Contacts of the helix formed by residues 17 - 43 (chain A) in PDB entry 1DIP
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 GLU 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ALA* 5.7 6.1 - - + +
13A ARG* 4.7 22.4 - - + +
14A GLU 4.9 3.1 + - - -
15A GLU 5.2 1.2 - - - +
16A VAL* 1.3 76.8 - - - +
18A ILE* 1.3 61.6 + - + +
20A LYS* 3.6 11.0 - - + +
21A GLU* 3.0 36.8 + - - +
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Residues in contact with ILE 18 (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 VAL* 3.1 13.6 - - + -
17A GLU* 1.3 81.6 - - + +
19A LEU* 1.3 61.0 + - + +
21A GLU* 3.3 6.2 + - - +
22A GLN* 2.8 42.0 + - + +
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Residues in contact with LEU 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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16A VAL* 3.3 21.4 + - + +
18A ILE* 1.3 84.3 - - + +
20A LYS* 1.3 58.3 + - - +
22A GLN* 3.3 24.0 - - - +
23A ILE* 3.0 37.5 + - + +
16B VAL* 5.4 7.0 - - + -
19B LEU* 3.1 59.0 - - + +
20B LYS* 5.9 1.8 - - + -
23B ILE* 5.0 8.7 - - + -
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Residues in contact with LYS 20 (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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9A MET 5.6 1.6 + - - -
10A TYR 4.6 6.3 + - - -
11A ALA* 3.6 41.3 - - + +
12A VAL* 3.8 15.7 - - + -
16A VAL 2.8 18.0 + - - +
17A GLU* 3.6 11.9 - - + +
19A LEU* 1.3 78.9 - - - +
21A GLU* 1.3 88.1 + - - +
23A ILE* 3.4 5.8 + - - +
24A ARG* 2.9 46.5 + - + +
19B LEU* 5.8 1.1 - - - -
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Residues in contact with GLU 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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17A GLU* 3.0 22.9 + - - +
18A ILE* 3.6 4.6 - - - +
20A LYS* 1.3 104.5 + - - +
22A GLN* 1.3 57.8 + - - +
24A ARG* 3.7 5.2 - - + +
25A GLU* 2.6 48.7 + - - +
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Residues in contact with GLN 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 ILE* 2.8 24.8 + - + +
19A LEU* 3.3 30.9 - - - +
20A LYS 3.1 0.2 - - - -
21A GLU* 1.3 78.3 - - - +
23A ILE* 1.3 65.9 + - + +
25A GLU* 3.4 4.6 + - + -
26A LEU* 2.8 44.2 + - + +
23B ILE* 3.3 26.1 - - - +
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Residues in contact with ILE 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 LEU* 3.0 20.6 + - + +
20A LYS* 4.0 4.9 - - - +
22A GLN* 1.3 83.1 - - + +
24A ARG* 1.3 62.8 + - - +
26A LEU* 5.2 0.2 - - + -
27A VAL* 2.9 41.0 + - + +
19B LEU* 4.1 15.3 - - + -
22B GLN* 4.1 22.2 - - + -
23B ILE* 3.8 31.2 - - + -
26B LEU* 3.5 24.0 - - + +
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Residues in contact with ARG 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 LYS* 2.9 39.1 + - - +
21A GLU* 3.8 10.8 - - - +
23A ILE* 1.3 81.3 - - - +
25A GLU* 1.3 79.7 + - - +
27A VAL* 3.5 5.2 + - - +
28A GLU* 2.9 55.1 + - - +
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Residues in contact with GLU 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 GLU* 2.6 51.3 + - - +
22A GLN* 3.9 4.9 - - - +
24A ARG* 1.3 99.2 + - - +
26A LEU* 1.3 64.1 + - + +
28A GLU* 3.7 8.2 - - + +
29A LYS* 2.8 45.5 + - + +
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Residues in contact with LEU 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 GLN* 2.8 37.6 + - + +
23A ILE* 4.0 0.4 - - + -
24A ARG 3.2 0.2 - - - -
25A GLU* 1.3 85.6 - - + +
27A VAL* 1.3 58.6 + - - +
29A LYS* 4.4 3.4 - - + -
30A ASN* 2.9 29.6 + - - +
23B ILE* 5.1 4.3 - - + +
26B LEU* 3.2 58.0 - - + +
27B VAL* 3.9 18.4 - - + +
30B ASN* 3.9 17.0 - - + +
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Residues in contact with VAL 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 ILE* 2.9 31.9 + - + +
24A ARG* 4.0 6.1 - - + +
26A LEU* 1.3 77.8 - - - +
28A GLU* 1.3 59.0 + - - +
30A ASN* 4.0 4.8 - - - +
31A SER* 2.9 29.8 + - - +
26B LEU* 3.4 24.7 - - + -
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Residues in contact with GLU 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 ARG* 2.9 45.4 + - - +
25A GLU* 4.1 12.8 - - + +
27A VAL* 1.3 79.4 - - - +
29A LYS* 1.3 61.4 + - + +
31A SER* 3.9 7.0 - - - -
32A GLN* 3.0 38.1 + - - +
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Residues in contact with LYS 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 GLU* 2.8 36.2 + - + +
26A LEU* 4.1 7.2 - - + +
28A GLU* 1.3 76.1 - - + +
30A ASN* 1.3 61.6 + - - +
32A GLN* 4.0 21.1 + - - +
33A LEU* 2.8 44.4 + - + +
30B ASN* 3.9 12.8 - - - +
