Contacts of the helix formed by residues 27 - 50 (chain E) in PDB entry 4KNF
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 27 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ASP* 3.0 25.0 + - + +
25E ILE 4.2 2.0 - - - -
26E SER* 1.3 77.0 + - - +
28E THR* 1.3 61.7 + - - +
29E VAL* 3.5 3.8 + - - +
30E GLY* 2.6 30.9 + - - -
31E VAL* 3.0 21.1 + - - +
83E TRP* 2.8 30.3 + - - +
84E ILE* 3.9 12.1 - - + +
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Residues in contact with THR 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ILE 4.5 6.3 + - - +
26E SER 3.0 12.4 + - - -
27E ASP* 1.3 72.1 + - - +
29E VAL* 1.3 63.4 + - - +
31E VAL* 3.2 7.7 + - + +
32E SER* 2.9 25.1 + - - -
218E SER* 6.3 0.2 - - - -
222E LEU* 4.3 18.4 - - + -
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Residues in contact with VAL 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E ASP* 3.2 1.7 - - - +
28E THR* 1.3 73.9 - - - +
30E GLY* 1.3 66.3 + - - +
32E SER* 3.0 9.2 + - - -
33E PHE* 2.8 37.2 + - + -
83E TRP* 2.9 52.5 - - + +
218E SER* 3.8 29.6 - - - +
221E ASN* 4.2 13.2 - - + -
222E LEU* 3.8 17.5 - - + -
225E ASN* 5.4 0.7 - - - +
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Residues in contact with GLY 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E ASP* 2.6 33.0 + - - -
29E VAL* 1.3 73.9 - - - +
31E VAL* 1.3 59.3 + - - +
33E PHE* 3.3 3.4 + - - +
34E TRP 3.2 5.5 + - - -
80E ARG* 3.0 36.0 + - - -
83E TRP* 3.2 14.8 - - - +
84E ILE* 4.5 4.0 - - - -
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 4.9 1.8 - - + -
96A ILE* 3.9 24.5 - - + -
23E LEU* 4.4 17.5 - - + -
24E ASP 4.0 14.6 - - - +
25E ILE* 4.1 26.9 - - + +
27E ASP 3.0 15.4 + - - +
28E THR* 3.4 9.9 - - - +
30E GLY* 1.3 72.1 - - - +
32E SER* 1.3 67.0 + - - +
34E TRP* 3.1 9.9 + - + +
35E LEU* 3.0 32.6 + - + +
80E ARG* 4.8 1.1 - - - +
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Residues in contact with SER 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E THR 2.9 7.1 + - - -
29E VAL 3.0 8.7 + - - -
31E VAL* 1.3 78.7 - - - +
33E PHE* 1.3 62.3 + - - +
35E LEU* 3.2 14.5 + - - +
36E VAL* 3.2 26.9 - - - +
222E LEU* 3.5 31.1 + - - +
225E ASN* 2.8 30.0 + - - +
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Residues in contact with PHE 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E VAL* 2.8 36.8 + - + -
30E GLY 3.4 2.9 - - - +
32E SER* 1.3 75.9 - - - +
34E TRP* 1.3 59.4 + - - +
36E VAL* 4.1 1.4 - - - +
37E THR* 2.5 35.9 + - - -
76E TYR* 3.8 20.8 - + - -
79E MET* 3.8 24.9 - - + -
80E ARG* 3.4 27.4 - - + -
83E TRP* 3.6 35.7 - + + -
90E PRO* 4.2 8.7 - - + -
94E ARG* 3.5 30.3 - - - -
221E ASN* 4.0 11.2 - - + -
225E ASN* 3.6 11.9 - - - +
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Residues in contact with TRP 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 6.0 1.8 - - + -
75A HIS* 2.8 35.9 + + - -
78A TYR* 3.5 40.6 - + - -
93A PHE* 3.6 28.0 - + - -
96A ILE* 3.3 24.6 - - + +
100A LEU* 4.7 2.0 - - + +
23E LEU* 3.9 17.5 - - + -
30E GLY 3.2 4.2 + - - +
31E VAL* 3.1 10.9 + - + +
33E PHE* 1.3 79.5 - - - +
35E LEU* 1.3 63.1 + - + +
37E THR* 3.7 5.7 - - - -
38E ALA* 3.3 21.2 + - + +
80E ARG* 3.8 41.8 - - - +
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Residues in contact with LEU 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 4.0 32.5 - - + +
