Contacts of the helix formed by residues 27 - 60 (chain A) in PDB entry 3RK3
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 27 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A SER* 1.3 60.6 + - - -
29A ASN* 3.9 10.1 - - - +
30A ARG* 2.7 58.0 + - - +
31A ARG* 3.3 2.8 + - - +
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY* 1.3 70.8 - - - -
29A ASN* 1.3 62.8 + - - +
31A ARG* 2.9 24.6 + - - +
32A LEU* 2.9 12.3 + - - +
147D ASP* 4.1 29.9 + - - +
150D LEU* 5.4 4.2 - - - +
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Residues in contact with ASN 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY* 3.9 10.7 - - - +
28A SER* 1.3 77.0 - - - +
30A ARG* 1.3 61.0 + - - +
32A LEU* 2.8 28.8 + - - +
33A GLN* 2.9 28.0 + - - +
198B ARG* 5.2 12.9 - - + +
201B GLU* 3.1 30.1 + - - -
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY* 2.7 35.5 + - - +
29A ASN* 1.3 76.5 + - - +
31A ARG* 1.3 59.3 + - - +
33A GLN* 3.3 12.5 + - + +
34A GLN* 3.1 26.1 + - - +
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Residues in contact with ARG 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY 3.3 2.7 + - - +
28A SER* 2.9 25.1 + - - +
30A ARG* 1.3 80.3 - - - +
32A LEU* 1.3 57.5 + - - +
34A GLN* 3.7 31.9 - - - +
35A THR* 2.9 28.5 + - - +
150D LEU* 5.7 3.4 - - + -
151D GLU* 3.5 48.5 + - - +
154D SER* 3.8 24.8 + - - -
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Residues in contact with LEU 32 (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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28A SER 2.9 8.4 + - - +
29A ASN* 2.8 14.9 + - - +
31A ARG* 1.3 74.4 - - - +
33A GLN* 1.3 69.6 + - - +
34A GLN 3.2 0.2 - - - -
35A THR* 3.1 5.7 + - - -
36A GLN* 3.0 19.2 + - + +
198B ARG* 4.6 10.5 - - + +
201B GLU* 3.8 39.9 - - + +
202B ILE* 4.3 18.2 - - + -
205B LEU* 3.8 33.9 - - + -
150D LEU* 4.3 22.9 - - + -
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Residues in contact with GLN 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 ASN* 2.9 31.0 + - - +
30A ARG* 3.3 10.7 + - + +
32A LEU* 1.3 78.1 - - - +
34A GLN* 1.3 66.0 + - - +
36A GLN* 2.8 15.3 + - - +
37A ALA* 3.0 12.5 + - - +
201B GLU* 3.3 26.7 + - - +
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Residues in contact with GLN 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG 3.1 12.7 + - - +
31A ARG* 3.7 34.5 + - - +
33A GLN* 1.3 80.4 - - - +
35A THR* 1.3 62.5 + - - +
37A ALA* 3.3 9.1 + - - +
38A GLN* 2.9 31.0 + - + +
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Residues in contact with THR 35 (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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31A ARG* 2.9 19.6 + - - +
32A LEU* 3.1 14.3 + - - +
34A GLN* 1.3 78.0 - - - +
36A GLN* 1.3 66.2 + - - +
38A GLN* 3.0 28.3 + - - +
39A VAL* 3.1 10.5 + - + +
205B LEU* 3.9 27.6 - - + -
150D LEU* 4.8 9.8 + - + +
153D VAL* 4.6 13.5 - - + -
154D SER* 3.6 27.3 + - - +
157D ILE* 5.7 0.7 - - + -
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Residues in contact with GLN 36 (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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32A LEU* 3.0 9.0 + - + +
