Contacts of the helix formed by residues 25 - 58 (chain A) in PDB entry 4MBS
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 VAL 25 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.4 19.0 + - + +
24A ASN* 1.3 74.0 - - - +
26A LYS* 1.4 54.1 + - - +
27A GLN 3.3 2.7 - - - -
28A ILE* 3.3 22.6 + - + +
29A ALA* 2.8 36.5 + - + +
276A ASP* 6.0 1.8 - - - +
277A GLN* 4.7 23.6 - - + -
280A GLN* 5.9 7.4 - - + -
186B GLN* 5.1 11.2 - - + +
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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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24A ASN* 3.4 19.4 - - - +
25A VAL* 1.4 76.7 - - - +
27A GLN* 1.3 59.4 - - - +
29A ALA* 3.8 6.5 - - - +
30A ALA* 3.0 30.3 + - - +
90A ALA 4.7 2.1 - - - +
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Residues in contact with GLN 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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24A ASN* 3.8 19.8 + - - +
25A VAL 3.3 0.2 - - - -
26A LYS* 1.3 77.4 - - - +
28A ILE* 1.3 65.1 + - + +
30A ALA* 3.9 9.2 - - - +
31A ARG* 3.7 33.5 + - - +
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Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASN 4.3 16.8 - - - +
25A VAL* 3.3 19.6 + - + +
27A GLN* 1.3 78.9 - - + +
29A ALA* 1.4 60.5 + - - +
31A ARG* 3.0 10.8 + - - +
32A LEU* 3.0 33.6 + - + +
1107A OLC 5.9 2.0 - - - +
166B PHE* 4.5 18.8 - - + -
183B PRO* 3.7 35.7 - - + -
184B TYR 5.7 1.3 - - - +
186B GLN* 4.6 20.4 - - + +
190B TRP* 4.8 13.0 - - + -
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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
----------------------------------------------------------
25A VAL* 2.8 23.4 + - + +
26A LYS* 3.8 8.7 - - - +
28A ILE* 1.4 73.1 - - + +
30A ALA* 1.4 58.2 + - - +
32A LEU* 4.5 3.4 - - - +
33A LEU* 2.9 57.0 + - + +
34A PRO* 3.4 1.7 - - - +
90A ALA* 4.1 5.5 - - + +
1107A OLC 6.1 2.0 - - - +
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Residues in contact with ALA 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 LYS 3.0 17.1 + - - +
27A GLN* 3.9 11.2 - - - +
28A ILE 3.3 0.2 - - - -
29A ALA* 1.4 73.7 - - - +
31A ARG* 1.3 60.4 + - + +
34A PRO* 3.3 19.7 - - - +
90A ALA 3.3 27.7 + - - +
91A ALA* 3.9 16.2 - - - +
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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 GLN* 3.7 29.8 + - - +
28A ILE* 3.0 7.6 + - - +
30A ALA* 1.3 80.7 - - + +
32A LEU* 1.3 57.5 + - - +
34A PRO* 4.1 1.3 - - - +
35A PRO* 3.4 18.4 - - - +
165B ILE* 3.3 35.0 + - + +
166B PHE* 4.8 9.9 - - + -
168B ARG* 5.3 14.1 - - - +
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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 ILE* 3.0 24.5 + - + +
29A ALA* 4.6 2.2 - - - +
31A ARG* 1.3 77.1 - - - +
33A LEU* 1.4 69.3 + - + +
34A PRO 3.6 0.2 - - - -
35A PRO* 3.4 9.1 - - - +
36A LEU* 3.7 16.1 + - + +
1107A OLC 3.7 42.4 - - - +
162B PRO* 4.3 21.8 - - + -
165B ILE* 3.9 14.5 - - + +
166B PHE* 3.7 28.9 - - + -
190B TRP* 4.2 15.7 - - + -
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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 ALA* 2.9 44.5 + - + +
32A LEU* 1.4 73.3 - - + +
34A PRO* 1.4 67.0 - - + +
36A LEU* 3.2 7.7 + - + +
37A TYR* 2.9 66.5 + - + +
