Contacts of the helix formed by residues 14 - 39 (chain A) in PDB entry 3J2I
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 14 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLU 4.2 3.3 - - - +
10A GLN* 3.5 18.4 - - - +
11A THR* 3.0 28.6 + - - +
12A ILE 4.2 1.6 - - - -
13A ALA* 1.3 83.8 - - + +
15A ASP* 1.3 66.3 + - - +
16A LEU* 4.4 5.1 - - + +
17A VAL* 3.0 29.4 + - + +
18A VAL* 3.2 13.2 + - - +
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Residues in contact with ASP 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 4.4 5.5 - - - +
14A GLU* 1.3 71.7 - - - +
16A LEU* 1.3 57.5 + - - +
18A VAL* 3.2 11.2 + - - +
19A THR* 2.9 32.0 + - - +
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 3.2 5.2 - - + +
15A ASP* 1.3 79.1 - - - +
17A VAL* 1.3 59.1 + - + +
19A THR* 3.4 12.5 + - + -
20A LYS* 3.0 56.4 + - + +
64A PHE* 4.5 13.9 - - + -
67A GLU* 5.9 2.5 - - - +
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 4.1 10.5 - - + +
11A THR* 3.3 35.4 - - - +
12A ILE* 4.0 1.6 - - + -
14A GLU* 3.0 23.6 + - + +
16A LEU* 1.3 76.3 - - + +
18A VAL* 1.3 65.4 + - - +
20A LYS* 3.2 9.9 + - + +
21A TYR* 3.0 33.8 + - + -
117A PHE* 3.4 46.0 - - + -
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 3.4 39.3 - - + +
14A GLU 3.2 8.0 + - - +
15A ASP* 3.6 10.3 - - - +
17A VAL* 1.3 75.4 - - - +
19A THR* 1.3 56.6 + - - +
21A TYR* 3.2 4.5 + - - +
22A LYS* 2.9 56.1 + - + +
324A LEU* 4.1 8.7 - - + -
326A MET* 3.9 19.7 - - + -
331A MET* 3.8 14.4 - - + -
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Residues in contact with THR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 2.9 15.4 + - - +
16A LEU* 3.5 17.4 - - + +
17A VAL 3.2 0.2 - - - -
18A VAL* 1.3 76.7 - - - +
20A LYS* 1.3 57.5 + - - +
22A LYS* 3.2 10.1 + - - +
23A MET* 2.8 58.6 + - + +
64A PHE* 4.7 7.9 - - + -
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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
----------------------------------------------------------
10A GLN* 4.8 5.5 + - - -
16A LEU* 3.0 48.4 + - + +
17A VAL* 3.2 7.5 + - - +
19A THR* 1.3 75.2 - - - +
21A TYR* 1.3 63.2 + - - +
23A MET* 3.5 2.6 + - - +
24A GLY* 3.0 18.7 + - - -
64A PHE* 3.8 19.3 - - + -
67A GLU* 5.5 1.0 + - - -
70A MET* 3.7 24.7 - - - +
114A VAL* 3.8 25.8 - - + +
115A ASP* 2.8 27.0 + - + -
117A PHE* 3.9 34.5 - - + +
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Residues in contact with TYR 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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12A ILE* 3.6 30.5 - - + -
17A VAL* 3.0 24.6 + - + -
18A VAL 3.5 5.8 - - - +
20A LYS* 1.3 76.4 - - - +
22A LYS* 1.3 57.4 + - - +
24A GLY* 3.3 1.2 + - - -
25A GLY 2.8 24.9 + - - -
117A PHE* 3.5 31.9 - + + +
118A ILE 3.1 42.3 + - - -
119A ALA* 4.2 1.5 - - - +
190A LEU* 4.1 16.0 + - + +
191A LYS* 4.3 7.4 - - - -
192A GLN 4.6 0.2 + - - -
223A VAL* 3.9 28.4 - - + +
324A LEU* 4.1 13.0 - - + -
333A ILE* 3.4 27.3 - - + +
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Residues in contact with LYS 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 VAL* 2.9 35.9 + - + +
19A THR* 3.7 8.7 - - - +
21A TYR* 1.3 73.4 - - + +
23A MET* 1.3 58.8 + - + +
25A GLY* 3.2 1.4 + - - +
26A ASP* 2.8 39.5 + - - +
331A MET* 3.3 35.9 - - + -
