Contacts of the helix formed by residues 27 - 51 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ASP* 3.5 31.0 + - + +
25D ILE 3.1 3.1 - - - -
26D SER* 1.3 75.2 + - - +
28D THR* 1.3 62.2 + - - +
29D VAL* 3.6 2.8 + - - +
30D GLY* 3.2 15.6 + - - -
31D VAL* 3.3 14.6 + - - +
83D TRP* 2.9 39.6 + - - -
84D ILE* 4.2 11.6 - - - +
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Residues in contact with THR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ILE 4.4 6.7 + - - -
26D SER 2.9 15.3 + - - -
27D ASP* 1.3 70.7 + - - +
29D VAL* 1.3 63.7 + - - +
31D VAL* 3.3 16.4 + - - +
32D SER* 3.3 13.3 + - - -
222D LEU* 4.3 24.2 - - + -
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Residues in contact with VAL 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ASP* 3.2 1.4 + - - +
28D THR* 1.3 76.2 - - - +
30D GLY* 1.3 62.8 + - - +
32D SER* 3.2 5.2 + - - -
33D PHE* 3.0 41.3 + - + -
83D TRP* 3.3 42.4 - - + +
218D SER* 3.7 28.5 - - - +
221D ASN* 3.9 16.8 - - + -
222D LEU* 3.6 23.3 - - + -
225D ASN* 5.0 1.1 - - - +
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Residues in contact with GLY 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 5.3 0.4 - - - -
24D ASP 5.9 0.2 - - - -
27D ASP* 3.2 24.5 + - - -
29D VAL* 1.3 76.8 - - - +
31D VAL* 1.3 61.7 + - - +
33D PHE* 3.4 5.5 + - - +
34D TRP* 2.9 14.6 + - - +
80D ARG* 2.8 32.0 + - - -
83D TRP* 3.6 10.0 - - - +
84D ILE* 5.1 0.4 - - - -
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Residues in contact with VAL 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 5.3 7.4 - - + -
24D ASP 3.9 15.0 - - - +
25D ILE* 4.6 18.2 - - + +
27D ASP 3.3 14.1 + - - +
28D THR* 3.3 12.1 + - - +
30D GLY* 1.3 75.0 - - - +
32D SER* 1.3 52.5 + - - +
34D TRP* 3.1 7.6 + - - +
35D LEU* 2.8 56.0 + - + +
92E VAL* 5.2 4.7 - - + -
96E ILE* 4.1 25.4 - - + -
99E LEU* 6.2 0.7 - - + -
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Residues in contact with SER 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D THR* 3.3 9.5 + - - -
29D VAL 3.2 8.2 + - - -
31D VAL* 1.3 76.1 - - - +
33D PHE* 1.3 63.9 + - - +
35D LEU* 3.4 11.3 + - - +
36D VAL* 3.0 29.2 + - - +
222D LEU* 4.1 18.3 + - - +
225D ASN* 2.6 37.5 + - - +
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Residues in contact with PHE 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D VAL* 3.0 39.5 + - + -
30D GLY* 3.6 3.4 - - - +
32D SER* 1.3 75.4 + - - +
34D TRP* 1.3 58.8 + - - +
36D VAL* 3.8 0.3 - - - -
37D THR* 2.4 36.7 + - - -
76D TYR* 3.9 17.1 - + - -
79D MET* 4.1 13.0 - - + -
80D ARG* 3.5 37.7 - - + -
83D TRP* 3.7 26.5 - + + -
90D PRO* 4.1 13.5 - - + -
94D ARG* 3.6 7.2 - - - -
221D ASN* 3.9 20.9 - - - -
225D ASN* 3.3 30.1 - - - +
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Residues in contact with TRP 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 3.9 15.5 - - + -
30D GLY 2.9 14.3 + - - +
31D VAL* 3.2 12.3 - - - +
33D PHE* 1.3 77.4 - - - +
35D LEU* 1.3 67.3 + - - +
37D THR* 3.3 6.3 - - - -
38D ALA* 3.1 19.5 + - + +
80D ARG* 3.6 42.8 - - - +
74E TRP* 6.1 0.7 - - + -
75E HIS* 2.8 39.7 + + - -
78E TYR* 3.8 34.5 - + - -
93E PHE* 3.4 29.2 - + - -
96E ILE* 3.4 21.5 - - + +
100E LEU* 4.7 1.8 - - + +
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Residues in contact with LEU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D VAL* 2.8 42.4 + - + +
32D SER* 3.7 9.2 - - - +
