Contacts of the helix formed by residues 27 - 50 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ASP* 3.2 27.5 + - + +
25A ILE 3.2 2.7 - - - -
26A SER* 1.3 77.7 + - - +
28A THR* 1.3 63.0 + - - +
29A VAL* 3.7 3.3 + - - +
30A GLY* 3.0 10.0 + - - -
31A VAL* 2.9 18.7 + - - +
83A TRP* 2.9 39.3 + - - -
84A ILE* 3.7 14.6 - - + +
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Residues in contact with THR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE 4.5 5.5 + - - -
26A SER 3.0 13.2 + - - -
27A ASP* 1.3 70.2 + - - +
29A VAL* 1.3 56.4 + - - +
31A VAL* 2.8 27.5 + - + +
32A SER* 2.9 13.8 + - - -
222A LEU* 4.2 23.6 - - + -
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASP* 3.7 1.1 + - - +
28A THR* 1.3 76.3 - - - +
30A GLY* 1.3 62.1 + - - +
32A SER* 3.1 3.1 + - - -
33A PHE* 3.0 40.6 + - + -
83A TRP* 3.2 40.2 - - + +
218A SER* 3.6 39.5 - - - +
221A ASN* 4.0 13.5 - - + -
222A LEU* 3.6 24.7 - - + +
225A ASN* 5.1 1.3 - - - +
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Residues in contact with GLY 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 5.8 0.2 - - - -
24A ASP 5.8 0.2 - - - -
27A ASP* 3.0 30.5 + - - -
29A VAL* 1.3 78.5 - - - +
31A VAL* 1.3 58.7 + - - +
33A PHE* 3.5 3.3 + - - +
34A TRP 3.3 7.8 + - - -
80A ARG* 2.4 37.2 + - - -
83A TRP* 3.6 3.3 - - - +
84A ILE* 4.1 9.4 - - - -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 5.1 9.9 - - + -
24A ASP 4.1 15.0 - - - +
25A ILE* 4.4 25.8 - - + +
27A ASP 2.9 11.6 + - - +
28A THR* 2.8 15.0 + - + +
30A GLY* 1.3 70.0 - - - -
32A SER* 1.3 60.4 + - - +
34A TRP* 3.2 9.1 + - + +
35A LEU* 2.9 48.6 + - + +
80A ARG* 4.6 0.2 - - - +
92B VAL* 4.9 9.4 - - + -
96B ILE* 4.1 16.2 - - + -
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 2.9 11.6 + - - -
29A VAL 3.4 8.5 - - - -
31A VAL* 1.3 78.5 - - - +
33A PHE* 1.3 61.1 - - - +
35A LEU* 3.3 10.4 + - - +
36A VAL* 3.1 29.7 + - - +
222A LEU* 3.8 19.3 + - - +
225A ASN* 2.6 35.1 + - - +
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Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.0 43.2 + - + +
30A GLY 3.8 1.3 - - - +
31A VAL 3.2 0.2 - - - -
32A SER* 1.3 72.9 - - - +
34A TRP* 1.3 56.3 - - - +
36A VAL* 4.0 0.2 - - - +
37A THR* 2.5 43.8 + - - +
76A TYR* 3.5 25.0 - + - -
79A MET* 3.9 14.4 - - + -
80A ARG* 3.4 36.1 - - + -
83A TRP* 3.9 21.5 - + + -
90A PRO* 4.2 13.7 - - + -
94A ARG* 3.5 20.9 - - - -
221A ASN* 4.0 9.0 - - + -
225A ASN* 3.3 23.6 - - - +
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Residues in contact with TRP 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.0 19.0 - - + +
30A GLY 3.3 3.0 + - - +
31A VAL* 3.2 12.1 + - - +
33A PHE* 1.3 80.3 - - - +
35A LEU* 1.3 63.9 + - + +
37A THR* 3.6 4.9 + - - -
38A ALA* 3.2 21.6 + - + +
80A ARG* 3.7 40.2 - - - +
74B TRP* 6.0 1.8 - - + -
75B HIS* 2.9 38.7 + + - -
78B TYR* 3.6 38.6 - + - -
93B PHE* 3.6 26.7 - + - -
96B ILE* 3.4 24.3 - - + +