333A ILE* 4.2 21.2 - - + +
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Residues in contact with MET 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR* 2.8 41.3 + - + +
20A LYS* 4.1 3.8 - - - +
22A LYS* 1.3 75.1 - - + +
24A GLY* 1.3 62.2 + - - +
26A ASP* 3.4 12.8 + - - +
27A ILE* 3.2 28.1 + - - +
63A ILE* 3.8 43.7 - - + -
64A PHE* 3.7 23.6 - - + +
114A VAL* 4.6 1.3 - - + -
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Residues in contact with GLY 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS 3.0 12.8 + - - -
21A TYR 3.8 2.7 - - - -
23A MET* 1.3 75.9 - - - +
25A GLY* 1.3 57.6 + - - +
27A ILE* 3.3 4.2 + - - +
28A ALA* 2.9 28.9 + - - +
112A VAL* 3.7 17.3 - - - +
114A VAL* 3.8 20.3 - - - +
117A PHE 5.6 1.6 - - - -
119A ALA* 3.7 9.9 - - - -
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Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR 2.8 14.5 + - - -
22A LYS 3.2 3.6 + - - -
24A GLY* 1.3 74.1 - - - +
26A ASP* 1.3 58.8 + - - +
28A ALA* 3.3 1.4 + - - +
29A ASN* 2.8 35.7 + - - +
119A ALA* 3.4 15.8 - - - +
333A ILE* 3.5 22.9 - - - -
334A THR* 3.7 3.6 - - - -
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Residues in contact with ASP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 2.8 28.8 + - - +
23A MET* 3.6 11.8 - - - +
25A GLY* 1.3 73.0 - - - +
27A ILE* 1.3 59.0 + - + +
29A ASN* 3.5 9.6 + - - +
30A ARG* 3.0 48.7 + - - +
333A ILE 5.2 1.7 - - - +
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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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23A MET 3.2 16.3 + - - +
24A GLY* 3.6 6.7 - - - +
25A GLY 3.2 0.2 - - - -
26A ASP* 1.3 74.1 - - + +
28A ALA* 1.3 65.5 + - - +
30A ARG* 3.2 16.9 + - - +
31A VAL* 2.9 36.9 + - + +
56A ILE* 4.6 7.0 - - - -
59A GLU* 3.6 51.6 - - + +
60A THR* 3.9 10.5 - - + +
63A ILE* 3.8 25.4 - - + -
112A VAL* 4.0 20.4 - - + -
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Residues in contact with ALA 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 GLY 2.9 16.0 + - - +
25A GLY 3.7 4.7 - - - +
27A ILE* 1.3 75.5 - - - +
29A ASN* 1.3 58.3 + - - +
31A VAL* 3.5 0.8 + - - -
32A LEU* 2.9 32.7 + - - +
110A LEU* 3.9 17.5 - - + +
112A VAL* 3.8 19.0 - - + +
119A ALA 3.9 15.5 - - - +
121A VAL* 4.0 7.0 - - + -
334A THR* 4.0 13.5 - - + -
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Residues in contact with ASN 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 GLY 2.8 17.7 + - - +
26A ASP* 3.7 10.1 + - - +
28A ALA* 1.3 78.3 - - - +
30A ARG* 1.3 58.1 + - - +
32A LEU* 3.8 2.1 - - - +
33A ARG* 3.0 57.1 + - - +
121A VAL* 4.2 2.6 - - - +
333A ILE 3.6 16.6 + - - -
334A THR* 3.3 11.5 - - - +
335A SER* 2.9 32.9 + - - +
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Residues in contact with ARG 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 ASP* 3.0 35.9 + - - +
27A ILE* 3.6 20.0 - - - +
29A ASN* 1.3 74.8 - - - +
31A VAL* 1.3 67.8 + - - +
33A ARG* 3.3 6.6 + - - +
34A SER* 2.9 23.5 + - - -
55A MET* 5.6 2.9 - - + -
59A GLU* 3.0 37.9 + - - +
62A LYS* 5.0 7.6 - - - +
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 2.9 29.4 + - + +
28A ALA* 4.0 3.6 - - - +
30A ARG* 1.3 76.8 - - - +
32A LEU* 1.3 63.7 + - - +