90A ALA* 4.2 17.5 - - + -
284A THR* 4.4 2.7 - - - +
1101A MRV 5.0 5.4 - - - +
1107A OLC 3.4 32.5 - - - +
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Residues in contact with PRO 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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29A ALA 3.4 5.8 - - - +
30A ALA 3.3 27.6 - - - +
32A LEU 3.8 0.7 - - - -
33A LEU* 1.4 87.3 - - + +
35A PRO* 1.4 69.4 - - + +
37A TYR* 3.5 1.4 + - - +
38A SER* 3.0 28.9 + - - +
87A ALA* 3.5 34.6 - - + +
90A ALA* 4.4 2.0 - - + -
91A ALA* 3.7 13.5 - - + +
1105A OLC 5.4 5.2 - - - +
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Residues in contact with PRO 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 3.4 18.6 - - - +
32A LEU 3.4 13.5 - - - +
34A PRO* 1.4 92.1 - - + +
36A LEU* 1.3 60.5 + - - +
38A SER* 3.4 7.7 + - - -
39A LEU* 3.0 28.4 + - + +
161B LEU* 4.2 14.1 - - + -
165B ILE* 3.8 23.1 - - + -
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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 LEU* 3.7 14.3 + - + +
33A LEU* 3.2 10.7 + - + +
35A PRO* 1.3 79.2 - - - +
37A TYR* 1.3 66.9 + - + +
39A LEU* 3.2 6.1 + - - +
40A VAL* 3.1 36.7 + - + +
284A THR* 3.7 30.1 - - + -
287A MET* 5.4 1.6 - - + -
288A THR* 5.4 1.1 - - - +
1107A OLC 3.9 38.4 - - + +
158B PHE* 3.7 28.3 - - + -
161B LEU* 3.8 16.9 - - + +
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Residues in contact with TYR 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 58.0 + - + +
36A LEU* 1.3 85.0 - - + +
38A SER* 1.3 60.2 + - - +
40A VAL* 3.5 4.1 + - - -
41A PHE* 2.9 25.3 + - - +
83A VAL* 3.3 31.7 - - + +
84A PRO* 6.2 0.9 - - - -
86A TRP* 3.8 12.6 - - + -
87A ALA* 3.7 33.9 - - + -
284A THR* 3.6 8.6 + - + -
287A MET* 4.1 19.1 - - + -
1101A MRV 3.1 47.7 + + + +
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Residues in contact with SER 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 PRO* 3.0 20.6 + - - +
35A PRO* 3.5 8.0 - - - +
37A TYR* 1.3 75.3 - - - +
39A LEU* 1.3 61.9 + - - +
41A PHE* 3.5 5.5 + - - +
42A ILE* 3.1 34.8 + - - +
84A PRO* 6.5 0.7 - - - -
87A ALA* 5.1 1.8 - - - +
1105A OLC 3.6 38.7 - - - +
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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 PRO* 3.0 18.4 + - + +
36A LEU 3.2 9.2 + - - +
38A SER* 1.3 73.0 - - - +
40A VAL* 1.4 63.5 - - - +
42A ILE* 3.2 8.7 + - - +
43A PHE* 3.0 26.9 + - + +
154B VAL* 4.8 5.6 - - + +
157B VAL* 3.7 27.6 - - + -
158B PHE* 3.4 40.6 - - + -
161B LEU* 3.7 31.9 - - + -
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Residues in contact with VAL 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* 3.1 24.8 + - + +
37A TYR 3.9 4.7 - - - +
39A LEU* 1.4 72.4 - - - +
41A PHE* 1.3 58.0 + - - +
43A PHE* 4.8 0.9 - - - -
44A GLY* 2.9 29.3 + - - -
80A LEU* 3.7 1.3 - - + +
83A VAL* 4.9 2.7 - - + -
287A MET* 4.0 24.9 - - + -
288A THR* 4.0 32.3 - - + +
290A CYS* 3.9 25.1 - - - -
291A CYS* 4.0 10.6 - - - +
1107A OLC 5.0 0.2 - - + -
158B PHE* 4.1 19.3 - - + -
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Residues in contact with PHE 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 TYR 2.9 19.4 + - - +
38A SER* 3.7 4.9 - - - +
39A LEU 3.3 0.2 - - - -
40A VAL* 1.3 77.2 - - - +
42A ILE* 1.4 59.9 + - + +
