Contacts of the helix formed by residues 22 - 48 (chain A) in PDB entry 5PNZ
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 SER 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A MET* 1.3 63.1 + - - +
24A GLU* 3.5 7.9 + - - +
25A GLN* 3.1 37.8 + - - +
26A VAL* 3.3 24.4 + - - +
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Residues in contact with MET 23 (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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22A SER* 1.3 71.7 - - - +
24A GLU* 1.3 66.2 + - - +
26A VAL* 3.2 30.3 + - + -
27A ALA* 3.0 29.9 + - + +
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Residues in contact with GLU 24 (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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22A SER* 3.3 7.7 + - - +
23A MET* 1.3 78.5 - - - +
25A GLN* 1.3 66.0 + - - +
27A ALA* 3.2 8.6 + - - +
28A MET* 3.0 29.3 + - + +
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Residues in contact with GLN 25 (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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22A SER* 3.1 29.0 + - - +
24A GLU* 1.3 80.1 - - - +
26A VAL* 1.3 57.4 + - + +
28A MET* 3.3 16.4 + - - +
29A GLU* 3.0 46.7 + - - +
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Residues in contact with VAL 26 (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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22A SER 3.3 14.1 + - - +
23A MET* 3.2 31.9 + - + +
25A GLN* 1.3 78.0 - - + +
27A ALA* 1.3 57.0 + - - +
29A GLU* 3.2 17.0 + - - +
30A LEU* 2.9 29.4 + - + +
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Residues in contact with ALA 27 (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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23A MET* 3.0 19.6 + - + +
24A GLU* 3.2 11.4 + - - +
26A VAL* 1.3 77.6 - - - +
28A MET* 1.3 62.7 + - + +
30A LEU* 3.2 9.3 + - - +
31A ARG* 3.0 21.7 + - - +
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Residues in contact with MET 28 (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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24A GLU* 3.0 20.2 + - + +
25A GLN* 3.5 21.5 - - - +
27A ALA* 1.3 75.3 - - + +
29A GLU* 1.3 59.1 + - + +
31A ARG* 3.3 41.3 + - - +
32A LEU* 3.0 27.2 + - - +
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Residues in contact with GLU 29 (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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25A GLN* 3.0 33.5 + - - +
26A VAL* 3.5 21.5 - - - +
28A MET* 1.3 74.5 - - + +
30A LEU* 1.3 61.0 + - - +
32A LEU* 3.4 11.8 + - + +
33A THR* 2.9 33.2 + - - +
87A GLN* 4.9 2.4 - - - +
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Residues in contact with LEU 30 (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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26A VAL* 2.9 16.2 + - + +
27A ALA* 3.2 11.6 + - - +
29A GLU* 1.3 75.8 - - - +
31A ARG* 1.3 58.4 + - - +
33A THR* 3.3 7.5 + - - -
34A GLU* 2.8 35.0 + - + +
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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
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27A ALA 3.0 11.9 + - - +
28A MET* 3.4 36.8 + - - +
30A LEU* 1.3 76.9 - - - +
32A LEU* 1.3 57.9 + - - +
34A GLU* 3.2 8.4 + - - +