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Residues in contact with ASN 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 LEU 2.9 21.4 + - - +
27A VAL* 4.0 6.1 - - + +
29A LYS* 1.3 77.2 - - - +
31A SER* 1.3 60.8 + - - +
33A LEU* 3.5 1.4 - - - +
34A GLU* 2.7 38.1 + - - +
26B LEU* 4.4 4.9 + - + +
29B LYS* 3.4 36.4 + - - +
30B ASN* 3.4 26.4 - - + +
33B LEU* 4.6 6.6 - - - +
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Residues in contact with SER 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 VAL* 2.9 22.7 + - - +
28A GLU* 4.0 9.6 - - - -
30A ASN* 1.3 79.8 - - - +
32A GLN* 1.3 57.4 + - - +
34A GLU* 3.5 10.7 + - - +
35A ARG* 3.0 28.6 + - - +
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Residues in contact with GLN 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 GLU* 3.0 28.3 + - - +
29A LYS* 4.0 23.1 + - - +
31A SER* 1.3 76.9 - - - +
33A LEU* 1.3 62.0 + - + +
35A ARG* 4.1 4.6 - - + +
36A GLU* 2.9 39.7 + - + +
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Residues in contact with LEU 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 LYS* 2.8 37.5 + - + +
30A ASN 3.8 3.4 - - - +
32A GLN* 1.3 79.4 - - + +
34A GLU* 1.3 60.8 + - - +
36A GLU* 4.1 13.0 - - - +
37A ASN* 2.9 18.0 + - - +
30B ASN* 3.5 18.6 - - - +
33B LEU* 2.8 43.1 - - + +
34B GLU* 3.0 34.5 - - + +
37B ASN* 4.0 14.8 - - + +
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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 ASN* 2.7 26.4 + - - +
31A SER* 3.2 13.0 + - - +
33A LEU* 1.3 79.9 - - - +
35A ARG* 1.3 55.8 + - - +
37A ASN* 4.1 1.9 - - - +
38A THR* 2.6 44.1 + - - +
33B LEU* 4.0 20.0 - - + -
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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 SER 3.0 15.7 + - - +
32A GLN* 4.1 5.8 - - + +
34A GLU* 1.3 78.0 - - - +
36A GLU* 1.3 63.1 + - - +
38A THR* 3.8 5.5 - - + -
39A LEU* 2.8 50.0 + - + +
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Residues in contact with GLU 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 GLN* 2.9 29.4 + - + +
33A LEU* 4.1 14.3 - - - +
35A ARG* 1.3 83.3 - - - +
37A ASN* 1.3 57.6 + - - +
39A LEU* 3.4 9.5 + - + +
40A LEU* 3.0 36.8 + - + +
37B ASN* 3.8 17.6 + - - +
41B LYS* 4.7 12.6 + - - -
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Residues in contact with ASN 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 LEU 2.9 20.9 + - - +
34A GLU* 4.1 2.3 + - - +
36A GLU* 1.3 77.3 - - - +
38A THR* 1.3 63.2 + - - +
40A LEU* 3.7 1.9 - - - +
41A LYS* 2.8 50.2 + - - +
33B LEU* 3.0 24.7 - - + +
36B GLU* 3.2 34.8 + - - +
37B ASN* 3.2 25.9 - - + +
40B LEU* 3.6 6.3 - - - +
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Residues in contact with THR 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* 2.6 32.9 + - - +
35A ARG* 4.0 6.7 - - + -
37A ASN* 1.3 79.0 + - - +
39A LEU* 1.3 51.2 + - - +
41A LYS* 3.7 20.2 + - - +
42A THR* 2.4 45.9 + - + +
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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 ARG* 2.8 39.0 + - - +
36A GLU* 3.6 11.0 - - + +
38A THR* 1.3 79.5 - - - +
40A LEU* 1.3 62.6 + - + +
42A THR* 3.1 4.8 + - - +
43A LEU* 2.9 55.6 + - + +
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Residues in contact with LEU 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 GLU* 3.0 21.0 + - + +
37A ASN 4.1 3.1 - - - +
39A LEU* 1.3 81.1 - - + +
41A LYS* 1.3 60.1 + - - +
43A LEU* 3.8 20.4 - - + +
44A ALA* 3.0 31.4 + - - +
37B ASN* 3.7 17.3 - - - +
40B LEU* 4.2 17.3 - - + +
41B LYS* 3.6 45.3 - - + +
44B ALA* 4.6 9.5 - - + +
45B SER* 5.4 6.1 - - - +
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Residues in contact with LYS 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 ASN* 2.8 36.7 + - - +
38A THR* 3.7 19.8 + - - +
39A LEU 3.2 0.2 - - - -
40A LEU* 1.3 81.1 - - - +
42A THR* 1.3 60.5 + - + +
44A ALA* 3.6 1.5 - - - -
45A SER* 3.0 34.3 + - - +
36B GLU* 4.2 9.9 + - - +
40B LEU* 3.1 24.9 - - + +
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Residues in contact with THR 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 THR* 2.4 39.4 + - + +
39A LEU* 3.1 14.7 + - - +
41A LYS* 1.3 76.7 - - + +
43A LEU* 1.3 59.5 + - - +
45A SER* 3.4 7.5 - - - +
46A PRO* 2.6 34.7 - - - +
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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* 2.9 47.3 + - + +
40A LEU* 4.0 22.9 - - + +
41A LYS 3.3 0.2 - - - -
42A THR* 1.3 85.9 - - - +
44A ALA* 1.3 59.3 + - - +
45A SER 3.2 1.1 + - - -
46A PRO* 3.5 9.7 - - - +
48A GLN* 3.2 47.6 - - + +
44B ALA* 5.6 1.6 - - + -
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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