Contacts of the helix formed by residues 14 - 42 (chain A) in PDB entry 2MFR
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 SER 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A PRO* 1.3 71.9 - - - +
15A ASN* 1.3 57.2 + - - +
16A ILE 2.9 0.7 - - - -
17A ALA* 2.6 39.5 + - - +
18A LYS* 3.1 22.2 + - - +
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Residues in contact with ASN 15 (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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13A PRO* 2.8 27.1 + - + +
14A SER* 1.3 75.6 + - - +
16A ILE* 1.3 57.6 + - + +
18A LYS* 3.4 7.1 + - - +
19A ILE* 2.9 45.9 + - + +
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Residues in contact with ILE 16 (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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12A VAL* 4.3 29.6 - - + +
13A PRO* 2.9 15.4 + - + +
15A ASN* 1.3 79.0 - - + +
17A ALA* 1.3 52.2 + - - +
18A LYS 3.3 0.2 - - - -
19A ILE* 4.2 16.6 - - + -
20A ILE* 2.5 61.4 + - + +
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Residues in contact with ALA 17 (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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13A PRO 4.2 0.6 + - - -
14A SER* 2.6 26.5 + - - +
16A ILE* 1.3 81.3 - - - +
18A LYS* 1.3 62.3 + - + +
20A ILE* 4.0 5.8 - - - +
21A ILE* 2.8 30.8 + - - +
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Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 3.1 25.4 + - - +
15A ASN* 3.9 10.1 - - - +
16A ILE 3.3 0.2 - - - -
17A ALA* 1.3 81.1 - - + +
19A ILE* 1.3 62.7 + - + +
20A ILE 3.2 1.3 - - - -
21A ILE* 4.0 8.5 - - + -
22A GLY* 2.8 28.8 + - - -
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Residues in contact with ILE 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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15A ASN* 2.9 38.3 + - + +
16A ILE* 3.7 17.7 - - + +
18A LYS* 1.3 78.0 - - + +
20A ILE* 1.3 56.6 + - + +
23A PRO* 2.6 33.7 - - + +
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Residues in contact with ILE 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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16A ILE* 2.5 45.3 + - + +
17A ALA* 4.0 6.3 - - - +
18A LYS 3.2 0.4 - - - -
19A ILE* 1.3 81.0 - - + +
21A ILE* 1.3 66.3 + - + +
23A PRO* 3.4 11.0 - - - +
24A LEU* 4.4 8.3 + - - +
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Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA 2.8 25.6 - - - +
18A LYS* 4.0 11.4 - - + -
20A ILE* 1.3 79.6 - - + +
22A GLY* 1.3 62.3 - - - +
23A PRO* 3.2 2.7 - - - -
24A LEU* 2.7 36.7 + - + +
25A ILE* 2.9 28.1 + - + +
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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 LYS 2.8 16.9 + - - -
21A ILE* 1.3 80.2 - - - +
23A PRO* 1.3 68.6 - - - +
25A ILE* 2.9 27.1 + - - +
26A PHE* 3.2 18.0 + - - -
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Residues in contact with PRO 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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18A LYS 3.7 0.7 - - - +
19A ILE* 2.6 35.7 - - + +
20A ILE* 3.4 8.1 - - - +
21A ILE 3.2 3.8 - - - -
22A GLY* 1.3 93.5 - - - +
24A LEU* 1.3 58.8 + - - +
26A PHE* 3.4 15.7 - - + +
27A VAL* 3.4 17.6 - - - +
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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 ILE 4.4 7.8 + - - +
21A ILE* 2.7 26.7 + - + +
23A PRO* 1.3 72.2 - - + +
25A ILE* 1.3 57.7 + - - +
26A PHE 2.9 2.0 - - - -
27A VAL* 2.6 43.4 + - + +
28A PHE* 2.8 14.5 + - + +
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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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21A ILE* 2.9 26.1 + - + +
22A GLY* 2.9 22.7 + - - +
24A LEU* 1.3 75.3 - - - +
26A PHE* 1.3 66.5 + - + +
28A PHE* 3.4 10.0 + - + +
29A LEU* 3.1 43.7 + - + +
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Residues in contact with PHE 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* 3.2 12.7 + - - -
23A PRO* 3.4 14.8 - - + +
25A ILE* 1.3 87.2 - - + +
27A VAL* 1.3 63.9 + - + +
29A LEU* 3.3 16.2 + - + +
30A PHE* 3.2 29.3 + + + +
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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 PRO 3.4 16.6 - - - +
24A LEU* 2.6 29.6 + - + +
26A PHE* 1.3 75.4 - - + +
28A PHE* 1.3 55.5 + - - +
30A PHE* 3.3 8.4 + - + +
31A SER* 3.1 27.9 + - - -
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Residues in contact with PHE 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* 2.8 13.0 + - + +
