Contacts of the helix formed by residues 23 - 49 (chain B) in PDB entry 5PQR
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 MET 23 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B SER* 1.3 74.5 - - - +
24B GLU* 1.3 68.1 + - - +
26B VAL* 3.6 30.0 - - + +
27B ALA* 2.9 30.7 + - - +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER* 3.7 20.4 - - - +
23B MET* 1.3 87.3 + - - +
25B GLN* 1.3 57.4 + - + +
27B ALA* 3.7 5.7 + - - +
28B MET* 3.1 33.4 + - + +
31B ARG* 5.0 1.6 + - - -
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Residues in contact with GLN 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER* 3.1 37.8 + - - +
24B GLU* 1.3 76.8 - - + +
26B VAL* 1.3 61.1 + - + +
28B MET* 3.8 11.6 - - + +
29B GLU* 3.0 31.2 + - - +
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B SER 3.3 12.8 + - - +
23B MET* 3.6 34.3 - - + +
25B GLN* 1.3 76.3 - - + +
27B ALA* 1.3 58.2 + - - +
29B GLU* 3.5 4.8 + - - +
30B LEU* 2.9 44.7 + - + +
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B MET* 2.9 17.8 + - + +
24B GLU* 3.8 6.3 - - - +
26B VAL* 1.3 75.3 - - - +
28B MET* 1.3 60.3 + - - +
30B LEU* 3.3 10.3 + - - +
31B ARG* 2.9 50.0 + - + +
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Residues in contact with MET 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 3.1 24.8 + - + +
25B GLN* 3.8 11.4 - - + +
26B VAL 3.4 0.2 - - - -
27B ALA* 1.3 74.5 - - - +
29B GLU* 1.3 58.3 + - - +
31B ARG* 3.2 29.9 + - + +
32B LEU* 2.9 29.0 + - + +
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLN 3.0 18.2 + - - +
26B VAL* 3.9 4.9 - - - +
28B MET* 1.3 75.8 - - - +
30B LEU* 1.3 62.7 + - + +
32B LEU* 3.4 22.2 + - - +
33B THR* 3.1 46.8 + - + +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 2.9 39.0 + - + +
27B ALA* 3.6 9.2 - - - +
28B MET 3.3 0.4 - - - -
29B GLU* 1.3 76.5 - - + +
31B ARG* 1.3 62.7 + - + +
33B THR* 3.2 11.4 + - - +
34B GLU* 3.0 33.7 + - + +
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Residues in contact with ARG 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU 5.0 1.4 + - - -
27B ALA* 2.9 40.1 + - + +
28B MET* 3.2 40.4 + - - +
30B LEU* 1.3 75.0 - - + +
32B LEU* 1.3 63.4 + - - +
34B GLU* 3.6 0.6 + - - -
35B LEU* 3.1 25.3 + - - +
142B GLY 4.0 18.8 - - - +
143B LEU* 3.7 35.5 + - + +
144B GLU 5.7 2.8 - - - -
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B MET* 2.9 13.2 + - + +
29B GLU* 3.5 26.5 - - - +
31B ARG* 1.3 78.2 - - - +
33B THR* 1.3 73.3 + - + +
35B LEU* 3.5 7.5 + - - +
36B THR* 2.9 34.1 + - + +
87B GLN* 3.5 44.1 + - + +
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Residues in contact with THR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLU* 3.1 34.6 + - + +
30B LEU* 3.2 17.7 + - - +
32B LEU* 1.3 84.5 - - + +
34B GLU* 1.3 67.4 + - - +
36B THR* 3.7 5.9 + - - -
37B ARG* 3.0 39.9 + - - +
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.0 24.7 + - + +
31B ARG* 5.3 0.2 - - - -
33B THR* 1.3 78.9 + - - +
35B LEU* 1.3 58.9 + - - +
37B ARG* 3.2 38.2 + - - +
38B LEU* 3.1 27.7 + - - +
141B ILE* 4.1 31.0 - - + +
143B LEU* 3.9 20.9 - - + +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ARG 3.1 19.0 + - - +
32B LEU* 3.6 7.9 - - - +
34B GLU* 1.3 70.4 - - - +
36B THR* 1.3 63.8 + - - +
38B LEU* 3.1 9.1 + - + +
39B LEU* 2.8 58.2 + - + +
89B TYR 3.8 11.7 - - - +
90B LYS* 3.4 33.7 - - - +
91B ASN* 4.0 2.9 - - - +
92B LEU* 4.3 16.6 - - + +
138B VAL* 5.1 2.7 - - + -
143B LEU* 3.7 22.9 - - + +
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Residues in contact with THR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 2.9 18.7 + - - +
33B THR* 3.8 7.9 - - - -
35B LEU* 1.3 81.2 - - - +
37B ARG* 1.3 55.9 + - - +
39B LEU* 4.0 1.3 - - - +
40B ARG* 2.9 60.5 + - - +
84B LEU* 4.1 25.6 - - + +
85B GLU* 5.1 1.8 - - - +
87B GLN* 3.0 27.2 + - - +
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Residues in contact with ARG 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B THR* 3.0 28.4 + - - +
34B GLU* 3.2 31.1 + - - +
36B THR* 1.3 77.0 - - - +
38B LEU* 1.3 61.8 + - - +
40B ARG* 3.4 21.7 + - - +
41B SER* 3.0 23.4 + - - -
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLU 3.1 14.1 + - - +