33A GLN* 2.8 12.2 + - - +
35A THR* 1.3 74.8 - - - +
37A ALA* 1.3 68.7 + - - +
39A VAL* 2.8 14.2 + - - +
40A ASP* 2.9 32.5 + - - +
201B GLU 3.9 2.9 - - - +
204B LYS* 3.3 32.6 + - + +
205B LEU* 3.2 43.3 + - + +
208B SER* 2.5 39.0 + - - -
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Residues in contact with ALA 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 GLN 3.0 11.3 + - - +
34A GLN* 3.4 12.6 - - - +
36A GLN* 1.3 77.4 - - - +
38A GLN* 1.3 57.2 + - - +
40A ASP* 3.0 9.5 + - - +
41A GLU* 2.9 33.1 + - - +
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Residues in contact with GLN 38 (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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34A GLN* 2.9 19.8 + - + +
35A THR* 3.0 17.5 + - - +
37A ALA* 1.3 75.6 - - - +
39A VAL* 1.3 58.7 + - - +
41A GLU* 3.5 15.1 - - - +
42A VAL* 3.3 25.0 + - + +
154D SER* 2.8 47.7 + - - +
157D ILE* 3.8 11.2 - - + +
158D GLY* 3.0 20.3 + - - -
161D ARG* 4.1 14.1 + - - +
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Residues in contact with VAL 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 THR* 3.1 14.2 + - + +
36A GLN* 2.8 9.4 + - - +
38A GLN* 1.3 72.1 - - - +
40A ASP* 1.3 59.3 + - - +
41A GLU 2.8 1.6 - - - -
42A VAL* 2.4 30.8 + - - +
43A VAL* 2.9 26.9 + - + +
205B LEU* 4.3 15.3 - - + -
208B SER* 3.6 32.5 - - - +
209B ILE* 4.5 10.1 - - + +
212B LEU* 4.8 9.2 - - + -
157D ILE* 3.9 29.2 - - + -
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Residues in contact with ASP 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLN* 2.9 46.3 + - - +
37A ALA* 3.7 9.0 + - - +
39A VAL* 1.3 74.5 - - - +
41A GLU* 1.3 65.2 + - - +
43A VAL* 3.5 10.8 + - - +
44A ASP* 3.0 32.2 + - - +
204B LYS* 4.9 8.0 + - - -
208B SER* 4.2 8.7 + - - -
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA 2.9 15.2 + - - +
38A GLN* 3.5 15.9 - - - +
39A VAL 2.8 0.2 - - - -
40A ASP* 1.3 75.9 - - - +
42A VAL* 1.3 60.3 + - + +
44A ASP* 3.0 18.8 + - - +
45A ILE* 2.6 37.5 + - + +
161D ARG* 4.1 22.4 - - - +
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Residues in contact with VAL 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 GLN 3.3 16.4 - - - +
39A VAL* 2.4 18.3 + - - +
41A GLU* 1.3 75.5 - - + +
43A VAL* 1.3 50.7 + - - +
45A ILE* 3.1 10.0 + - - +
46A MET* 2.8 43.6 + - + +
212B LEU* 3.2 28.3 - - + -
216B PHE* 4.6 1.6 - - + -
157D ILE* 4.2 12.8 - - + +
160D LEU* 4.3 16.6 - - + +
161D ARG* 3.8 31.6 - - + +
164D ALA* 4.5 4.7 - - + -
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 2.9 35.1 + - + +
40A ASP* 3.6 15.5 - - - +
42A VAL* 1.3 73.0 - - - +
44A ASP* 1.3 67.0 + - - +
46A MET 3.1 1.6 + - - -
47A ARG* 2.9 40.3 + - - +
208B SER* 4.5 6.7 - - - +
211B GLU* 4.5 18.4 - - + +
212B LEU* 3.3 14.3 - - + +
215B MET* 3.6 22.6 - - - +
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Residues in contact with ASP 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 ASP* 3.0 21.6 - - - +
41A GLU* 3.0 9.0 + - - +
43A VAL* 1.3 76.4 - - - +
45A ILE* 1.3 68.3 + - + +
47A ARG* 3.0 40.1 + - - +
48A VAL* 3.2 18.2 + - + +