33D PHE 3.3 0.2 - - - -
34D TRP* 1.3 76.7 - - - +
36D VAL* 1.3 58.7 + - + +
38D ALA* 3.1 9.1 + - - +
39D GLY* 2.9 23.2 + - - -
229D PHE* 5.3 3.9 - - + -
96E ILE* 4.1 23.3 - - + +
99E LEU* 4.3 24.9 - - + -
100E LEU* 3.9 30.5 - - + +
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Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D SER* 3.0 19.5 + - - +
35D LEU* 1.3 76.7 - - + +
37D THR* 1.3 56.0 + - - +
39D GLY* 2.9 4.3 + - - +
40D MET* 2.7 44.8 + - + +
76D TYR* 3.3 40.2 - - + +
225D ASN* 3.6 28.7 - - + +
226D LEU* 5.6 0.4 - - - -
228D ASP* 4.9 0.2 - - + -
229D PHE* 3.9 26.5 - - + +
233D ILE* 5.0 0.4 - - + +
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Residues in contact with THR 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D PHE 2.4 25.7 + - - -
34D TRP* 3.3 9.4 - - - -
36D VAL* 1.3 77.2 - - - +
38D ALA* 1.3 61.9 + - - +
40D MET* 3.3 2.2 + - - +
41D LEU 3.0 18.5 + - - -
73D PHE* 3.4 35.2 - - + +
76D TYR* 3.4 32.7 + - + +
77D LEU* 4.1 21.3 - - + +
80D ARG* 4.9 3.1 - - - -
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Residues in contact with ALA 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TRP* 3.1 8.8 + - - +
35D LEU 3.1 11.2 + - - +
37D THR* 1.3 78.8 - - - +
39D GLY* 1.3 53.5 + - - +
41D LEU* 3.3 10.5 + - - +
42D ALA* 2.8 34.7 + - - +
73D PHE* 5.7 0.2 - - - -
71E ILE* 5.1 11.2 - - + +
75E HIS* 4.8 9.6 - - + -
100E LEU* 3.7 29.2 - - + -
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Residues in contact with GLY 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LEU 2.9 10.4 + - - -
36D VAL* 2.9 8.1 + - - -
38D ALA* 1.3 74.8 - - - +
40D MET* 1.3 59.3 + - - +
42D ALA* 3.3 6.0 + - - +
43D ALA* 2.9 31.9 + - - +
229D PHE* 4.8 7.0 - - - -
233D ILE* 3.7 18.3 - - - +
100E LEU* 5.1 5.6 - - - -
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Residues in contact with MET 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D VAL* 2.7 36.9 + - + +
37D THR* 3.7 4.5 - - - +
39D GLY* 1.3 73.4 - - - +
41D LEU* 1.3 61.7 - - - +
43D ALA* 3.4 4.7 - - - +
44D THR* 2.7 31.4 + - - -
69D THR* 3.2 39.5 - - + +
72D ALA* 2.5 45.5 - - + -
73D PHE* 3.8 11.7 - - + +
76D TYR* 4.5 5.2 - - + -
228D ASP 4.8 4.0 - - - +
232D LYS* 3.7 20.2 - - + -
233D ILE* 4.1 20.4 - - - -
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Residues in contact with LEU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D THR 3.0 9.4 + - - +
38D ALA* 3.4 12.1 - - - +
40D MET* 1.3 78.4 - - - +
42D ALA* 1.3 64.7 + - - +
44D THR* 3.4 7.6 + - - -
45D VAL* 3.3 30.3 + - + +
73D PHE* 3.6 44.9 - - + -
71E ILE* 6.1 5.2 - - + -
74E TRP* 4.2 31.0 - - + +
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Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ALA 2.8 18.8 + - - +
39D GLY* 3.8 6.3 - - - +
41D LEU* 1.3 71.0 - - - +
43D ALA* 1.3 52.1 + - - +
45D VAL* 2.9 10.4 + - - +
46D PHE* 2.8 32.0 + - - -
67E LEU* 3.7 27.7 - - + +
71E ILE* 4.0 26.8 - - + +
104E LEU* 5.5 2.5 - - + -
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Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D GLY 2.9 21.7 + - - +
40D MET 3.4 4.7 - - - +
42D ALA* 1.3 72.2 - - - +
44D THR* 1.3 57.7 + - - +
46D PHE* 3.5 7.6 - - - +
47D PHE* 2.8 45.3 + - + -
69D THR* 3.8 20.2 - - + -
233D ILE* 3.9 21.5 - - + -
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Residues in contact with THR 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D MET 2.7 25.4 + - - -