34A SER* 3.1 7.6 + - - -
35A LEU* 3.0 24.6 + - + +
52A GLY* 3.8 30.3 - - - +
55A MET* 4.0 18.2 - - + -
56A ILE* 4.2 12.3 - - + +
59A GLU* 4.0 23.1 - - - +
110A LEU* 3.9 18.4 - - + -
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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
----------------------------------------------------------
28A ALA 2.9 18.8 + - - +
29A ASN* 3.8 3.1 - - - +
31A VAL* 1.3 76.4 - - - +
33A ARG* 1.3 60.6 + - - +
35A LEU* 3.1 5.9 + - - +
36A VAL* 2.9 40.4 + - + +
108A ILE* 3.7 36.8 - - + +
110A LEU* 4.1 10.3 - - + +
121A VAL* 3.7 34.3 - - + -
123A HIS* 3.7 31.0 - - + +
335A SER 4.0 3.8 - - - +
336A GLY* 3.8 14.4 - - - -
337A PRO* 4.3 3.1 - - + -
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Residues in contact with ARG 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASN* 3.0 48.4 + - - +
30A ARG* 3.9 5.6 - - - +
31A VAL 3.3 0.2 - - - -
32A LEU* 1.3 78.9 - - - +
34A SER* 1.3 63.6 + - - +
36A VAL* 3.4 7.6 + - - +
37A GLU* 3.0 25.1 + - - +
335A SER* 2.9 42.0 + - - -
336A GLY* 3.5 13.1 + - - -
337A PRO* 3.6 33.6 - - + +
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Residues in contact with SER 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 2.9 14.3 + - - -
31A VAL 3.4 8.5 - - - -
33A ARG* 1.3 76.4 - - - +
35A LEU* 1.3 59.4 + - - +
37A GLU* 3.4 10.1 + - - +
38A ALA* 3.0 28.5 + - - +
51A LYS* 3.7 11.3 + - - -
55A MET* 3.6 33.7 - - - +
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Residues in contact with LEU 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 VAL* 3.0 15.6 + - + +
32A LEU* 3.1 6.7 + - - +
34A SER* 1.3 73.2 - - - +
36A VAL* 1.3 65.0 + - - +
38A ALA* 3.2 5.0 + - - +
39A SER* 2.9 27.4 + - - -
48A LEU* 3.6 30.9 - - + +
51A LYS* 4.1 21.5 - - + -
52A GLY* 3.8 21.1 - - - +
55A MET* 5.1 2.0 - - - -
78A THR* 3.7 29.4 - - + -
80A ILE* 5.2 0.9 - - + -
108A ILE* 3.8 19.3 - - + -
110A LEU* 3.9 20.2 - - + -
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 2.9 30.2 + - + +
33A ARG* 3.7 10.5 - - - +
35A LEU* 1.3 76.6 - - - +
37A GLU* 1.3 62.8 + - - +
39A SER* 3.1 24.3 + - - +
108A ILE* 4.3 1.3 - - + -
123A HIS* 3.9 27.4 - - + +
125A PHE* 3.9 36.1 - - + -
337A PRO* 4.8 10.3 - - + -
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG 3.0 17.2 + - - +
34A SER* 3.7 9.0 - - - +
36A VAL* 1.3 77.7 - - - +
38A ALA* 1.3 60.2 + - - +
39A SER 3.4 6.1 + - - +
40A SER* 5.5 1.2 - - - -
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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
----------------------------------------------------------
34A SER 3.0 17.3 + - - +
35A LEU* 3.2 7.1 + - - +
37A GLU* 1.3 74.1 - - - +
39A SER* 1.3 63.1 + - - +
40A SER* 3.4 5.6 + - - -
43A VAL* 3.5 21.1 - - - +
48A LEU* 3.7 16.4 - - + -
51A LYS* 4.6 16.6 - - + -
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU 2.9 13.8 + - - -
36A VAL 3.1 16.2 + - - +
37A GLU 3.9 4.5 - - - +
38A ALA* 1.3 76.1 - - - +
40A SER* 1.3 62.7 + - - +
48A LEU* 3.6 16.7 - - - +
100A LEU* 3.8 16.5 - - - +
106A VAL* 5.1 0.9 - - - +
108A ILE* 4.2 3.6 - - - +
125A PHE* 3.4 32.9 - - - -
127A VAL* 5.0 3.1 - - - +
128A ASP* 4.1 5.7 + - - +
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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