Contacts of the helix formed by residues 42 - 73 (chain A) in PDB entry 2LP8
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 42 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 2.6 40.8 + - - +
4A SER* 3.3 19.2 + - - +
41A THR* 1.3 82.3 + - - +
43A SER* 1.3 72.5 + - - +
44A GLU* 3.0 5.4 + - - +
45A ALA* 3.4 11.6 + - - +
46A VAL* 3.3 13.6 - - + +
148A TRP* 3.3 33.9 + - - +
149A ASP* 4.5 9.5 + - + +
182A HIS* 6.2 4.3 - - + +
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 3.1 24.1 + - - -
7A GLU* 2.9 36.1 + - - -
8A LEU* 3.2 18.3 - - - +
41A THR 3.5 0.4 - - - -
42A GLU* 1.3 77.1 - - - +
44A GLU* 1.3 61.2 + - - +
45A ALA 3.0 0.2 - - - -
46A VAL* 2.7 13.2 + - - +
47A LYS* 2.5 36.6 + - - +
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLY* 3.5 26.4 + - - +
41A THR 4.9 2.0 - - - +
42A GLU 3.0 2.5 + - - +
43A SER* 1.3 75.8 - - - +
45A ALA* 1.3 56.6 + - - +
47A LYS* 3.8 11.1 - - - +
48A GLN* 3.0 32.0 + - + +
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU 3.4 7.1 + - - +
43A SER 3.0 0.4 - - - -
44A GLU* 1.3 80.3 - - - +
46A VAL* 1.3 60.9 + - + +
48A GLN* 3.3 5.5 + - - +
49A ALA* 2.8 28.6 + - - +
149A ASP* 5.6 4.5 - - - +
152A VAL* 3.6 26.2 - - + +
157A ASN* 5.1 1.2 + - - +
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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
----------------------------------------------------------
8A LEU* 3.2 40.6 - - + -
42A GLU* 3.3 27.1 - - + +
43A SER* 2.7 11.8 + - - +
45A ALA* 1.3 73.4 - - + +
47A LYS* 1.3 51.9 + - - +
49A ALA* 3.1 2.8 + - - +
50A LEU* 2.6 43.1 + - + +
148A TRP* 3.6 40.8 - - + +
149A ASP* 4.3 3.8 - - - +
151A PHE* 5.3 0.2 - - - -
152A VAL* 3.4 11.6 - - + +
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 2.7 46.9 + - - +
8A LEU* 3.8 17.7 - - + +
11A ASP* 4.3 30.7 + - + +
39A GLU 2.8 21.9 + - - +
43A SER* 2.5 37.9 + - - +
44A GLU* 3.8 10.8 - - - +
46A VAL* 1.3 71.7 - - - +
48A GLN* 1.3 64.2 + - + +
50A LEU* 3.4 9.0 - - - +
51A ARG* 2.9 37.6 + - - +
104A PHE* 5.6 0.4 - - + -
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Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU* 3.0 25.5 + - + +
45A ALA* 3.3 8.0 + - - +
46A VAL 3.2 0.2 - - - -
47A LYS* 1.3 86.2 - - + +
49A ALA* 1.3 56.1 + - - +
51A ARG* 3.1 42.1 + - - +
52A GLU* 2.9 28.0 + - - +
157A ASN* 2.7 50.0 + - + +
160A ALA* 6.4 0.4 - - + -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA 2.8 13.2 + - - +
46A VAL 3.5 7.4 - - - +
48A GLN* 1.3 74.8 - - - +
50A LEU* 1.3 66.1 + - - +
52A GLU* 3.3 4.7 + - - +
53A ALA* 3.1 19.4 + - - +
151A PHE* 3.5 26.4 - - + -
152A VAL* 3.7 5.6 - - + -
155A TYR 4.0 2.8 - - - +
156A GLY* 3.3 28.3 - - - -
157A ASN* 3.7 9.4 - - - +
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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
