Contacts of the helix formed by residues 18 - 41 (chain A) in PDB entry 2M6X
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 18 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ASN 2.5 10.3 + - - +
17A HIS* 1.3 74.6 - - - +
19A PHE* 1.3 57.8 + - - -
20A PHE* 3.0 25.4 - - - -
21A TRP* 2.7 32.2 + - - +
22A GLY 3.3 3.1 + - - -
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Residues in contact with PHE 19 (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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18A GLY* 1.3 71.7 - - - -
20A PHE* 1.3 95.4 + + + +
22A GLY* 3.0 11.2 + - - +
23A LEU* 2.8 39.6 + - + +
49E PRO* 6.1 0.9 - - + -
50E LEU* 4.8 17.5 - - + -
53E VAL* 3.8 33.8 - - + +
56E LEU* 6.0 3.1 - - - -
30F TRP* 4.1 23.1 - + - -
33F LYS* 5.7 4.7 - - - -
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Residues in contact with PHE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY 4.3 13.9 - - - -
17A HIS 4.9 1.1 - - - -
18A GLY* 3.5 20.6 - - - -
19A PHE* 1.3 104.0 - + + +
21A TRP* 1.3 92.9 + - + +
23A LEU* 3.1 23.1 + - - +
24A LEU 3.5 1.6 + - - -
56D LEU* 6.1 5.8 - - + -
25F VAL* 4.1 22.2 - - + -
26F VAL* 4.7 17.7 - - + -
29F ALA* 3.3 29.4 - - + +
30F TRP* 3.5 30.3 - + + -
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Residues in contact with TRP 21 (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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16A ASN* 3.5 44.8 + - + +
18A GLY 2.7 16.0 + - - +
20A PHE* 1.3 90.6 - - + +
22A GLY* 1.3 62.7 + - - -
24A LEU* 3.2 46.8 + - + +
25A VAL* 3.7 7.1 + - + +
25F VAL* 3.4 40.2 - - + -
28F LEU* 5.8 1.1 - - + -
29F ALA* 4.7 1.6 - - + -
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Residues in contact with GLY 22 (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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18A GLY 3.3 4.4 + - - -
19A PHE* 3.0 9.6 + - - -
21A TRP* 1.3 83.5 - - - +
23A LEU* 1.3 63.1 + - - +
24A LEU 3.3 0.3 + - - -
25A VAL* 3.3 24.2 - - - +
26A VAL* 3.5 8.9 - - - +
56E LEU* 4.5 26.4 - - - +
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Residues in contact with LEU 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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19A PHE* 2.8 44.3 + - + +
20A PHE* 3.1 12.2 + - - +
22A GLY* 1.3 78.3 - - - +
24A LEU* 1.3 54.8 + - - +
26A VAL* 2.8 19.7 - - + +
27A THR* 2.6 28.8 + - - +
49E PRO* 4.2 24.9 - - + +
52E LEU* 6.1 4.5 - - + -
53E VAL* 3.8 24.5 - - + -
29F ALA 5.1 8.7 - - - +
32F VAL* 5.0 2.2 - - + -
33F LYS* 4.4 23.6 - - + +
36F LEU* 5.0 14.4 - - + -
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Residues in contact with LEU 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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20A PHE 3.5 4.5 + - - +
21A TRP* 3.2 46.7 + - + +
23A LEU* 1.3 80.7 - - - +
25A VAL* 1.3 63.1 + - - +
27A THR* 3.4 3.5 + - - -
28A LEU* 3.1 43.5 + - + +
28F LEU* 4.5 22.9 - - + +
29F ALA* 4.6 8.5 - - - +
32F VAL* 3.5 35.6 - - + +
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Residues in contact with VAL 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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21A TRP* 3.7 6.3 + - + +
22A GLY* 3.3 16.9 + - - +
24A LEU* 1.3 80.7 - - - +