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Residues in contact with ILE 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 GLU* 2.6 61.9 + - + +
42A VAL* 3.3 10.8 - - + +
44A ASP* 1.3 78.9 - - + +
46A MET* 1.3 62.5 + - - +
48A VAL* 3.2 10.1 + - - +
49A ASN* 3.1 24.2 + - - +
161D ARG* 5.6 3.1 - - + -
164D ALA* 3.3 31.4 - - + -
165D LEU* 4.1 23.8 - - + +
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Residues in contact with MET 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 2.8 30.7 + - + +
43A VAL* 3.7 1.6 - - - +
45A ILE* 1.3 72.8 - - - +
47A ARG* 1.3 65.3 + - - +
49A ASN* 2.7 8.7 + - - +
50A VAL* 2.7 26.5 + - + +
212B LEU* 4.5 2.2 - - + -
215B MET* 3.0 32.5 - - + +
216B PHE* 3.5 65.3 - - + +
219B MET* 4.4 11.0 - - + -
164D ALA* 4.1 19.5 - - + -
167D MET* 4.1 17.7 - - - -
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Residues in contact with ARG 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 VAL* 2.9 22.2 + - - +
44A ASP* 3.0 45.0 + - - +
46A MET* 1.3 74.1 - - - +
48A VAL* 1.3 67.4 + - + +
50A VAL* 2.9 5.6 + - - +
51A ASP* 2.9 21.3 + - - +
211B GLU* 4.4 11.7 + - - -
215B MET* 2.7 24.0 - - + +
70E TYR* 3.8 35.0 + - + +
71E GLY 5.5 0.9 - - - -
72E ILE* 3.8 18.5 - - + +
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Residues in contact with VAL 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 ASP* 3.2 18.2 - - + +
45A ILE* 3.4 8.1 - - - +
46A MET 3.1 0.2 - - - -
47A ARG* 1.3 77.7 - - + +
49A ASN* 1.3 58.3 + - - +
51A ASP* 3.2 13.8 - - + +
52A LYS* 2.8 46.9 + - + +
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Residues in contact with ASN 49 (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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45A ILE* 3.1 16.0 + - - +
46A MET* 2.7 17.6 + - - +
48A VAL* 1.3 73.3 - - - +
50A VAL* 1.3 63.7 + - - +
52A LYS* 3.2 15.6 + - - +
53A VAL* 2.9 19.9 + - - +
219B MET* 3.6 16.7 - - + +
164D ALA* 2.9 38.6 + - - +
167D MET* 3.6 13.0 - - + +
168D GLY* 3.2 29.4 - - - +
171D ILE* 4.8 3.0 - - + +
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A MET* 2.7 22.2 + - + +
47A ARG* 3.4 7.4 - - - +
49A ASN* 1.3 70.0 - - - +
51A ASP* 1.3 65.9 + - - +
53A VAL* 2.9 5.6 + - - +
54A LEU* 2.8 27.1 + - + +
215B MET* 3.9 34.1 - - + +
218B ASP* 5.9 4.0 - - + -
219B MET* 3.5 22.9 - - + +
222B LEU* 5.4 7.4 - - + -
66E ILE* 4.0 27.1 - - + -
70E TYR* 4.6 12.1 - - + -
72E ILE* 5.1 4.3 - - + -
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Residues in contact with ASP 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG 2.9 11.6 + - - +
48A VAL* 3.2 17.3 - - + +
50A VAL* 1.3 75.0 - - - +
52A LYS* 1.3 68.1 + - - +
54A LEU* 2.7 22.1 + - - +
55A GLU* 3.1 28.4 + - - +
67E ARG* 3.9 14.6 + - - -
72E ILE* 3.6 35.7 - - + +
73E LYS 4.8 0.9 - - - +
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Residues in contact with LYS 52 (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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48A VAL* 2.8 37.6 + - + +
49A ASN* 3.2 19.1 + - - +
51A ASP* 1.3 74.8 - - - +
53A VAL* 1.3 58.6 + - - +
55A GLU* 3.1 20.2 + - - +
56A ARG 2.9 22.5 + - - -
168D GLY* 3.6 24.2 + - - +
169D ASN* 4.2 3.4 + - - +