----------------------------------------------------------
8A LEU* 4.0 24.2 - - + -
46A VAL* 2.6 29.4 + - + +
47A LYS* 3.4 10.1 - - - +
49A ALA* 1.3 73.5 - - - +
51A ARG* 1.3 51.4 + - - +
53A ALA* 3.4 1.4 + - - +
54A GLY 2.7 30.3 + - - -
97A TRP 6.0 0.2 - - - +
100A ILE* 5.3 8.7 - - + +
101A VAL* 4.5 9.4 - - + +
104A PHE* 2.9 57.6 - - + -
134A LEU* 6.2 1.8 - - + -
148A TRP* 5.7 3.6 - - + -
151A PHE* 3.3 33.0 - - + -
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 2.7 38.9 + - - +
12A PHE* 4.2 16.4 - - + -
15A TYR* 5.4 19.5 - - + +
47A LYS* 2.9 18.6 + - - +
48A GLN* 3.1 50.7 + - - +
50A LEU* 1.3 74.6 - - - +
52A GLU* 1.3 69.1 + - - +
54A GLY 3.8 0.2 - - - -
55A ASP* 2.9 27.7 + - - +
104A PHE* 4.0 9.2 - - + -
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 2.9 21.0 + - - +
49A ALA* 3.5 5.6 - - - +
51A ARG* 1.3 95.3 - - - +
53A ALA* 1.3 64.0 + - - +
55A ASP* 3.3 7.6 + - - +
56A GLU* 3.1 27.4 + - - +
155A TYR* 4.8 7.2 - - + +
156A GLY 5.5 0.7 - - - +
157A ASN* 3.1 33.7 + - - +
158A ASN 5.0 3.6 + - - +
159A ALA* 4.9 8.7 + - - +
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA 3.1 5.1 + - - +
50A LEU 3.8 0.7 - - - +
52A GLU* 1.3 76.5 - - - +
54A GLY* 1.3 65.5 + - - +
56A GLU* 3.2 7.7 + - - +
57A PHE* 3.1 16.3 + - - +
101A VAL* 3.3 39.4 - - + +
151A PHE* 3.6 17.9 - - + -
155A TYR* 3.6 24.8 - - + -
1015B ILE* 4.3 5.8 - - + +
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Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 4.2 4.0 - - - -
50A LEU 2.7 22.1 + - - -
51A ARG 3.8 2.0 - - - -
53A ALA* 1.3 74.0 - - - +
55A ASP* 1.3 55.9 + - - +
57A PHE* 2.9 2.9 + - - +
58A GLU* 2.9 27.2 + - - +
101A VAL* 3.6 6.7 - - - +
104A PHE* 3.8 16.8 - - - -
105A SER* 3.0 18.6 + - - -
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Residues in contact with ASP 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG 2.9 19.1 + - - +
52A GLU* 3.4 8.5 - - - +
54A GLY* 1.3 73.5 - - - +
56A GLU* 1.3 72.8 + - - +
58A GLU* 3.0 30.2 + - - +
59A LEU* 3.2 25.5 + - - +
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU 3.1 16.1 + - - +
53A ALA* 3.2 14.1 + - - +
55A ASP* 1.3 84.0 - - - +
57A PHE* 1.3 56.1 + - - +
59A LEU* 2.9 24.4 - - - +
60A ARG* 2.8 49.7 + - - +
155A TYR* 3.5 25.9 + - + +
1015B ILE* 4.9 3.8 - - + -
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Residues in contact with PHE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA 3.1 9.6 + - - +
54A GLY* 2.9 11.3 + - - +
56A GLU* 1.3 78.6 - - - +
58A GLU* 1.3 65.9 + - - +
60A ARG* 3.3 16.1 + - + +
61A TYR* 3.0 45.7 + + + -
90A LEU* 6.0 0.4 - - + -
102A ALA* 3.3 39.7 - - + -
105A SER* 3.5 10.1 - - - +
106A PHE* 4.1 6.1 - - + -
1008B LEU* 3.5 35.4 - - + -
1011B PHE* 3.9 10.5 - - + -