26A VAL* 1.3 76.5 + - + +
28A LEU* 3.4 10.3 + - + +
29A ALA* 3.2 21.0 + - - +
15B GLY 6.0 2.2 - - - +
16B ASN* 6.3 0.7 - - - -
21B TRP* 3.9 31.0 - - + +
24B LEU* 4.9 7.9 - - + +
56E LEU* 5.4 6.3 - - + -
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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 GLY 3.5 6.1 - - - +
23A LEU* 2.8 37.0 - - + +
25A VAL* 1.3 89.5 - - + +
27A THR* 1.3 66.9 + - - +
29A ALA* 3.2 7.0 + - - +
30A TRP* 3.0 48.4 + - + -
20B PHE* 5.8 9.2 - - + -
52E LEU* 4.6 16.6 - - + -
56E LEU* 5.1 15.5 - - + -
36F LEU* 4.6 9.2 - - + -
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Residues in contact with THR 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 LEU* 2.6 21.2 + - - +
24A LEU* 3.6 5.4 - - - -
25A VAL 3.3 0.2 - - - -
26A VAL* 1.3 80.0 - - - +
28A LEU* 1.3 63.5 + - + +
30A TRP* 3.3 4.8 + - - +
31A HIS* 3.1 21.9 + - + +
32F VAL* 3.8 27.4 - - + +
35F ARG* 4.1 13.9 - - + -
36F LEU* 3.1 55.3 - - - +
39F GLY* 6.0 0.2 - - - -
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Residues in contact with LEU 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 LEU* 3.1 43.5 + - + +
25A VAL* 3.7 8.3 - - + +
26A VAL 3.3 0.2 - - - -
27A THR* 1.3 80.8 - - + +
29A ALA* 1.3 63.7 + - - +
31A HIS* 3.4 5.4 + - + +
32A VAL* 3.3 28.8 + - + +
24B LEU* 4.1 22.2 - - + -
32F VAL* 5.8 0.4 - - + -
35F ARG* 4.1 27.6 - - - +
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Residues in contact with ALA 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 VAL 3.2 9.9 + - - +
26A VAL* 3.2 11.2 + - - +
27A THR 3.2 0.2 - - - -
28A LEU* 1.3 80.8 - - - +
30A TRP* 1.3 59.0 + - - +
32A VAL* 2.7 27.1 - - - +
33A LYS* 4.0 7.4 + - - +
20B PHE* 4.0 43.1 - - + +
21B TRP* 5.6 0.4 - - - -
23B LEU* 5.8 2.7 - - + +
24B LEU* 4.5 11.6 - - + +
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Residues in contact with TRP 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* 3.0 43.9 + - + +
27A THR* 3.8 6.5 - - - +
28A LEU 3.3 0.2 - - - -
29A ALA* 1.3 77.3 - - - +
31A HIS* 1.3 63.9 + - - +
33A LYS* 3.2 39.8 + - - +
20B PHE* 3.5 46.0 - + - -
48E TRP* 6.3 1.3 - + - -
52E LEU* 4.8 16.6 - - + -
36F LEU* 5.2 14.4 - - + -
39F GLY* 3.3 41.8 - - - +
40F ALA* 3.8 11.1 - - + +
42F TYR* 3.6 18.5 - + - -
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Residues in contact with HIS 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 THR 3.1 15.8 + - - +
28A LEU* 3.8 6.3 - - - +
29A ALA 3.3 0.2 - - - -
30A TRP* 1.3 78.8 - - - +
32A VAL* 1.3 62.9 + - + +
33A LYS 3.0 1.7 + - - -
34A GLY* 3.5 9.4 + - - -
35A ARG* 3.8 36.2 + - + +
35F ARG* 3.7 48.6 + - + +
38F PRO* 5.7 4.0 - - + -
39F GLY* 4.6 13.6 - - - -
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Residues in contact with VAL 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 LEU* 3.4 15.3 - - + +
29A ALA* 2.7 32.8 - - - +
31A HIS* 1.3 73.4 - - + +
33A LYS* 1.3 67.6 + - + +
34A GLY 3.2 0.2 - - - -
35A ARG* 2.8 34.0 + - + +
36A LEU* 2.9 14.0 + - - +
23B LEU* 5.4 0.9 - - + -
24B LEU* 3.7 22.2 - - + -
27B THR* 3.4 31.3 - - + +
28B LEU* 4.1 17.3 - - + -
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Residues in contact with LYS 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 ALA 4.2 5.0 + - - +