35A LEU* 2.8 28.5 + - - +
142A GLY 3.8 17.4 + - - +
143A LEU* 3.5 30.3 + - + +
144A GLU* 3.5 27.6 + - - +
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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 MET 3.0 14.0 + - - +
29A GLU* 3.7 12.6 - - + +
31A ARG* 1.3 77.6 - - - +
33A THR* 1.3 56.2 + - - +
35A LEU* 3.3 9.1 + - + +
36A THR* 2.8 36.3 + - - +
87A GLN* 3.7 41.7 - - + +
89A TYR 3.5 24.9 - - - +
90A LYS* 4.2 13.2 - - + +
143A LEU 5.4 0.4 - - - -
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Residues in contact with THR 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 GLU* 2.9 21.5 + - - +
30A LEU* 3.6 7.8 - - - -
32A LEU* 1.3 75.0 - - - +
34A GLU* 1.3 64.1 + - + +
36A THR* 3.3 4.1 + - - -
37A ARG* 3.0 22.9 + - + +
87A GLN* 3.0 29.0 + - - +
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Residues in contact with GLU 34 (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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30A LEU* 2.8 17.4 + - + +
31A ARG* 3.2 10.5 + - - +
33A THR* 1.3 76.6 - - - +
35A LEU* 1.3 64.8 + - - +
37A ARG* 3.2 12.9 + - - +
38A LEU* 3.1 21.3 + - - +
143A LEU* 3.7 25.2 - - + +
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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
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31A ARG 2.8 17.2 + - - +
32A LEU* 3.6 10.8 - - + +
34A GLU* 1.3 72.4 - - - +
36A THR* 1.3 59.5 + - - +
38A LEU* 3.2 3.5 + - + +
39A LEU* 2.9 46.5 + - + +
89A TYR 3.5 19.1 - - - +
90A LYS* 3.4 28.9 - - - +
91A ASN* 3.7 9.0 - - - +
92A LEU 4.8 5.4 - - - +
138A VAL* 4.2 28.5 - - + -
143A LEU* 3.8 31.8 - - + +
144A GLU* 5.0 0.2 - - - +
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Residues in contact with THR 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* 2.8 25.0 + - - +
33A THR* 3.5 8.5 - - - -
34A GLU 3.2 0.2 - - - -
35A LEU* 1.3 77.3 - - - +
37A ARG* 1.3 57.3 + - - +
39A LEU* 4.5 1.8 - - - -
40A ARG* 2.9 48.0 + - - +
84A LEU* 3.3 41.5 - - + +
85A GLU* 5.2 0.7 - - - -
87A GLN* 3.6 29.2 - - + +
89A TYR 5.0 2.3 + - - -
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Residues in contact with ARG 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 THR* 3.0 13.4 + - + +
34A GLU* 3.2 18.4 + - - +
36A THR* 1.3 74.5 - - - +
38A LEU* 1.3 64.4 + - - +
40A ARG* 3.4 21.3 + - - +
41A SER* 3.3 19.1 + - - -
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Residues in contact with LEU 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 GLU 3.1 10.5 + - - +
35A LEU* 3.2 6.5 + - + +
37A ARG* 1.3 78.4 - - - +
39A LEU* 1.3 69.4 + - + +
41A SER* 3.1 9.4 + - - -
42A VAL* 3.0 46.4 + - + +
134A ALA* 4.6 7.9 - - + -
137A GLU* 3.8 35.7 - - + +
138A VAL* 4.0 23.3 - - + +
141A ILE* 5.9 0.4 - - + -
143A LEU* 3.7 25.1 - - + -
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Residues in contact with LEU 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 43.5 + - + +
36A THR* 4.9 0.9 - - - -
38A LEU* 1.3 85.5 - - + +
40A ARG* 1.3 60.5 + - - +
42A VAL* 3.6 6.5 - - + +
43A LEU* 2.7 32.2 + - - +
84A LEU* 3.6 20.6 - - + -
89A TYR* 3.8 30.1 - - + +
91A ASN 4.6 2.2 - - - +
92A LEU* 3.8 30.3 - - + -
95A PHE* 3.9 26.5 - - + -
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Residues in contact with ARG 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 THR* 2.9 38.2 + - - +