25A ILE* 3.6 13.0 - - + +
27A VAL* 1.3 76.9 - - - +
29A LEU* 1.3 63.5 + - + +
31A SER* 3.4 12.1 + - - -
32A VAL* 2.9 55.7 + - + +
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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 ILE* 3.1 34.2 + - + +
26A PHE* 3.6 19.3 - - + +
27A VAL 3.3 0.2 - - - -
28A PHE* 1.3 78.8 - - + +
30A PHE* 1.3 66.0 + - + +
32A VAL* 3.5 12.7 + - + +
33A VAL* 3.0 32.7 + - + +
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Residues in contact with PHE 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 PHE* 3.2 18.0 + + + +
27A VAL* 3.5 12.6 - - + +
28A PHE 3.2 0.2 - - - -
29A LEU* 1.3 80.0 - - + +
31A SER* 1.3 61.9 + - - +
33A VAL* 3.3 9.3 + - + +
34A ILE* 3.0 38.4 + - + +
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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* 3.1 17.7 + - - -
28A PHE* 3.5 16.7 + - - -
30A PHE* 1.3 74.5 - - - +
32A VAL* 1.3 66.5 + - - +
34A ILE* 3.3 12.9 + - - +
35A GLY* 3.0 25.3 + - - -
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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 PHE* 2.9 49.3 + - + +
29A LEU* 3.6 15.3 - - + +
30A PHE 3.3 0.2 - - - -
31A SER* 1.3 84.3 + - - +
33A VAL* 1.3 64.8 + - + +
35A GLY* 3.3 1.9 + - - -
36A SER* 3.3 22.4 + - - -
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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 LEU* 3.0 19.5 + - + +
30A PHE* 3.6 11.7 - - + +
31A SER 3.2 0.4 - - - -
32A VAL* 1.3 78.3 - - + +
34A ILE* 1.3 59.0 + - + +
35A GLY 3.0 4.3 - - - -
36A SER* 3.3 6.3 + - - +
37A ILE* 2.9 47.6 + - + +
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Residues in contact with ILE 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 PHE* 3.0 33.1 + - + +
31A SER* 3.8 9.9 - - - +
33A VAL* 1.3 78.1 - - + +
35A GLY* 1.3 56.7 + - - +
37A ILE* 3.9 9.4 - - + -
38A TYR* 2.8 48.7 + - + +
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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 SER 3.0 13.4 + - - -
32A VAL 3.3 4.5 + - - -
33A VAL 3.0 0.6 - - - -
34A ILE* 1.3 74.8 - - - +
36A SER* 1.3 64.2 + - - +
37A ILE 3.0 0.9 - - - -
38A TYR* 3.1 20.6 + - - +
39A LEU* 3.6 4.3 + - - +
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Residues in contact with SER 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* 3.3 12.8 + - - +
33A VAL* 3.3 10.7 + - - +
35A GLY* 1.3 74.5 - - - +
37A ILE* 1.3 67.0 + - - +
39A LEU* 3.4 22.2 - - - +
40A PHE* 4.3 5.7 + - - -
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Residues in contact with ILE 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* 2.9 37.4 + - + +
34A ILE* 3.9 11.7 - - + +
36A SER* 1.3 80.5 + - - +
38A TYR* 1.3 69.1 - - + +
39A LEU 3.0 2.2 - - - -
40A PHE* 2.9 30.5 + - + +
41A LEU* 3.3 12.2 + - + +
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Residues in contact with TYR 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 ILE* 2.8 41.3 + - + +
35A GLY* 3.2 11.0 - - - +
37A ILE* 1.3 78.3 - - + +
39A LEU* 1.3 55.8 + - - +
41A LEU* 2.6 60.7 + - + +
42A ARG* 3.3 17.6 + - - +
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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 GLY 3.6 3.8 + - - +
36A SER* 3.4 18.5 + - - +
37A ILE 3.0 0.4 + - - -
38A TYR* 1.3 77.3 - - - +
40A PHE* 1.3 60.3 + - + +
42A ARG* 3.0 30.8 + - + +
43A LYS* 3.7 7.7 + - - +
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Residues in contact with PHE 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 SER 4.9 7.4 - - - -
37A ILE* 2.9 23.2 + - + +
39A LEU* 1.3 82.1 - - + +
41A LEU* 1.3 57.1 + - - +
42A ARG 3.0 1.1 - - - -
43A LYS* 3.1 62.6 + - + +
44A ARG* 3.9 10.2 - - - +
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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 ILE* 3.3 8.2 + - + +
38A TYR* 2.6 66.6 + - + +
40A PHE* 1.3 73.4 - - - +
42A ARG* 1.3 60.3 + - - -
43A LYS 3.4 0.4 - - - -
44A ARG* 3.9 20.2 - - - +
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Residues in contact with ARG 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 TYR* 3.3 17.0 + - - +
39A LEU* 3.0 18.3 + - + +
41A LEU* 1.3 82.4 - - - +
43A LYS* 1.3 54.6 + - - +
44A ARG 3.0 13.3 + - - -
45A GLN* 4.1 8.0 + - - +
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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
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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