45A PHE* 2.9 61.9 + + + +
80A LEU* 3.3 41.7 - - + +
81A LEU* 4.4 8.3 - - + -
83A VAL* 4.3 7.6 - - + -
84A PRO* 3.6 26.5 - - + -
1104A OLC 4.1 18.8 - - + -
1105A OLC 3.9 34.1 - - + -
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Residues in contact with ILE 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 SER* 3.1 24.7 + - - +
39A LEU* 3.8 5.4 - - - +
41A PHE* 1.4 75.0 - - + +
43A PHE* 1.3 64.4 + - - +
45A PHE* 4.0 2.5 - - - +
46A VAL* 3.1 39.7 + - + +
1105A OLC 4.0 39.3 - - + -
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Residues in contact with PHE 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* 3.0 18.0 + - + +
40A VAL* 4.2 3.1 - - - +
42A ILE* 1.3 77.4 - - - +
44A GLY* 1.3 56.9 + - - +
46A VAL* 4.1 4.8 - - + +
47A GLY* 3.0 24.9 + - - -
291A CYS* 3.7 30.6 - - + +
295A ILE* 3.4 39.5 - - + -
1107A OLC 4.3 11.4 - - + -
150B VAL* 5.2 7.4 - - + -
151B ILE* 4.6 13.0 - - + -
154B VAL* 3.9 40.2 - - + -
158B PHE* 5.3 2.7 - + + -
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Residues in contact with GLY 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 VAL 2.9 16.4 + - - -
43A PHE* 1.3 75.4 - - - +
45A PHE* 1.4 58.2 + - - +
47A GLY* 4.9 0.9 - - - -
48A ASN* 2.9 37.0 + - - +
80A LEU* 3.5 14.1 - - - +
291A CYS* 3.4 26.8 - - - +
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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 PHE* 2.9 51.4 + + + +
42A ILE* 4.0 3.1 - - - +
44A GLY* 1.4 69.0 - - - +
46A VAL* 1.3 71.4 + - + +
48A ASN 4.1 0.2 - - - -
49A MET* 3.1 56.4 + - + +
77A LEU* 4.1 20.7 - - + +
80A LEU* 3.9 8.1 - - + +
81A LEU* 5.4 11.2 - - + -
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Residues in contact with VAL 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 ILE* 3.1 31.0 + - + +
43A PHE* 4.1 5.6 - - + +
45A PHE* 1.3 82.9 - - + +
47A GLY* 1.3 62.9 + - - +
49A MET* 3.9 3.4 - - - +
50A LEU* 3.1 42.1 + - + +
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Residues in contact with GLY 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 PHE 3.0 19.2 + - - -
44A GLY* 3.8 0.9 - - - -
45A PHE 3.4 0.2 - - - -
46A VAL* 1.3 78.8 - - - +
48A ASN* 1.4 56.9 + - - +
50A LEU* 3.5 9.9 + - - +
51A VAL* 3.2 28.9 + - - +
291A CYS 6.0 0.2 - - - -
294A PRO* 3.5 23.7 - - - +
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Residues in contact with ASN 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 GLY* 2.9 30.4 + - - +
47A GLY* 1.4 70.1 - - - +
49A MET* 1.3 64.9 + - - +
51A VAL* 3.5 6.0 + - - +
52A ILE* 3.1 30.4 + - - +
73A ALA* 3.6 20.6 - - + +
76A ASP* 3.4 25.4 - - - +
77A LEU* 3.7 18.2 - - + -
80A LEU* 3.6 5.2 - - - +
290A CYS 2.9 26.3 + - - -
293A ASN* 5.6 0.5 - - - +
294A PRO* 4.0 19.0 - - - +
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Residues in contact with MET 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* 3.1 53.2 + - + +
46A VAL* 3.9 4.0 - - - +
48A ASN* 1.3 73.9 - - - +
50A LEU* 1.4 64.2 + - + +
52A ILE* 3.4 13.3 + - + +
53A LEU* 3.0 53.6 + - + +
77A LEU* 4.0 23.8 - - + -
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Residues in contact with LEU 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 VAL* 3.1 36.8 + - + +
47A GLY* 3.6 9.0 - - - +
49A MET* 1.4 74.2 - - - +
51A VAL* 1.4 64.1 + - + +
