Contacts of the helix formed by residues 23 - 53 (chain A) in PDB entry 2YEV
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 ASP 23 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A THR* 3.1 12.6 + - - +
22A VAL* 1.3 78.1 - - - +
24A HIS* 1.3 66.0 + - - +
25A LYS* 2.8 50.8 + - - +
26A LYS* 3.2 21.7 + - + +
27A ILE* 3.1 23.3 + - - +
103A ASP* 4.3 4.3 - - - -
514A ALA* 4.1 16.0 - - - +
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Residues in contact with HIS 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 VAL 3.3 1.8 + - - -
23A ASP* 1.3 78.1 + - - +
25A LYS* 1.3 76.3 + - + +
27A ILE* 4.3 0.2 - - - -
28A GLY* 2.9 24.4 + - - -
92A ASN* 2.7 35.8 + - - +
93A PHE 3.3 19.4 + - - -
96A PRO* 3.4 19.8 - - + +
97A LEU* 4.1 4.3 - - + -
102A ARG 4.1 1.3 - - - -
103A ASP* 2.9 41.1 + - - +
104A VAL* 3.8 17.7 - - + -
110A ASN* 4.1 15.9 - - - +
516A ASN* 3.0 26.7 + - - -
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Residues in contact with LYS 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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23A ASP* 2.8 33.4 + - - +
24A HIS* 1.3 99.3 + - + +
26A LYS* 1.3 58.9 + - + +
28A GLY 3.3 0.2 + - - -
29A LEU* 3.0 28.0 + - + +
93A PHE* 3.2 36.6 - - + +
97A LEU* 4.7 0.9 - - + -
512A PRO* 3.7 35.4 - - + -
513A LYS 3.5 13.9 - - - -
514A ALA* 2.9 18.3 + - - +
516A ASN* 2.6 28.8 + - - +
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Residues in contact with LYS 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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17A ASP* 2.9 34.8 + - - +
18A LEU* 4.7 12.3 - - + -
21A THR* 3.6 29.6 + - + +
23A ASP* 3.2 23.1 + - + +
25A LYS* 1.3 76.6 - - + +
27A ILE* 1.3 64.2 + - - +
29A LEU* 3.2 13.6 + - + +
30A MET* 2.9 32.6 + - + +
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Residues in contact with ILE 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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21A THR* 4.0 10.8 - - + +
22A VAL 4.6 5.6 - - - -
23A ASP 3.1 19.6 + - - +
24A HIS 3.9 4.0 - - - +
26A LYS* 1.3 75.6 - - - +
28A GLY* 1.3 57.7 + - - +
30A MET* 3.2 25.2 + - + +
31A TYR* 3.0 53.1 + - + -
92A ASN* 4.5 1.6 - - - +
110A ASN* 3.8 30.5 - - + +
111A ALA* 3.7 31.0 - - + +
114A TYR* 4.0 8.3 - - + -
115A TRP* 5.2 2.9 - - - +
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Residues in contact with GLY 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 HIS 2.9 19.6 + - - -
25A LYS 3.7 2.0 - - - -
26A LYS 3.2 0.2 - - - -
27A ILE* 1.3 77.6 - - - +
29A LEU* 1.3 52.3 + - - +
31A TYR 3.5 0.3 + - - -
32A THR* 2.7 37.9 + - - -
88A THR 4.2 2.5 - - - -
89A GLY* 3.6 18.8 - - - +
92A ASN* 3.8 10.1 - - - -
93A PHE* 4.2 7.0 - - - -
409A MET* 6.1 0.2 - - - -
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Residues in contact with LEU 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 LYS* 3.0 22.4 + - + +
26A LYS* 3.2 13.0 + - + +
28A GLY* 1.3 76.7 - - - +
30A MET* 1.3 58.8 + - + +
32A THR* 3.7 6.5 - - + -
33A ALA* 2.9 32.1 + - - +
93A PHE* 4.0 13.5 - - + -
409A MET* 3.9 43.3 - - + +
410A THR* 5.5 4.5 - - + -
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Residues in contact with MET 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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18A LEU* 4.1 37.2 - - + +
