Contacts of the helix formed by residues 23 - 47 (chain A) in PDB entry 2Q06
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 THR 23 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA* 1.3 75.7 - - - +
24A GLU* 1.3 60.4 + - - +
25A ILE 3.2 0.7 - - - +
26A ARG* 3.6 26.9 - - + -
27A ALA* 2.9 29.0 + - + +
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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 ALA* 3.6 19.4 + - + +
23A THR* 1.3 76.2 - - - +
25A ILE* 1.3 79.1 + - - +
26A ARG 3.0 1.5 + - - -
27A ALA* 3.2 5.4 + - - +
28A SER* 2.7 38.8 + - - +
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Residues in contact with ILE 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 ALA 3.4 24.7 + - - +
23A THR 3.2 0.4 - - - -
24A GLU* 1.3 97.8 + - - +
26A ARG* 1.3 64.1 + - + +
28A SER* 3.5 10.2 + - - -
29A VAL* 3.2 27.6 - - + +
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR* 3.2 28.4 + - + +
24A GLU 3.0 0.6 - - - -
25A ILE* 1.3 81.9 - - + +
27A ALA* 1.3 61.1 + - - +
28A SER 3.2 1.8 - - - -
29A VAL 3.8 0.9 - - - -
30A GLY 3.3 9.7 + - - -
294A GLU 2.5 32.1 + - - -
295A GLY* 3.0 17.2 + - - -
296A TYR 3.0 45.7 + - - +
297A SER* 4.4 9.0 - - - +
301A ILE* 5.1 3.0 - - - +
302A ASP* 2.3 38.0 + - - -
305A ARG* 4.5 6.1 - - - +
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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 THR* 2.9 19.7 + - + +
24A GLU* 4.0 4.7 - - - +
26A ARG* 1.3 77.1 - - - +
28A SER* 1.3 59.1 + - - +
29A VAL 3.4 0.2 - - - -
30A GLY 4.1 0.6 - - - -
31A ARG* 3.2 22.2 + - - +
292A GLU* 4.3 24.1 - - + +
295A GLY* 4.5 9.0 - - - -
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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
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24A GLU* 2.7 28.6 + - - +
25A ILE* 3.5 10.0 + - - -
27A ALA* 1.3 75.8 - - - +
29A VAL* 1.3 65.7 + - - +
31A ARG* 3.5 21.5 - - - +
32A MET* 3.6 11.1 + - - +
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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
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25A ILE* 3.2 21.7 + - + +
26A ARG 3.6 1.0 + - - +
27A ALA 3.4 0.2 - - - -
28A SER* 1.3 78.8 + - - +
30A GLY* 1.3 59.5 + - - +
32A MET* 3.1 18.6 - - + +
33A VAL* 3.0 23.6 + - - +
296A TYR* 3.2 38.8 - - + +
297A SER* 5.4 0.7 - - - -
298A LEU* 3.8 37.2 - - + -
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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
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26A ARG 3.3 9.4 + - - -
27A ALA 4.0 1.1 + - - -
29A VAL* 1.3 76.9 - - - +
31A ARG* 1.3 58.2 + - - +
33A VAL* 4.2 3.1 - - - -
34A GLY* 2.7 32.6 + - - -
291A PHE* 3.6 23.7 - - - +
296A TYR* 3.7 22.2 - - - -
368B ASN* 3.9 1.4 - - - +
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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 3.2 20.6 + - - +
28A SER* 3.5 15.7 - - - +
30A GLY* 1.3 76.1 - - - +
32A MET* 1.3 59.8 + - - +
34A GLY 3.5 0.2 + - - -
35A GLY* 3.0 21.8 + - - -
38A ARG* 3.6 7.6 + - - -
124A ASN* 3.2 23.3 + - - +
125A ASN* 4.5 6.9 + - - +
127A GLU* 2.3 36.2 + - - +
129A ALA* 3.9 25.3 - - - +
292A GLU* 4.8 8.4 - - + +
368B ASN* 3.9 23.8 + - - +
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Residues in contact with MET 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 3.6 10.5 + - - +
29A VAL* 3.1 24.2 + - + +
30A GLY 3.1 0.2 - - - -
31A ARG* 1.3 80.9 - - + +
33A VAL* 1.3 68.7 + - + +
35A GLY* 3.4 8.1 + - - +