99A LEU* 4.4 24.9 - - + -
100A LEU* 3.6 32.8 - - + +
31E VAL* 3.0 35.7 + - + +
32E SER* 3.2 9.4 + - - +
34E TRP* 1.3 80.3 - - + +
36E VAL* 1.3 59.5 + - + +
38E ALA 3.4 0.3 + - - -
39E GLY* 3.1 20.1 + - - -
229E PHE* 6.0 0.7 - - - -
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Residues in contact with VAL 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E SER* 3.2 18.9 + - - +
33E PHE 4.3 0.9 - - - +
35E LEU* 1.3 76.3 - - + +
37E THR* 1.3 57.1 + - - +
38E ALA 3.2 0.9 - - - -
39E GLY* 3.6 3.6 - - - +
40E MET* 2.8 44.9 + - + +
76E TYR* 2.9 49.8 - - + +
225E ASN* 3.8 28.3 - - + +
229E PHE* 4.9 18.4 - - + -
233E ILE* 4.5 0.5 - - - +
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Residues in contact with THR 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E PHE* 2.5 29.3 + - - +
34E TRP* 3.7 7.1 - - - -
36E VAL* 1.3 77.2 - - - +
38E ALA* 1.3 58.5 + - - +
40E MET* 3.1 7.0 + - - +
41E LEU 2.9 23.2 + - - -
73E PHE* 3.6 21.8 - - + +
76E TYR* 3.6 32.6 + - + +
77E LEU* 4.0 27.6 - - + +
80E ARG* 5.1 3.3 - - - -
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Residues in contact with ALA 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 4.9 11.5 - - + +
75A HIS* 4.8 8.5 - - + -
100A LEU* 3.9 24.7 - - + -
34E TRP* 3.3 17.2 + - + +
35E LEU 3.7 4.5 - - - +
36E VAL 3.2 0.6 - - - -
37E THR* 1.3 79.4 - - - +
39E GLY* 1.3 61.4 + - - +
41E LEU* 3.5 10.8 + - + +
42E ALA* 3.0 27.9 + - - +
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Residues in contact with GLY 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 5.2 4.7 - - - -
35E LEU 3.1 11.9 + - - -
36E VAL* 3.1 6.7 + - - -
38E ALA* 1.3 76.9 - - - +
40E MET* 1.3 58.6 + - - +
42E ALA* 3.4 6.7 + - - +
43E ALA* 3.0 31.0 + - - +
229E PHE* 5.3 4.9 - - - -
233E ILE* 3.5 17.6 - - - +
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Residues in contact with MET 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E VAL* 2.8 27.2 + - + +
37E THR* 3.1 5.1 + - - +
39E GLY* 1.3 75.3 - - - +
41E LEU* 1.3 60.5 - - - +
43E ALA* 3.9 1.9 - - - +
44E THR* 2.6 35.2 + - - -
69E THR* 3.6 22.8 - - - +
72E ALA* 3.6 24.0 - - + -
73E PHE* 3.8 13.5 - - + +
76E TYR* 4.3 11.7 - - + -
228E ASP* 3.5 44.0 - - + +
229E PHE* 4.3 1.3 - - - +
232E LYS* 4.0 8.7 - - + -
233E ILE* 3.9 22.4 - - + -
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Residues in contact with LEU 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 6.4 2.5 - - + -
74A TRP* 4.1 32.8 - - + +
37E THR 2.9 13.4 + - - +
38E ALA* 3.6 13.9 - - + +
39E GLY 3.3 0.2 - - - -
40E MET* 1.3 78.2 - - - +
42E ALA* 1.3 60.9 + - - +
44E THR* 3.9 6.0 - - - -
45E VAL* 3.2 37.8 + - + +
73E PHE* 3.8 40.5 - - + -
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Residues in contact with ALA 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.4 28.8 - - + +
71A ILE* 4.1 24.5 - - + -
104A LEU* 5.6 1.8 - - + -
38E ALA 3.0 18.0 + - - +
39E GLY* 3.7 7.6 - - - +
40E MET 3.2 0.2 - - - -
41E LEU* 1.3 78.0 - - - +
43E ALA* 1.3 53.4 + - - +
45E VAL* 3.4 1.3 + - - -
46E PHE* 2.8 31.0 + - - +
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Residues in contact with ALA 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E GLY 3.0 18.9 + - - +
40E MET 3.9 2.5 - - - +