21A THR* 3.8 15.9 - - + -
26A LYS 2.9 22.9 + - - +
27A ILE* 3.5 35.7 - - + +
29A LEU* 1.3 75.1 - - + +
31A TYR* 1.3 60.6 + - - +
33A ALA* 4.0 3.6 - - - +
34A THR* 2.7 33.3 + - - -
114A TYR* 3.6 35.2 - - + +
115A TRP* 4.5 8.1 - - + -
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Residues in contact with TYR 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 ILE* 3.0 30.6 + - + +
28A GLY 3.7 1.8 - - - +
30A MET* 1.3 75.4 - - - +
32A THR* 1.3 55.3 + - - +
34A THR* 3.2 1.8 + - - -
35A ALA* 2.8 38.1 + - - +
84A GLN* 3.8 9.0 - - + +
88A THR* 3.1 54.0 - - + +
89A GLY* 3.7 5.2 - - - -
92A ASN* 3.6 16.6 - - - -
113A SER* 2.5 39.6 + - - -
114A TYR* 3.5 27.7 - + + -
117A PHE* 3.7 35.0 - + + -
166A SER* 3.4 6.0 + - - -
170A GLY* 5.7 0.2 - - - -
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Residues in contact with THR 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 GLY 2.7 21.5 + - - -
29A LEU* 3.7 9.2 - - + -
31A TYR* 1.3 76.2 - - - +
33A ALA* 1.3 63.1 + - - +
35A ALA* 3.4 3.9 + - - +
36A PHE* 3.0 43.6 + - + -
85A ALA* 5.2 1.3 - - - +
89A GLY* 3.1 23.6 - - - -
90A PHE* 3.6 26.6 + - + -
402A LEU* 4.3 9.2 - - + -
409A MET* 4.7 10.6 - - + -
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Residues in contact with ALA 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 LEU 2.9 18.3 + - - +
30A MET* 4.0 4.3 - - - +
32A THR* 1.3 77.3 - - - +
34A THR* 1.3 58.5 + - - +
36A PHE* 3.9 4.0 - - - +
37A PHE* 2.9 28.9 + - - +
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Residues in contact with THR 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 MET 2.7 18.3 + - - -
31A TYR 3.8 2.2 - - - -
33A ALA* 1.3 74.9 - - - +
35A ALA* 1.3 59.0 + - - +
37A PHE* 3.2 12.7 + - + +
38A ALA* 2.8 28.5 + - - +
80A PHE 4.7 0.2 - - - -
114A TYR* 2.7 28.1 + - - +
117A PHE* 3.7 12.8 - - + -
118A LEU* 4.5 11.2 - - + -
121A ILE* 3.6 29.4 - - + -
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Residues in contact with ALA 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 TYR 2.8 22.5 + - - +
32A THR 3.7 3.6 - - - +
34A THR* 1.3 72.9 - - - +
36A PHE* 1.3 56.6 + - - +
38A ALA* 3.0 5.9 + - - +
39A PHE 3.0 22.3 + - - -
80A PHE 3.3 20.0 - - - +
81A PHE* 3.3 14.5 - - - +
84A GLN* 3.8 19.3 - - + -
85A ALA* 3.8 19.5 - - + +
117A PHE* 4.6 1.0 - - + -
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Residues in contact with PHE 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 THR* 3.0 38.7 + - + +
33A ALA* 4.3 3.4 - - - +
35A ALA* 1.3 73.8 - - - +
37A PHE* 1.3 66.5 + - - +
39A PHE* 3.3 6.6 + + - +
40A ALA* 3.1 17.0 + - - +
81A PHE* 3.8 17.0 - + - -
85A ALA* 3.8 21.5 - - + -
90A PHE* 3.8 21.5 - + - -
398A ALA* 3.8 24.5 - - + -
399A PHE* 3.7 28.0 - + - -
402A LEU* 4.0 13.5 - - + -
480A TRP* 3.6 40.5 - + + -
484A MET* 6.3 0.4 - - - -
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Residues in contact with PHE 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 ALA 2.9 19.8 + - - +
34A THR* 3.4 11.7 - - + +
36A PHE* 1.3 76.6 - - - +
38A ALA* 1.3 66.4 + - - +
40A ALA* 3.0 11.7 + - + +
41A LEU* 2.9 47.0 + - + +
121A ILE* 6.5 1.1 - - + -
125A LEU* 6.0 2.0 - - + -
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Residues in contact with ALA 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 THR 2.8 12.3 + - - +