36A ILE* 3.3 19.0 + - - +
120A TRP* 5.4 0.5 - - - -
124A ASN* 4.9 3.5 - - - +
129A ALA* 5.1 7.0 - - + +
131A ALA* 3.7 32.3 - - + +
132A GLY* 3.8 18.6 - - - +
135A HIS* 3.6 36.8 - - + +
298A LEU* 4.9 13.0 - - + -
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Residues in contact with VAL 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 17.0 + - - +
30A GLY* 3.2 4.5 + - - +
32A MET* 1.3 79.5 - - + +
34A GLY* 1.3 70.3 + - - +
35A GLY 2.9 1.1 - - - -
36A ILE* 2.8 21.1 + - + +
37A GLY* 3.1 9.7 + - - -
135A HIS* 4.4 12.6 - - + +
281A TYR* 3.7 40.2 - - + +
291A PHE* 3.4 41.3 - - + -
296A TYR* 4.3 15.3 - - + -
298A LEU* 5.1 0.7 - - + -
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Residues in contact with GLY 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 GLY 2.7 18.4 + - - -
33A VAL* 1.3 74.2 - - - +
35A GLY* 1.3 65.2 + - - +
37A GLY 3.1 1.9 + - - -
38A ARG* 3.0 44.7 + - - -
285A VAL* 4.5 3.7 - - - +
291A PHE* 4.0 21.3 - - - -
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Residues in contact with GLY 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 3.0 12.3 + - - -
32A MET 3.6 6.3 - - - -
33A VAL 2.9 1.4 - - - -
34A GLY* 1.3 79.1 - - - +
36A ILE* 1.3 62.2 + - - +
38A ARG* 3.2 9.5 + - - +
39A PHE* 3.2 20.4 + - - +
120A TRP* 4.6 1.3 - - - -
123A ALA 4.2 3.5 - - - +
124A ASN* 2.9 34.0 + - - -
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Residues in contact with ILE 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 MET* 3.3 14.6 + - - +
33A VAL* 2.8 21.5 + - + +
35A GLY* 1.3 70.3 - - - -
37A GLY* 1.3 57.3 + - - +
39A PHE* 3.2 6.2 - - + +
40A TYR* 2.9 28.6 + - + +
120A TRP* 3.9 16.8 - - + -
132A GLY* 3.9 9.2 - - - +
135A HIS* 4.6 11.2 - - + -
136A MET* 3.3 38.6 - - + -
278A ALA* 3.8 34.5 - - + +
281A TYR* 4.3 15.3 - - + -
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Residues in contact with GLY 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 VAL 3.1 4.6 + - - -
34A GLY 3.1 6.1 + - - -
36A ILE* 1.3 76.5 - - - +
38A ARG* 1.3 70.1 + - - +
40A TYR* 3.3 2.1 + - - +
41A ILE* 3.0 23.0 + - - +
281A TYR* 3.5 30.7 - - - +
282A GLY* 3.9 2.2 - - - -
285A VAL* 3.6 12.3 - - - -
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Residues in contact with ARG 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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31A ARG 3.6 3.6 + - - -
34A GLY* 3.0 42.4 + - - +
35A GLY* 3.2 6.3 - - - +
37A GLY* 1.3 71.7 - - - +
39A PHE* 1.3 66.2 + - - +
41A ILE* 2.9 5.1 + - - +
42A GLN* 2.8 24.6 + - - +
123A ALA* 3.2 32.3 + - + +
124A ASN* 4.7 1.4 - - - +
125A ASN* 3.6 9.9 + - - -
285A VAL* 4.0 20.6 - - + +
361B ARG* 4.8 10.9 + - - +
366B ALA* 6.4 0.7 - - - -
368B ASN* 3.0 60.2 + - - +
369B GLU* 4.5 24.2 - - + +
370B ASN 5.0 2.0 - - - +
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Residues in contact with PHE 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 GLY 3.2 11.3 + - - +
36A ILE* 3.2 14.8 - - + +
38A ARG* 1.3 76.6 - - - +
40A TYR* 1.3 67.9 + + + +
42A GLN* 3.0 6.6 + - - +
43A MET* 2.7 56.1 + - + +
63A ILE* 4.1 15.9 - - + -
64A GLU* 6.0 0.2 - - - -
67A VAL* 3.3 39.5 - - + -
116A ILE* 4.1 7.2 - - + -
119A ILE* 3.9 14.4 - - + -
120A TRP* 3.5 60.3 - + + -
123A ALA* 3.7 12.3 - - + +
136A MET* 6.3 1.6 - - - -
278A ALA* 6.2 1.8 - - + -
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Residues in contact with TYR 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 ILE 2.9 14.7 + - - +