41D LEU* 3.7 9.4 - - - -
43D ALA* 1.3 72.2 - - - +
45D VAL* 1.3 64.7 + - + +
47D PHE* 4.0 1.6 - - - +
48D PHE* 3.0 44.0 + - + -
66D GLY* 3.4 17.9 - - - +
69D THR* 3.0 27.6 + - - -
70D GLY* 3.3 11.4 + - - -
73D PHE* 4.8 0.9 - - - +
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Residues in contact with VAL 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LEU* 3.3 26.4 + - + +
42D ALA* 2.9 7.4 + - - +
44D THR* 1.3 74.3 - - + +
46D PHE* 1.3 67.5 + - - +
48D PHE* 3.9 2.9 - - - -
49D VAL* 2.9 39.9 + - + +
48E PHE* 3.5 34.5 - - + -
67E LEU* 3.9 8.7 - - + -
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Residues in contact with PHE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ALA 2.8 12.1 + - - +
43D ALA* 3.3 12.1 + - - +
45D VAL* 1.3 77.3 - - - +
47D PHE* 1.3 70.3 + + - +
49D VAL* 3.9 0.3 - - - -
50D GLU* 3.0 51.7 + - + +
237D LEU* 3.7 26.9 - - + -
240D TRP* 3.5 50.7 - + + -
60E THR* 3.9 15.9 - - + -
63E THR* 4.1 18.4 - - + -
64E VAL* 4.9 9.2 - - + -
67E LEU* 4.0 19.4 - - + +
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Residues in contact with PHE 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ALA* 2.8 31.9 + - + +
44D THR 4.1 0.2 - - - +
46D PHE* 1.3 92.6 - + - +
48D PHE* 1.3 64.7 + - - +
50D GLU* 3.6 2.0 + - - -
51D ARG* 3.6 17.2 + - - +
62D LEU* 3.7 35.9 - - + +
65D SER* 3.6 29.8 - - - -
66D GLY* 3.8 5.6 - - - -
69D THR* 3.6 28.9 - - + -
232D LYS 4.2 2.7 - - - -
233D ILE* 3.7 12.3 - - + -
236D GLY* 3.4 42.2 - - - -
237D LEU* 3.8 8.3 - - + -
240D TRP* 4.9 5.6 - - + -
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Residues in contact with PHE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C VAL* 3.6 29.6 - - + -
49C VAL* 4.2 16.9 - - + +
44D THR* 3.0 46.2 + - + +
45D VAL* 4.1 3.1 - - - +
47D PHE* 1.3 79.1 - - - +
49D VAL* 1.3 64.1 + - + +
51D ARG* 3.5 30.1 + - - +
63D THR* 3.7 44.0 - - + -
66D GLY* 3.7 9.2 - - - -
67D LEU* 3.8 12.3 - - + -
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Residues in contact with VAL 49 (chain D).
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* 2.9 38.3 + - + +
46D PHE 4.0 1.6 - - - +
48D PHE* 1.3 78.9 - - + +
50D GLU* 1.3 58.4 + - - +
51D ARG 3.1 3.7 + - - -
52D ASP* 3.0 20.8 + - - +
48E PHE* 4.1 14.8 - - + +
51E ARG* 3.3 34.8 + - - +
63E THR* 4.0 17.0 - - + -
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Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D PHE* 3.0 37.6 + - + +
47D PHE 3.6 3.3 + - - +
48D PHE 3.4 0.2 - - - -
49D VAL* 1.3 70.9 - - - +
51D ARG* 1.3 51.9 + - - +
52D ASP* 3.0 8.5 - - - -
53D GLN* 2.8 43.2 + - - +
54D VAL* 3.9 2.6 + - - +
62D LEU* 3.9 6.0 - - + +
240D TRP* 3.2 34.2 + - + +
51E ARG* 3.2 10.0 + - - -
60E THR* 2.8 31.8 + - - -
63E THR* 2.7 31.7 + - + +
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Residues in contact with ARG 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C VAL* 3.1 30.8 + - - +
50C GLU* 2.7 12.1 + - - -
52C ASP* 2.6 44.4 + - - +
47D PHE 3.6 7.7 + - - +
48D PHE* 3.5 24.3 + - - +
49D VAL 3.1 1.2 + - - -
50D GLU* 1.3 76.5 - - - +
52D ASP* 1.3 56.4 + - - +
53D GLN 3.1 0.9 - - - -
54D VAL* 3.2 18.7 - - - +
59D LYS* 2.9 47.0 + - + +
62D LEU* 3.6 28.9 - - + +
63D THR* 2.7 37.8 + - - +
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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