37A ARG* 3.6 23.3 + - - +
38A LEU 3.2 0.2 - - - -
39A LEU* 1.3 76.5 - - - +
41A SER* 1.3 57.9 + - - +
43A LEU* 3.4 1.9 + - - +
44A ASP* 3.0 45.4 + - - +
81A ARG* 4.5 10.3 - - - +
84A LEU* 3.6 16.5 - - + +
85A GLU* 2.7 40.4 + - - +
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Residues in contact with SER 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 ARG 3.3 8.5 + - - -
38A LEU* 3.1 12.4 + - - -
40A ARG* 1.3 75.8 - - - +
42A VAL* 1.3 64.9 + - - +
44A ASP* 3.3 8.5 + - - +
45A GLN* 3.0 43.7 + - - +
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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 LEU* 3.0 38.9 + - + +
39A LEU* 3.6 11.9 - - + +
41A SER* 1.3 76.1 - - - +
43A LEU* 1.3 58.3 + - - +
45A GLN* 3.1 12.4 + - - +
46A LEU* 2.9 38.2 + - + +
92A LEU* 5.6 0.2 - - + -
95A PHE* 3.8 23.8 - - + -
130A VAL* 4.0 16.6 - - + -
131A LEU* 4.0 11.4 - - + -
134A ALA* 3.8 16.8 - - + -
137A GLU* 5.9 0.9 - - - +
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Residues in contact with LEU 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 LEU 2.7 20.6 + - - +
40A ARG* 3.7 5.8 - - - +
42A VAL* 1.3 73.8 - - - +
44A ASP* 1.3 57.6 + - - +
46A LEU* 3.3 4.1 + - + +
47A GLN* 2.9 29.3 + - - +
77A PHE* 3.7 31.9 - - + +
80A MET* 4.3 13.9 - - + -
81A ARG* 3.8 56.5 - - + +
84A LEU* 4.1 13.5 - - + -
95A PHE* 3.9 23.8 - - + -
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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 ARG* 3.0 29.6 + - - +
41A SER* 3.7 7.6 - - - +
42A VAL 3.2 0.2 - - - -
43A LEU* 1.3 75.6 - - - +
45A GLN* 1.3 63.5 + - + +
47A GLN* 3.4 3.5 + - - +
48A ASP* 3.1 34.3 + - - +
81A ARG* 3.1 32.9 + - - +
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Residues in contact with GLN 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 SER* 3.0 39.2 + - - +
42A VAL* 3.6 11.0 - - - +
44A ASP* 1.3 76.5 - - + +
46A LEU* 1.3 62.6 + - - +
48A ASP* 3.4 19.1 + - - +
49A LYS* 3.4 20.6 - - - +
130A VAL* 4.1 30.1 - - + +
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Residues in contact with LEU 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 VAL* 2.9 25.5 + - + +
43A LEU* 3.8 4.7 - - + +
45A GLN* 1.3 75.8 - - - +
47A GLN* 1.3 57.6 + - - +
49A LYS* 3.0 27.6 + - - +
77A PHE* 4.1 8.7 - - + -
95A PHE* 3.9 30.7 - - + -
99A PHE* 3.9 36.1 - - + -
123A LEU* 3.4 11.0 - - + +
127A GLY* 3.5 39.0 - - - +
130A VAL* 3.9 13.7 - - + -
131A LEU* 4.3 7.0 - - + -
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Residues in contact with GLN 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 LEU 2.9 16.6 + - - +
44A ASP* 3.4 4.9 + - - +
46A LEU* 1.3 75.0 - - - +
48A ASP* 1.3 67.6 + - - +
50A ASP* 3.1 23.4 + - + +
51A PRO* 5.1 0.3 - - - +
53A ARG* 3.8 33.2 - - + +
56A ALA* 3.9 11.5 + - - +
77A PHE* 3.5 52.4 - - + +
81A ARG* 3.0 27.2 + - - -
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Residues in contact with ASP 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* 3.1 24.5 + - - +
45A GLN* 3.6 13.7 - - - +
46A LEU 3.2 0.4 - - - -
47A GLN* 1.3 77.5 - - - +
49A LYS* 1.3 63.2 + - + +
50A ASP 3.1 4.1 + - - -
51A PRO* 3.9 14.5 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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