100B LEU* 4.6 1.8 - - + +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 2.9 40.8 + - + +
32A SER* 3.9 8.1 - - - +
33A PHE 3.3 0.2 - - - -
34A TRP* 1.3 73.7 - - - +
36A VAL* 1.3 55.6 + - + +
38A ALA* 3.2 5.7 + - - +
39A GLY* 2.9 30.0 + - - -
229A PHE* 5.9 1.2 - - - -
96B ILE* 3.8 36.3 - - + -
99B LEU* 3.9 23.3 - - + -
100B LEU* 4.0 25.2 - - + +
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER* 3.1 20.3 + - - +
33A PHE 4.0 0.2 - - - +
35A LEU* 1.3 76.6 - - + +
37A THR* 1.3 66.5 + - - +
39A GLY* 3.6 2.2 - - - +
40A MET* 2.8 36.5 + - + +
76A TYR* 3.3 43.5 - - + +
225A ASN* 4.0 27.8 - - + +
226A LEU* 5.7 0.4 - - - -
229A PHE* 4.8 23.3 - - + +
233A ILE* 4.7 0.3 - - - +
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Residues in contact with THR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 2.5 32.8 + - - +
34A TRP* 3.7 7.9 + - - -
36A VAL* 1.3 77.8 - - - +
38A ALA* 1.3 57.4 - - - +
40A MET* 3.1 4.8 + - - +
41A LEU 2.9 22.5 + - - -
73A PHE* 3.8 34.2 - - + +
76A TYR* 3.5 28.0 + - + +
77A LEU* 4.3 18.6 - - + -
80A ARG* 4.8 4.4 - - - +
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 3.2 13.3 + - + +
35A LEU 3.5 8.1 - - - +
37A THR* 1.3 76.7 - - - +
39A GLY* 1.3 66.9 + - - +
41A LEU* 3.3 11.4 + - - +
42A ALA* 3.0 23.8 + - - +
71B ILE* 5.1 9.8 - - + +
75B HIS* 4.9 7.0 - - + -
100B LEU* 3.8 26.5 - - + -
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Residues in contact with GLY 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU 2.9 15.3 + - - -
36A VAL* 3.1 4.0 + - - -
38A ALA* 1.3 75.0 - - - +
40A MET* 1.4 57.1 + - - +
42A ALA* 3.4 6.4 + - - +
43A ALA* 3.0 30.7 + - - +
229A PHE* 5.1 6.3 - - - -
233A ILE* 3.4 17.2 - - - +
100B LEU* 5.0 5.1 - - - +
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Residues in contact with MET 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 2.8 31.0 + - + +
37A THR* 3.5 6.1 - - - +
39A GLY* 1.4 73.3 - - - +
41A LEU* 1.3 60.8 + - - +
44A THR* 2.6 35.2 + - - -
69A THR* 3.0 60.0 - - + +
72A ALA* 3.7 17.0 - - + -
73A PHE* 3.9 15.5 - - - +
76A TYR* 4.4 11.2 - - + -
228A ASP* 5.0 4.0 - - - +
232A LYS* 4.2 15.3 - - + -
233A ILE* 3.5 20.9 - - + -
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A THR 2.9 12.1 + - - +
38A ALA* 3.4 13.5 - - - +
40A MET* 1.3 78.5 - - - +
42A ALA* 1.3 62.5 + - - +
44A THR* 3.3 9.2 + - + -
45A VAL* 3.2 28.0 + - + +
73A PHE* 3.9 43.1 - - + -
71B ILE* 6.4 2.0 - - + -
74B TRP* 4.0 35.0 - - + +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA 3.0 17.6 + - - +
39A GLY* 3.4 6.9 + - - +
41A LEU* 1.3 74.5 - - - +
43A ALA* 1.3 58.4 + - - +
45A VAL* 3.4 1.5 + - - -
46A PHE* 2.8 30.1 + - - +
67B LEU* 3.5 33.0 - - + +
71B ILE* 4.4 21.3 - - + +
104B LEU* 5.7 1.3 - - + -
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLY 3.0 16.8 + - - +
40A MET 4.0 1.1 - - - +
42A ALA* 1.3 74.1 - - - +
44A THR* 1.3 58.2 + - - +
46A PHE* 3.5 7.4 - - - +
47A PHE* 2.8 61.4 + - + -
