C ASN* 1.3 72.7 - - - +
40C GLY* 1.3 66.6 + - - +
42C ARG* 3.1 6.1 + - - +
43C VAL* 3.0 26.5 + - - +
121C PHE* 3.8 11.2 - - + -
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Residues in contact with GLY 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU 3.1 10.5 + - - -
37C GLU 3.4 2.5 - - - -
39C MET* 1.3 74.2 - - - +
41C PHE* 1.3 54.0 + - - +
43C VAL 3.2 0.3 + - - -
44C GLY 2.8 31.7 + - - -
121C PHE* 3.3 39.7 - - - -
124C GLY 3.3 7.2 - - - -
125C LEU* 3.3 9.9 + - - +
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Residues in contact with PHE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLU* 2.8 16.3 + - - +
38C ASN* 3.4 9.4 - - - +
39C MET 3.3 0.2 - - - -
40C GLY* 1.3 73.4 - - - +
42C ARG* 1.3 83.5 + - - +
45C GLN* 3.1 54.2 + - - +
124C GLY* 3.1 11.8 + - - +
127C ARG* 3.4 50.9 - - + +
128C GLY* 3.4 26.1 - - - -
131C SER* 3.6 28.9 - - - -
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 5.4 1.7 - - - +
25A ALA* 4.7 10.5 - - + -
38C ASN 3.1 13.7 + - - +
39C MET* 3.1 11.0 + - - +
41C PHE* 1.3 93.0 - - - +
43C VAL* 1.3 61.7 + - - +
45C GLN* 2.7 43.4 + - - +
46C GLY* 3.2 18.4 + - - -
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Residues in contact with VAL 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.0 14.8 - - + -
21A LEU* 3.5 40.6 - - + +
22A THR* 3.6 27.4 - - - +
25A ALA* 4.0 5.8 - - + -
39C MET 3.0 19.3 + - - +
40C GLY 3.2 3.6 + - - +
42C ARG* 1.3 73.9 - - - +
44C GLY* 1.3 59.0 + - - +
46C GLY* 3.1 2.1 + - - -
47C LEU* 2.8 32.8 + - + +
121C PHE* 3.8 7.9 - - + -
125C LEU* 3.5 20.0 - - + -
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Residues in contact with GLY 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C GLY 2.8 16.5 + - - -
41C PHE 3.8 0.7 - - - -
43C VAL* 1.3 73.1 - - - +
45C GLN* 1.3 60.9 + - - +
47C LEU* 3.3 4.6 + - - +
48C ILE* 3.2 26.2 + - - +
72C PHE* 4.2 7.1 - - - -
125C LEU* 3.5 31.3 - - - +
129C GLY* 3.6 9.6 - - - -
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Residues in contact with GLN 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PHE* 3.1 38.1 + - + +
42C ARG* 2.7 45.5 + - - +
43C VAL 3.3 0.2 - - - -
44C GLY* 1.3 78.2 - - - +
46C GLY* 1.3 61.5 + - - +
48C ILE 3.4 0.9 + - - -
49C GLU* 3.0 13.5 + - - +
128C GLY* 3.5 20.3 - - - +
131C SER* 4.2 6.1 + - - -
132C ASN* 3.0 46.5 + - - +
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Residues in contact with GLY 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 5.1 0.3 - - - +
21A LEU* 3.6 23.7 - - - +
42C ARG 3.2 7.6 + - - -
43C VAL 3.1 6.8 + - - -
45C GLN* 1.3 78.8 - - - +
47C LEU* 1.3 62.3 + - - +
49C GLU* 3.3 15.9 + - - +
50C ARG* 3.1 24.4 + - - +
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 4.5 2.5 - - + -
18A LEU* 4.1 33.2 - - + +
21A LEU* 3.7 16.6 - - + +
43C VAL* 2.8 24.3 + - + +
44C GLY 3.7 4.9 - - - +
45C GLN 3.2 0.2 - - - -
46C GLY* 1.3 77.4 - - - +
48C ILE* 1.3 50.8 + - - +
50C ARG* 3.3 1.6 + - - -
51C PHE* 2.2 80.0 + - + -
72C PHE* 4.0 18.8 - - + -
75C THR* 4.4 2.5 - - + -
76C VAL* 3.6 31.0 - - + -
125C LEU* 4.4 3.4 - - + -
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Residues in contact with ILE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLY 3.2 5.1 + - - +
45C GLN 3.7 7.2 - - - +
47C LEU* 1.3 73.1 - - - +
49C GLU* 1.3 63.0 + - - +
51C PHE* 4.6 1.8 - - + -
52C THR* 2.9 61.1 + - + +
67C PHE* 3.7 31.6 - - + -
68C ILE* 5.3 0.2 - - + -
72C PHE* 3.8 18.2 - - + -
129C GLY* 3.5 33.7 - - - +
132C ASN* 3.6 22.0 - - + +
133C LEU* 3.9 18.2 - - + -
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Residues in contact with GLU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLN* 3.0 14.3 + - - +
46C GLY* 3.4 19.7 - - - +
47C LEU 3.3 0.2 - - - -
48C ILE* 1.3 79.7 - - - +
50C ARG* 1.3 59.3 + - - +
52C THR 4.4 5.9 - - - +
53C LYS* 5.6 2.4 - - - +
132C ASN* 4.1 11.4 + - - +
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Residues in contact with ARG 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 3.7 43.2 + - + +
46C GLY 3.1 16.4 + - - +
47C LEU* 3.9 3.1 - - - +
49C GLU* 1.3 78.0 - - - +
51C PHE* 1.3 73.3 + - + +
52C THR 5.3 0.2 - - - -
53C LYS* 5.6 5.3 - - - +
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Residues in contact with PHE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 5.3 7.9 - - + -
47C LEU* 2.2 75.2 + - + +
48C ILE* 4.6 1.8 - - + -
50C ARG* 1.3 84.8 - - + +
52C THR* 1.3 72.0 + - + +
53C LYS* 3.4 8.0 + - - +
67C PHE* 5.3 2.7 - - + -
72C PHE* 5.9 2.0 - + - -
75C THR* 2.4 44.9 - - + -
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Residues in contact with THR 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE* 2.9 47.1 + - + +
49C GLU* 4.4 6.0 - - - +
51C PHE* 1.3 76.4 - - + +
53C LYS* 1.3 64.0 + - - +
58C PHE* 4.5 17.5 - - + -
67C PHE* 2.8 46.9 - - + -
133C LEU* 4.1 4.0 - - + +
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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