35A ALA 3.0 10.1 + - - +
37A PHE* 1.3 81.2 - - - +
39A PHE* 1.3 57.3 + - - +
41A LEU* 3.3 4.7 + - - +
42A ALA* 2.9 32.4 + - - +
76A THR* 3.6 14.4 - - + +
80A PHE* 3.5 38.1 - - + +
81A PHE* 4.2 1.6 - - + -
121A ILE* 5.4 3.8 - - + -
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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 ALA 3.0 5.5 + - - -
36A PHE* 3.5 6.7 - + - +
38A ALA* 1.3 77.6 - - - +
40A ALA* 1.3 60.0 + - - +
43A GLY* 2.8 29.5 + - - -
77A MET* 3.5 30.7 - - + +
81A PHE* 3.3 48.4 - + + +
391A MET* 4.5 20.0 - - + -
395A GLY* 6.3 1.1 - - - -
399A PHE* 3.8 22.7 - + - -
426A PHE* 3.9 28.9 - + - -
477A GLY* 6.2 0.7 - - - -
480A TRP* 3.8 25.8 - + - -
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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 PHE 3.1 12.0 + - - +
37A PHE* 3.0 16.0 + - + +
39A PHE* 1.3 81.1 - - - +
41A LEU* 1.3 63.9 + - - +
43A GLY* 3.2 1.7 + - - -
44A VAL* 3.0 29.2 + - + +
480A TRP* 4.3 14.8 - - + -
481A ILE* 5.4 6.1 - - + -
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Residues in contact with LEU 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 PHE* 2.9 40.5 + - + +
38A ALA* 3.6 5.8 - - - +
40A ALA* 1.3 77.1 - - - +
42A ALA* 1.3 61.8 + - - +
44A VAL* 3.3 12.2 + - + +
45A PHE* 3.2 49.1 + - + -
76A THR* 4.9 10.1 - - + -
125A LEU* 3.8 30.5 - - + -
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Residues in contact with ALA 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 ALA 2.9 20.1 + - - +
41A LEU* 1.3 72.3 - - - +
43A GLY* 1.3 58.9 + - - +
44A VAL 3.4 0.2 - - - -
45A PHE* 3.3 12.4 + - - +
46A SER 3.1 12.5 + - - -
73A HIS* 2.9 36.3 + - - +
76A THR* 3.7 15.7 - - + +
77A MET* 3.6 31.9 - - + -
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Residues in contact with GLY 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* 2.8 20.7 + - - -
40A ALA* 3.6 2.2 - - - -
41A LEU 3.2 0.4 - - - -
42A ALA* 1.3 75.8 - - - +
44A VAL* 1.3 63.4 + - - +
46A SER* 2.6 25.5 + - - -
47A LEU* 3.1 12.5 + - - +
77A MET* 3.6 8.0 - - - +
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Residues in contact with VAL 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 ALA 3.0 15.8 + - - +
41A LEU* 3.5 13.2 - - + +
43A GLY* 1.3 76.7 - - - +
45A PHE* 1.3 66.3 + - + +
47A LEU* 2.9 27.9 + - + +
48A LEU* 3.1 24.2 + - + +
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Residues in contact with PHE 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 LEU* 3.2 40.4 + - + -
42A ALA* 3.3 21.5 - - + +
43A GLY 3.2 0.2 - - - -
44A VAL* 1.3 80.7 - - + +
46A SER* 1.3 57.9 + - - +
48A LEU* 3.1 16.6 + - + +
49A ILE* 3.0 30.5 + - - +
69A ILE* 3.6 32.6 - - + +
72A LEU* 3.7 33.0 - - + -
73A HIS* 4.0 23.8 - - + -
76A THR* 4.7 4.3 - - - -
125A LEU* 5.2 5.2 - - + -
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Residues in contact with SER 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 ALA 3.1 6.4 + - - -
43A GLY* 2.6 21.8 + - - -
45A PHE* 1.3 77.3 - - - +
47A LEU* 1.3 62.6 + - - +
49A ILE* 3.5 10.5 - - - +
50A ARG* 2.9 35.1 + - - +
73A HIS* 3.5 30.0 + - - -
77A MET* 5.8 0.2 - - - -
470A ALA* 5.5 2.9 - - - +
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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 GLY 3.1 12.5 + - - +