30A TRP* 3.2 34.5 - - - +
31A HIS 3.0 1.4 + - - -
32A VAL* 1.3 79.9 - - + +
34A GLY* 1.3 63.8 + - - +
36A LEU* 3.0 21.7 + - - +
37A VAL* 3.8 7.6 - - - +
20B PHE* 4.2 18.7 - - - -
23B LEU* 5.2 9.7 - - - +
27B THR* 5.7 1.3 - - - -
42F TYR* 3.5 62.7 + - + -
45F LEU* 4.2 29.2 + - + +
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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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31A HIS 3.5 6.7 + - - -
32A VAL 3.2 0.6 - - - -
33A LYS* 1.3 79.8 - - - +
35A ARG* 1.3 56.5 + - - +
36A LEU 3.3 0.3 + - - -
37A VAL* 3.3 9.7 - - - +
38A PRO* 2.7 27.2 - - - +
42F TYR* 5.9 0.8 - - - +
45F LEU* 5.1 1.3 - - - +
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Residues in contact with ARG 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 HIS* 3.8 24.9 + - + +
32A VAL* 2.8 34.3 + - + +
34A GLY* 1.3 79.0 - - - +
36A LEU* 1.3 62.4 + - - +
38A PRO* 3.1 17.2 - - - +
39A GLY* 3.5 6.2 + - - -
27B THR 5.3 2.5 - - - +
28B LEU* 4.1 23.1 - - - +
31B HIS* 3.6 49.4 + - + +
35B ARG* 5.4 5.0 - - - +
35F ARG* 4.0 20.2 - - - +
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Residues in contact with LEU 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 VAL 2.9 9.9 + - - +
33A LYS* 3.0 14.8 + - - +
35A ARG* 1.3 77.4 - - - +
37A VAL* 1.3 64.6 + - - +
39A GLY* 3.4 3.1 + - - -
40A ALA* 3.3 18.6 + - + +
23B LEU* 5.0 9.9 - - + -
26B VAL* 5.8 2.9 - - + -
27B THR* 3.7 38.1 + - + -
30B TRP* 4.3 29.5 - - + +
45F LEU* 5.5 9.2 - - + -
49F PRO* 5.0 13.2 - - + -
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Residues in contact with VAL 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 LYS 3.8 9.2 - - - +
34A GLY* 3.3 21.1 - - - +
36A LEU* 1.3 75.8 - - - +
38A PRO* 1.3 67.0 - - + +
40A ALA* 3.1 21.8 + - - +
41A THR* 3.7 10.2 + - + +
45F LEU* 4.8 18.1 - - + +
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Residues in contact with PRO 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 GLY 2.7 28.0 - - - +
35A ARG* 3.1 20.0 - - - +
37A VAL* 1.3 90.6 - - + +
39A GLY* 1.3 56.6 + - - +
41A THR* 2.9 34.8 + - + +
42A TYR* 5.2 0.2 - - - +
31B HIS* 4.7 8.1 - - + +
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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 ARG 3.5 3.9 + - - -
36A LEU 3.4 6.9 + - - -
37A VAL 3.2 1.0 - - - -
38A PRO* 1.3 85.0 - - - +
40A ALA* 1.3 61.5 + - - +
42A TYR* 3.0 18.5 - - - -
30B TRP* 3.4 36.2 - - - -
31B HIS* 4.3 6.2 - - - -
33B LYS* 3.6 8.6 - - - +
34B GLY 5.8 0.4 - - - -
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Residues in contact with ALA 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 LEU* 3.3 13.1 + - + +
37A VAL* 3.1 15.5 + - - +
39A GLY* 1.3 76.9 - - - +
41A THR* 1.3 62.9 + - + +
42A TYR* 2.9 20.3 + - - -
30B TRP* 3.7 17.7 - - + +
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Residues in contact with THR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 4.0 11.7 - - + +
38A PRO* 2.9 23.7 + - + +
40A ALA* 1.3 80.0 - - + +
42A TYR* 1.3 61.8 + - - +
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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
------------------------------------------------------------
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