53A LEU* 3.3 9.6 + - + +
54A ILE* 3.0 44.1 + - + +
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Residues in contact with VAL 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 GLY 3.2 15.5 + - - +
48A ASN* 3.7 10.1 - - - +
49A MET 3.4 0.2 - - - -
50A LEU* 1.4 73.9 - - + +
52A ILE* 1.3 56.4 + - - +
54A ILE* 3.2 8.7 + - - +
55A LEU* 2.9 50.3 + - + +
69A LEU 4.7 1.1 - - - +
73A ALA* 4.2 13.2 - - + -
294A PRO* 4.0 16.2 - - + -
297A TYR* 3.6 42.8 - - + -
304A PHE* 4.5 9.6 - - + -
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Residues in contact with ILE 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 ASN 3.1 22.5 + - - +
49A MET* 3.7 15.3 - - + +
50A LEU 3.3 0.2 - - - -
51A VAL* 1.3 76.1 - - - +
53A LEU* 1.4 67.3 + - + +
55A LEU* 3.4 2.6 + - - +
56A ILE* 2.9 52.0 + - + +
70A LEU* 3.9 18.2 - - + -
73A ALA* 3.8 24.2 - - + -
74A ILE* 4.4 13.2 - - + -
77A LEU* 3.9 27.4 - - + -
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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 MET* 3.0 45.5 + - + +
50A LEU* 4.1 8.1 - - + +
52A ILE* 1.4 81.4 - - + +
54A ILE* 1.4 58.7 + - + +
56A ILE* 4.8 2.9 - - + -
57A ASN* 2.9 50.9 + - - +
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Residues in contact with ILE 54 (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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50A LEU* 3.0 41.7 + - + +
51A VAL* 3.7 5.6 - - - +
53A LEU* 1.4 76.2 - - + +
55A LEU* 1.3 58.8 + - - +
58A TYR* 3.0 35.1 + - + +
59A LYS* 2.8 25.8 + - + +
304A PHE* 4.0 30.3 - - + -
307A TYR* 4.2 25.1 - - + -
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Residues in contact with LEU 55 (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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51A VAL* 2.9 41.5 + - + +
52A ILE* 3.8 5.4 - - - +
54A ILE* 1.3 76.9 - - - +
56A ILE* 1.3 59.7 + - + +
59A LYS* 3.5 12.5 - - + +
60A ARG 2.8 23.2 + - - -
61A LEU* 3.2 22.3 + - + +
66A ASP* 4.2 23.3 - - + +
69A LEU* 3.8 15.7 - - + -
70A LEU* 3.6 36.6 - - + +
304A PHE* 4.0 22.4 - - + -
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Residues in contact with ILE 56 (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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52A ILE* 2.9 41.4 + - + +
53A LEU* 4.6 3.4 - - + +
55A LEU* 1.3 76.6 - - - +
57A ASN* 1.4 72.1 + - - +
60A ARG* 3.4 21.8 - - - -
61A LEU* 4.1 21.3 - - + -
70A LEU* 3.7 22.2 - - + -
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Residues in contact with ASN 57 (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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53A LEU* 2.9 46.5 + - - +
56A ILE* 1.4 90.7 - - - +
58A TYR* 1.3 60.0 + - - +
60A ARG* 2.8 32.5 + - - +
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU 3.9 0.6 + - - -
54A ILE* 3.0 39.0 + - + +
57A ASN* 1.3 75.4 - - - +
59A LYS* 1.4 87.5 + - + +
60A ARG* 3.3 6.3 + - - +
62A LYS* 5.0 2.9 + - - -
303A GLU* 3.6 35.8 + - + +
304A PHE* 5.2 2.7 - + - -
306A ASN* 5.7 0.7 - - - +
307A TYR* 3.5 61.5 + + + +
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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
------------------------------------------------------------
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