1012B GLY* 3.6 26.9 - - - -
1015B ILE* 3.6 23.3 - - + +
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.4 12.6 - - - -
15A TYR* 5.5 0.5 - - - -
16A LYS* 2.7 44.4 + - - +
19A GLN* 4.0 6.9 + - - +
54A GLY 2.9 17.1 + - - +
55A ASP* 3.0 25.6 + - - +
57A PHE* 1.3 75.9 - - - +
59A LEU* 1.3 54.4 + - - +
61A TYR* 3.0 27.7 + - + +
62A ARG* 2.8 37.4 + - - +
105A SER* 3.2 11.4 - - - +
109A ALA* 5.6 0.3 - - - +
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 3.2 23.6 - - - +
56A GLU* 2.9 34.5 - - - +
58A GLU* 1.3 76.4 - - - +
60A ARG* 1.3 88.4 + - + +
62A ARG* 3.3 27.3 + - - +
63A ARG* 4.2 2.8 + - - +
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Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU* 2.8 60.5 + - - +
57A PHE* 3.4 11.9 - - + +
58A GLU 3.0 0.6 + - - -
59A LEU* 1.3 91.2 - - + +
61A TYR* 1.3 59.8 + - + +
63A ARG* 4.3 10.2 + - - +
155A TYR* 5.4 0.4 + - - -
1011B PHE* 4.3 29.3 - - + +
1014B CYS* 3.2 35.4 + - - +
1015B ILE* 3.8 12.1 - - - +
1016B ASN 4.6 4.6 - - - +
1017B ARG* 4.2 0.6 - - - +
1018B NH2 3.2 26.3 + - - -
1100B 33B 5.7 2.5 - - - +
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 3.0 57.8 + + + -
58A GLU* 3.0 36.0 + - + +
60A ARG* 1.3 75.3 - - - +
62A ARG* 1.3 56.5 + - + +
63A ARG* 3.0 3.8 - - - -
64A ALA* 2.8 13.2 + - + +
65A PHE* 2.8 64.5 + + + +
68A LEU* 5.8 1.3 - - + -
105A SER* 3.5 14.3 + - - -
106A PHE* 3.8 16.4 - + + -
109A ALA* 3.5 18.9 - - - +
1008B LEU* 3.9 20.4 - - + -
1011B PHE* 5.1 11.4 - - + -
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 5.4 9.1 - - - +
20A LYS* 6.1 1.4 - - - +
58A GLU* 2.8 17.7 + - - +
59A LEU* 3.4 19.6 - - - +
60A ARG 3.3 1.0 - - - -
61A TYR* 1.3 79.5 - - + +
63A ARG* 1.3 61.6 + - - +
64A ALA 3.4 0.3 + - - -
65A PHE* 3.5 26.9 + - + +
66A SER* 3.9 10.8 + - - -
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU 4.2 2.8 + - - +
60A ARG 4.4 10.3 - - - +
62A ARG* 1.3 81.0 - - - +
64A ALA* 1.3 59.5 + - + +
66A SER* 4.0 7.3 + - - -
67A ASP* 4.4 6.6 - - - +
1011B PHE* 5.8 10.6 - - + -
1100B 33B 5.9 0.6 + - - -
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 2.8 8.4 + - + +
63A ARG* 1.3 78.5 - - + +
65A PHE* 1.3 56.3 + - - +
66A SER 3.2 2.2 - - - -
67A ASP* 2.7 31.8 + - - +
68A LEU* 2.8 39.9 + - + +
1007B ALA* 6.0 1.6 - - + -
1011B PHE* 6.0 3.4 - - + -
1100B 33B 4.3 16.6 - - - +
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 5.4 9.9 - - - -
61A TYR* 2.8 39.8 + + + +
62A ARG* 3.5 18.3 + - + -
64A ALA* 1.3 75.8 - - - +
66A SER* 1.3 69.3 + - - +
67A ASP 3.3 0.5 + - - -
68A LEU* 3.3 20.5 + - - +
69A THR* 3.9 10.6 + - + +
106A PHE* 4.0 11.2 - + - -
109A ALA* 3.3 34.8 - - + -
112A VAL* 5.0 7.9 - - + -
113A GLU* 3.4 36.1 - - + +
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 3.9 11.6 + - - -
63A ARG 4.0 5.4 + - - -