171D ILE* 3.8 16.2 - - + -
172D ASP* 2.5 46.7 + - - +
175D ASN* 3.4 10.4 + - - +
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASN 2.9 6.2 + - - +
50A VAL* 2.9 11.2 + - - +
52A LYS* 1.3 75.7 - - - +
54A LEU* 1.3 58.7 + - - +
56A ARG* 3.0 12.1 + - - +
57A ASP* 2.7 27.8 + - + +
219B MET* 3.5 31.2 - - + -
222B LEU* 3.4 34.3 - - + -
223B VAL* 4.4 10.1 - - + -
226B GLN* 3.8 15.3 - - - +
171D ILE* 3.5 24.5 - - + -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 2.8 19.7 + - + +
51A ASP* 2.7 22.1 + - - +
53A VAL* 1.3 68.1 - - - +
55A GLU* 1.3 67.6 + - + +
57A ASP* 3.3 3.9 + - + +
58A GLN* 2.9 30.8 + - + +
222B LEU* 4.0 23.8 - - + -
63E ARG* 4.1 37.1 - - + +
66E ILE* 4.1 23.3 - - + -
67E ARG* 3.5 39.9 - - + +
72E ILE* 5.6 3.4 - - + -
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASP* 3.1 26.7 + - - +
52A LYS* 3.1 25.7 + - - +
54A LEU* 1.3 76.1 - - + +
56A ARG* 1.3 63.5 + - - +
58A GLN* 3.3 18.1 - - - +
59A LYS* 3.1 35.8 + - - +
175D ASN* 4.3 9.1 + - - +
67E ARG* 5.8 4.0 - - - +
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LYS 2.9 10.4 + - - +
53A VAL* 3.0 19.5 + - - +
55A GLU* 1.3 72.4 - - - +
57A ASP* 1.3 65.3 + - - +
59A LYS* 2.8 26.8 + - + +
60A LEU* 3.4 17.8 + - + +
223B VAL* 4.3 5.9 - - - +
226B GLN* 3.3 38.9 - - - +
230B ILE* 5.2 6.2 - - - +
50C LEU* 3.7 15.5 - - - +
53C GLN* 2.6 41.2 + - - +
57C LEU* 4.5 6.7 - - - +
171D ILE* 5.1 4.2 - - - +
174D GLN* 2.7 33.6 + - + +
175D ASN* 3.5 26.6 + - - +
178D ILE* 5.6 7.4 - - + +
----------------------------------------------------------
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Residues in contact with ASP 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 2.7 15.2 + - + +
54A LEU* 3.8 8.7 - - + +
56A ARG* 1.3 71.2 - - - +
58A GLN* 1.3 61.7 + - - +
60A LEU* 3.4 13.5 + - - +
222B LEU* 4.9 9.6 - - + +
225B SER* 3.9 10.9 + - - -
226B GLN* 2.7 41.6 + - - +
229B MET* 5.6 2.6 - - - +
59E ARG* 3.6 30.4 + - - +
63E ARG* 3.3 31.5 + - + +
----------------------------------------------------------
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 2.9 17.0 + - - +
55A GLU* 3.3 24.0 + - - +
57A ASP* 1.3 73.1 - - - +
59A LYS* 1.3 62.4 + - + +
60A LEU* 3.0 13.3 + - - +
56E GLU* 5.7 0.5 - - - +
59E ARG* 5.0 0.3 + - - -
60E GLU* 4.2 15.2 + - - -
63E ARG* 3.3 31.8 + - - +
67E ARG* 4.6 18.6 + - - +
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 3.1 30.4 + - - +
56A ARG* 2.8 22.2 + - - +
58A GLN* 1.3 70.5 - - + +
60A LEU* 1.3 61.1 + - + +
175D ASN* 3.6 27.1 - - - +
178D ILE* 3.5 31.0 - - + +
179D ASP* 3.1 29.7 + - - -
182D MET* 4.4 24.7 - - + +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ARG* 3.6 17.5 - - + +
57A ASP* 3.8 3.4 - - - +
58A GLN 3.0 8.9 + - - +
59A LYS* 1.3 84.9 - - + +
226B GLN* 3.7 39.7 - - + +
229B MET* 3.1 37.6 - - + +
230B ILE* 3.2 37.2 - - + -
233B ILE* 5.3 15.8 - - + +
57C LEU* 5.9 0.7 - - + -
178D ILE* 4.5 21.3 - - + -
52E TYR* 5.2 5.0 + - - -
56E GLU* 4.9 2.8 - - - +
59E ARG* 2.7 27.9 + - - -
----------------------------------------------------------
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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