69A THR* 3.9 11.7 - - + -
233A ILE* 4.1 20.9 - - + -
237A LEU* 6.3 0.7 - - + -
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Residues in contact with THR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A MET 2.6 23.8 + - - -
41A LEU* 3.4 10.1 - - + -
43A ALA* 1.3 77.1 - - - +
45A VAL* 1.3 66.8 + - + +
47A PHE* 3.9 0.9 - - - +
48A PHE* 3.0 53.6 + - + -
66A GLY* 3.7 8.5 - - - +
69A THR* 3.1 10.9 + - - -
70A GLY* 3.0 29.1 + - - -
73A PHE* 4.8 1.6 - - - +
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.2 20.4 + - + +
42A ALA 3.7 6.3 - - - +
44A THR* 1.3 82.1 - - + +
46A PHE* 1.3 62.9 + - - +
48A PHE* 5.0 3.1 - - - -
49A VAL* 2.9 31.3 + - + +
48B PHE* 3.6 37.9 - - + -
63B THR* 5.4 0.2 - - + -
67B LEU* 4.0 9.9 - - + -
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Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA 2.8 21.5 + - - +
43A ALA* 3.5 9.2 - - - +
45A VAL* 1.3 73.5 - - - +
47A PHE* 1.3 70.6 + + - +
49A VAL* 4.0 0.3 - - - -
50A GLU* 2.9 45.3 + - + +
237A LEU* 3.8 20.6 - - + -
240A TRP* 3.5 57.9 - + - -
60B THR* 4.3 12.3 - - + -
63B THR* 3.7 26.0 - - + -
64B VAL* 4.4 9.4 - - + -
67B LEU* 4.0 15.7 - - + +
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Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA* 2.8 33.8 + - + +
46A PHE* 1.3 78.3 - + - +
48A PHE* 1.3 67.6 + - - +
50A GLU* 3.8 4.9 + - - -
51A ARG* 3.7 5.0 + - - +
62A LEU* 3.6 45.4 - - + +
65A SER* 3.5 28.9 - - - -
66A GLY* 3.8 5.4 - - - +
69A THR* 3.5 26.7 - - + -
232A LYS 4.3 4.5 - - - -
233A ILE 3.7 8.3 - - - -
236A GLY* 3.5 39.7 - - - -
237A LEU* 3.7 22.2 - - + -
240A TRP* 4.6 7.6 - + + -
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Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR* 3.0 40.6 + - + +
45A VAL* 4.1 3.6 - - - +
47A PHE* 1.3 75.2 - - - +
49A VAL* 1.3 67.8 + - + +
50A GLU 3.1 1.0 + - - -
51A ARG* 3.2 23.8 + - - +
63A THR* 3.7 35.2 - - + -
66A GLY* 3.5 32.8 - - - -
67A LEU* 3.5 7.4 - - + -
70A GLY* 5.6 0.4 - - - -
45E VAL* 3.8 28.0 - - + -
49E VAL* 4.3 22.4 - - + -
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 2.9 32.0 + - + +
46A PHE 4.1 1.3 - - - +
48A PHE* 1.3 73.9 - - + +
50A GLU* 1.3 57.3 + - - +
51A ARG 3.2 4.2 + - - -
52A ASP* 3.6 8.3 + - - +
48B PHE* 4.0 23.6 - - + -
51B ARG* 3.2 50.8 + - - +
63B THR* 3.7 10.8 - - + +
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 2.9 38.0 + - + +
47A PHE 3.8 0.6 + - - +
48A PHE 3.1 0.6 + - - -
49A VAL* 1.3 73.8 - - - +
51A ARG* 1.3 59.1 + - - +
52A ASP 3.1 3.1 - - - -
53A GLN* 2.9 34.4 + - - +
54A VAL* 3.9 1.4 + - - +
62A LEU* 3.7 11.9 - - + +
240A TRP* 2.8 40.1 + - + +
51B ARG* 2.8 26.1 + - - +
60B THR* 2.6 33.6 + - - -
63B THR* 3.0 16.4 + - + +
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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) + - + + + + + -
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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