44A VAL* 2.9 20.9 + - + +
46A SER* 1.3 81.8 + - - +
48A LEU* 1.3 62.4 + - + +
50A ARG* 4.3 1.7 - - - +
51A THR* 2.7 35.7 + - - +
470A ALA* 3.4 34.3 - - + +
471A TYR* 3.7 28.0 - - + -
474A GLY* 4.5 16.4 - - - -
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Residues in contact with LEU 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 VAL* 3.1 22.7 + - + +
45A PHE* 3.1 25.5 + - + +
47A LEU* 1.3 76.1 - - + +
49A ILE* 1.3 64.4 + - - +
51A THR* 3.4 4.3 + - - +
52A GLN* 3.1 20.8 + - - +
60A PHE* 3.6 31.0 - - + -
61A LEU* 4.1 16.9 - - + +
69A ILE* 4.5 14.4 - - + -
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Residues in contact with ILE 49 (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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45A PHE 3.0 17.2 + - - +
46A SER* 3.5 10.3 - - - +
48A LEU* 1.3 77.1 - - - +
50A ARG* 1.3 68.6 + - + +
52A GLN* 3.2 6.8 + - - +
53A LEU* 3.1 30.9 + - + +
61A LEU* 4.7 1.3 - - + -
66A TYR* 3.4 35.9 - - + +
69A ILE* 3.9 12.1 - - + -
70A LEU* 3.9 36.8 - - + +
73A HIS* 4.0 23.1 - - + -
380A TYR* 5.4 1.1 - - - +
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Residues in contact with ARG 50 (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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46A SER* 2.9 21.4 + - - +
47A LEU* 4.3 2.9 - - + +
49A ILE* 1.3 80.4 - - + +
51A THR* 1.3 64.6 + - - +
53A LEU* 3.3 35.5 + - - +
54A ALA 3.1 9.7 + - - -
380A TYR* 4.5 6.3 + - - -
433A THR* 4.3 5.2 - - + -
437A GLN* 3.3 24.0 - - - +
440A LEU* 6.0 0.4 - - - +
463A ASN* 3.0 44.3 + - - +
466A SER* 3.2 34.9 + - - -
467A THR* 2.5 41.3 + - + +
470A ALA* 3.8 22.7 - - + -
471A TYR* 5.7 0.7 - - + -
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Residues in contact with THR 51 (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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47A LEU 2.7 23.4 + - - -
48A LEU* 3.6 5.4 - - - +
50A ARG* 1.3 74.3 - - - +
52A GLN* 1.3 67.1 + - - +
54A ALA* 3.2 15.3 + - + +
58A ASN* 3.1 14.2 + - - +
60A PHE* 3.8 32.6 - - + -
467A THR* 4.4 2.9 - - - +
471A TYR* 2.6 29.6 + - - +
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Residues in contact with GLN 52 (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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48A LEU 3.1 10.1 + - - +
49A ILE 3.2 9.2 + - - +
51A THR* 1.3 77.9 - - - +
53A LEU* 1.3 59.6 + - - +
54A ALA 3.5 0.2 + - - -
55A VAL 3.7 2.1 - - - +
58A ASN* 3.0 57.2 + - - +
60A PHE* 3.0 17.4 + - + -
61A LEU* 2.8 54.5 + - + +
66A TYR* 3.9 11.0 - - + -
450A TYR* 2.8 31.0 + - - +
451A THR* 4.0 7.3 - - - +
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Residues in contact with LEU 53 (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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49A ILE* 3.1 22.1 + - + +
50A ARG* 3.3 33.0 + - - +
51A THR 3.1 0.4 - - - -
52A GLN* 1.3 74.9 - - + +
54A ALA* 1.3 65.2 + - - +
55A VAL 3.2 4.0 - - - -
66A TYR* 3.6 15.5 - - + +
380A TYR* 3.3 27.8 - - + +
445A MET* 4.7 4.0 - - + -
449A TYR 3.5 22.2 - - - +
450A TYR 3.6 17.7 - - - +
451A THR* 4.7 0.4 - - - -
452A TYR* 3.0 34.8 + - + -
463A ASN* 3.3 14.7 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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