41E LEU 3.3 0.2 - - - -
42E ALA* 1.3 76.6 - - - +
44E THR* 1.3 66.1 + - - +
46E PHE* 3.6 7.5 - - - +
47E PHE* 3.0 37.8 + - + -
69E THR* 3.9 19.1 - - + -
233E ILE* 3.9 24.5 - - + -
237E LEU* 6.4 0.7 - - + -
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Residues in contact with THR 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E MET 2.6 22.9 + - - -
41E LEU* 3.9 8.4 - - + -
43E ALA* 1.3 77.1 - - - +
45E VAL* 1.3 64.8 + - + +
47E PHE* 4.0 0.9 - - - +
48E PHE* 3.2 46.4 + - + -
66E GLY* 3.5 19.1 - - - +
69E THR* 3.0 11.3 + - - -
70E GLY* 3.0 31.2 + - - -
73E PHE* 4.8 0.7 - - - +
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Residues in contact with VAL 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.8 33.0 - - + -
67A LEU* 3.8 9.2 - - + -
41E LEU* 3.2 25.2 + - + +
42E ALA* 3.6 7.2 - - - +
43E ALA 3.3 0.4 - - - -
44E THR* 1.3 78.8 - - + +
46E PHE* 1.3 65.8 + - - +
48E PHE* 4.1 2.4 - - - -
49E VAL* 3.0 39.3 + - + +
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Residues in contact with PHE 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A THR* 4.2 14.4 - - + -
63A THR* 3.9 16.8 - - + -
64A VAL* 4.6 9.4 - - + -
67A LEU* 3.9 22.4 - - + +
42E ALA 2.8 17.8 + - - +
43E ALA* 3.6 10.1 - - - +
45E VAL* 1.3 77.1 - - - +
47E PHE* 1.3 73.6 + + + +
49E VAL* 3.8 1.2 - - - +
50E GLU* 2.9 45.7 + - + +
237E LEU* 4.0 17.3 - - + -
240E TRP* 3.3 60.1 - + - -
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Residues in contact with PHE 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ALA* 3.0 28.1 + - + +
44E THR 4.0 0.2 - - - +
46E PHE* 1.3 81.5 - + - +
48E PHE* 1.3 65.8 + - - +
50E GLU* 3.6 8.0 + - - +
51E ARG* 3.7 16.5 + - - +
62E LEU* 3.6 29.3 - - + +
65E SER* 3.7 35.9 - - - -
66E GLY* 3.8 6.1 - - - +
69E THR* 3.9 17.7 - - + -
232E LYS 4.3 3.1 - - - -
233E ILE 3.8 7.0 - - - -
236E GLY* 3.3 43.1 - - - -
237E LEU* 3.5 22.2 - - + -
240E TRP* 4.2 11.0 - + + -
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Residues in contact with PHE 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D VAL* 3.5 29.8 - - + -
49D VAL* 4.1 23.4 - - + +
44E THR* 3.2 46.5 + - + +
45E VAL* 4.3 2.5 - - - +
47E PHE* 1.3 78.6 - - - +
49E VAL* 1.3 67.7 + - + +
50E GLU 3.3 0.3 + - - -
51E ARG* 3.5 20.5 + - - +
63E THR* 3.7 35.9 - - + -
66E GLY* 3.8 22.7 - - - -
67E LEU* 3.8 7.9 - - + -
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Residues in contact with VAL 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 4.3 13.5 - - + -
51A ARG* 3.0 54.9 + - - +
63A THR* 4.0 13.0 - - + +
45E VAL* 3.0 34.5 + - + +
46E PHE 3.8 2.7 - - - +
48E PHE* 1.3 79.6 - - + +
50E GLU* 1.3 57.5 + - - +
51E ARG 3.2 4.5 + - - -
52E ASP* 3.3 8.3 + - - +
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Residues in contact with GLU 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ARG* 3.3 13.5 + - - +
60A THR* 2.8 30.2 + - - -
63A THR* 2.6 29.5 + - + -
46E PHE* 2.9 45.4 + - + +
47E PHE 4.3 2.5 - - - +
48E PHE 3.2 0.8 - - - -
49E VAL* 1.3 75.0 - - - +
51E ARG* 1.3 58.9 + - - +
52E ASP 3.2 3.1 - - - -
53E GLN* 3.1 37.6 + - - +
54E VAL* 3.9 1.9 + - - +
62E LEU* 3.7 10.9 - - + +
240E TRP* 3.2 28.1 + - + +
244E VAL* 5.0 0.2 - - - +
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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