35B LEU* 3.5 11.2 - - + +
37B ARG* 1.3 74.1 - - - +
39B LEU* 1.3 71.9 + - + +
41B SER* 3.0 10.7 + - - -
42B VAL* 2.9 32.6 + - + +
92B LEU* 5.5 0.9 - - + -
134B ALA* 3.8 24.5 - - + +
137B GLU* 4.1 24.5 - - + +
138B VAL* 3.4 37.9 - - + +
141B ILE* 5.1 6.7 - - + -
143B LEU* 4.4 9.9 - - + -
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 2.8 48.2 + - + +
36B THR 5.2 0.2 - - - +
38B LEU* 1.3 77.9 - - + +
40B ARG* 1.3 57.1 + - - +
42B VAL* 3.2 6.0 + - + +
43B LEU* 2.8 32.4 + - - +
84B LEU* 3.7 23.6 - - + -
89B TYR* 3.9 27.6 - - + +
91B ASN 4.6 2.5 - - - +
92B LEU* 3.5 33.0 - - + -
95B PHE* 3.8 31.7 - - + -
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Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B THR* 2.9 46.3 + - - +
37B ARG* 3.6 24.0 - - - +
38B LEU 3.2 0.2 - - - -
39B LEU* 1.3 75.8 - - - +
41B SER* 1.3 62.2 + - - +
43B LEU* 3.6 1.3 + - - +
44B ASP* 3.1 40.6 + - - +
81B ARG* 4.6 9.0 - - - +
84B LEU* 3.7 12.3 - - + +
85B GLU* 2.8 42.4 + - - +
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Residues in contact with SER 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ARG 3.0 13.1 + - - -
38B LEU* 3.0 14.5 + - - +
40B ARG* 1.3 74.5 - - - +
42B VAL* 1.3 65.9 + - - +
44B ASP* 3.4 6.2 + - - +
45B GLN* 3.0 42.5 + - - +
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU* 2.9 25.5 + - + +
39B LEU* 3.5 13.5 - - + +
41B SER* 1.3 76.5 + - - +
43B LEU* 1.3 64.1 + - - +
45B GLN* 3.2 12.9 + - - +
46B LEU* 3.0 27.1 + - + +
92B LEU* 5.5 0.2 - - + -
95B PHE* 3.6 25.1 - - + -
130B VAL* 4.0 17.5 - - + -
131B LEU* 3.9 15.3 - - + -
134B ALA* 3.7 28.5 - - + -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU 2.8 20.2 + - - +
40B ARG 4.0 3.1 - - - +
42B VAL* 1.3 73.9 - - - +
44B ASP* 1.3 57.6 + - - +
46B LEU* 3.2 6.9 + - + +
47B GLN* 3.0 30.9 + - - +
77B PHE* 3.7 35.4 - - + +
80B MET* 4.2 13.7 - - + -
81B ARG* 3.6 59.0 - - + +
84B LEU* 4.0 13.9 - - + -
95B PHE* 4.1 19.3 - - + -
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Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ARG* 3.1 24.5 + - - +
41B SER* 3.7 7.0 - - - +
43B LEU* 1.3 75.0 - - - +
45B GLN* 1.3 56.9 + - + +
47B GLN* 4.0 2.0 - - - +
48B ASP* 3.0 42.7 + - - +
81B ARG* 2.7 42.2 + - - +
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Residues in contact with GLN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B SER* 3.0 41.1 + - - +
42B VAL* 3.6 12.8 - - - +
44B ASP* 1.3 77.8 - - + +
46B LEU* 1.3 61.9 + - - +
48B ASP* 3.8 7.5 + - - +
49B LYS* 3.5 35.2 + - - +
130B VAL* 3.8 32.1 - - + +
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL* 3.0 32.9 + - + +
43B LEU* 3.2 10.5 + - + +
45B GLN* 1.3 74.4 - - - +
47B GLN* 1.3 64.8 + - - +
49B LYS* 3.1 23.2 + - + +
50B ASP 3.8 2.3 + - - -
77B PHE* 4.0 21.9 - - + -
80B MET* 5.7 0.4 - - + -
95B PHE* 4.3 13.0 - - + -
99B PHE* 3.9 31.9 - - + -
123B LEU* 3.9 12.5 - - + +
126B GLN 5.1 0.2 - - - -
127B GLY* 3.6 32.8 - - - +
130B VAL* 4.5 13.9 - - + -
131B LEU* 5.3 3.4 - - + -
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Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 3.0 21.7 + - + +
44B ASP* 4.1 2.9 - - - +
46B LEU* 1.3 69.1 - - - +
48B ASP* 1.3 60.2 + - - +
49B LYS 3.0 1.6 - - - -
50B ASP* 2.7 35.3 + - + +
53B ARG* 3.9 35.6 + - - +
56B ALA* 4.2 10.3 + - - +
77B PHE* 3.5 50.1 - - + +
78B ALA* 5.3 0.9 - - - +
81B ARG* 3.0 34.8 + - - +
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Residues in contact with ASP 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ASP* 3.0 25.7 + - - +
45B GLN* 3.9 9.6 - - - +
46B LEU 3.3 0.2 - - - -
47B GLN* 1.3 77.5 - - - +
49B LYS* 1.3 61.0 + - + +
50B ASP 3.5 0.7 + - - -
51B PRO* 4.1 10.8 - - - +
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Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLN* 3.5 27.7 + - - +
46B LEU* 3.1 14.3 + - + +
47B GLN 3.0 1.2 + - - -
48B ASP* 1.3 78.1 - - + +
50B ASP* 1.3 56.3 + - - +
51B PRO* 3.3 9.0 - - - +
122B ARG* 2.8 33.2 + - - +
123B LEU* 4.1 10.2 - - + +
126B GLN* 3.8 48.7 - - + +
130B VAL* 4.6 15.1 - - + +
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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