65A PHE* 1.3 86.6 - - - +
67A ASP* 1.3 68.2 + - - +
69A THR* 3.3 17.2 + - - +
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Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG 4.4 6.1 - - - +
64A ALA* 2.7 11.0 + - - +
66A SER* 1.3 87.7 + - - +
68A LEU* 1.3 66.1 + - + +
69A THR 3.1 4.5 + - - -
70A SER* 3.2 23.4 + - - -
71A GLN* 4.2 4.7 + - - +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 5.1 2.0 - - + +
64A ALA* 2.8 49.3 + - + +
65A PHE* 3.3 12.7 + - - +
67A ASP* 1.3 76.0 - - + +
69A THR* 1.3 53.2 + - - +
70A SER 3.0 5.8 - - - -
71A GLN* 2.7 54.1 + - - +
72A LEU* 2.8 31.2 + - + +
106A PHE* 4.3 13.0 - - + -
1003B CYS* 4.5 7.2 - - + -
1004B VAL* 3.5 21.5 - - + +
1007B ALA* 5.4 3.1 - - + -
1008B LEU* 4.6 7.2 - - + -
1100B 33B 5.2 1.3 - - - +
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Residues in contact with THR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.9 9.1 + - + +
66A SER* 3.3 16.8 + - - +
67A ASP 4.1 0.5 + - - -
68A LEU* 1.3 76.9 - - - +
70A SER* 1.3 60.2 + - - +
73A HIS* 2.9 21.5 + - - -
74A ILE* 3.1 20.2 + - + -
113A GLU* 3.2 44.0 - - + +
116A ASP* 4.8 7.4 + - - +
117A LYS* 3.8 27.1 + - - -
----------------------------------------------------------
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 3.2 13.2 + - - -
68A LEU 3.0 0.2 - - - -
69A THR* 1.3 83.5 + - - +
71A GLN* 1.3 62.0 + - - +
73A HIS* 3.7 13.0 + - - +
117A LYS* 5.7 0.4 - - - +
----------------------------------------------------------
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Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 4.2 4.6 - - - +
68A LEU* 2.7 49.6 + - - +
70A SER* 1.3 73.0 - - - +
72A LEU* 1.3 64.8 + - - +
73A HIS* 3.1 3.9 + - - +
85A GLN* 4.9 7.1 + - - +
1001B ACE 3.9 28.4 - - - +
1002B GLY 2.9 28.7 + - - +
1003B CYS* 3.1 23.7 - - - +
1004B VAL* 4.1 6.2 - - + +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 2.8 45.9 + - + +
69A THR 4.0 0.2 - - - +
71A GLN* 1.3 74.2 - - - +
73A HIS* 1.3 67.0 + - - +
74A ILE* 3.5 14.1 - - + -
82A SER* 2.6 56.8 + - - +
83A PHE* 4.1 1.6 - - - +
85A GLN* 4.7 6.4 + - - -
86A VAL* 4.7 0.7 - - + -
106A PHE* 3.7 24.2 - - + -
110A LEU* 4.0 12.3 - - + -
113A GLU* 3.2 22.7 - - - +
1004B VAL* 3.7 20.0 - - + -
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Residues in contact with HIS 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR 2.9 12.3 + - - -
70A SER* 4.0 12.5 + - - +
71A GLN 3.1 5.3 - - - +
72A LEU* 1.3 82.7 - - - +
74A ILE* 1.3 66.8 + - - +
75A THR* 3.0 32.2 + - + +
79A ALA* 4.9 0.2 - - - +
82A SER* 4.2 3.9 + - - -
117A LYS* 4.9 0.9 - - - +
----------------------------------------------------------
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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