37A GLY 3.6 3.6 - - - +
39A PHE* 1.3 83.9 - + + +
41A ILE* 1.3 65.2 + - + +
43A MET* 3.1 6.0 + - - +
44A CYS* 2.8 42.8 + - - -
49A LEU* 5.4 0.9 - - - +
53A GLU 4.9 0.2 + - - -
54A GLY* 2.2 37.4 + - - -
56A LEU 4.7 0.2 + - - -
59A ASN* 5.0 0.7 - - - +
60A SER* 3.5 25.3 + - - -
63A ILE* 3.5 34.0 - - + +
278A ALA* 3.8 27.6 - - + +
279A CYS* 3.1 30.2 - - + +
282A GLY* 3.7 13.9 - - - -
283A LEU 5.2 1.3 - - - -
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Residues in contact with ILE 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 GLY 3.0 12.5 + - - +
38A ARG* 2.9 9.9 + - - +
40A TYR* 1.3 78.1 - - + +
42A GLN* 1.3 69.6 + - - +
44A CYS* 2.8 24.0 + - + +
45A THR* 3.6 9.1 + - + +
282A GLY* 3.2 29.6 - - - +
285A VAL* 3.9 8.7 - - + -
286A ALA* 3.2 33.0 - - + +
361B ARG* 3.5 27.8 - - - +
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Residues in contact with GLN 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 ARG 2.8 16.1 + - - +
39A PHE* 3.4 10.3 - - - +
41A ILE* 1.3 77.9 - - - +
43A MET* 1.3 62.1 + - - +
45A THR* 3.2 16.0 + - - -
46A GLU* 3.5 15.9 + - + +
119A ILE* 4.2 22.2 - - + -
123A ALA* 5.4 4.3 - - + -
318B PRO* 3.4 33.4 - - + +
319B ASN* 3.4 36.8 + - - +
361B ARG* 5.2 5.2 + - - -
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Residues in contact with MET 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 PHE* 2.7 39.5 + - + +
40A TYR* 3.2 14.1 - - - +
42A GLN* 1.3 73.3 - - - +
44A CYS* 1.3 58.9 + - - +
46A GLU* 2.9 31.3 + - + +
47A LEU* 3.1 24.9 - - + +
63A ILE* 3.7 26.5 - - + -
66A MET* 4.1 17.9 - - + -
111A TYR* 5.3 7.6 - - + -
116A ILE* 3.7 37.7 - - + -
119A ILE* 4.6 15.9 - - - +
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Residues in contact with CYS 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 TYR* 2.8 56.0 + - - -
41A ILE* 2.8 15.1 + - + +
43A MET* 1.3 76.5 - - - +
45A THR* 1.3 61.3 + - + +
47A LEU* 3.8 6.8 + - - -
48A LYS* 3.5 1.6 + - - -
49A LEU* 3.3 47.4 + - + +
54A GLY* 4.4 8.1 - - - -
63A ILE* 4.6 2.0 - - - -
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Residues in contact with THR 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 ILE* 3.6 8.5 + - + +
42A GLN* 3.2 14.2 + - - -
44A CYS* 1.3 77.1 - - + +
46A GLU* 1.3 57.7 + - - +
47A LEU 2.9 4.9 - - - -
48A LYS* 2.7 39.1 + - + +
49A LEU 6.1 0.2 - - - +
319B ASN* 3.4 34.4 + - - +
359B SER* 5.5 7.6 - - - +
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Residues in contact with GLU 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 GLN* 3.5 19.1 - - + +
43A MET* 2.9 21.5 + - + +
45A THR* 1.3 77.2 + - - +
47A LEU* 1.3 59.6 + - + +
48A LYS* 6.0 0.2 - - - -
111A TYR* 2.9 36.8 + - + +
115A GLU* 3.9 17.8 - - - +
118A ARG* 5.5 1.0 + - - -
119A ILE* 4.3 17.1 - - + +
319B ASN* 3.9 14.6 - - - +
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Residues in contact with LEU 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 MET* 3.1 38.0 + - + +
44A CYS 4.3 0.2 - - - +
45A THR 2.9 0.6 - - - -
46A GLU* 1.3 79.7 - - + +
48A LYS* 1.3 58.2 + - - +
49A LEU* 2.7 40.7 + - + -
63A ILE* 4.3 10.1 - - + -
66A MET* 5.9 2.0 - - - -
96A ILE* 4.0 20.4 - - + -
98A ARG* 2.3 39.3 + - - +
109A ILE* 4.8 14.4 - - + -
111A TYR* 3.8 28.3 - - + -
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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
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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