Contacts of the helix formed by residues 2 - 29 (chain B) in PDB entry 4A2N
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 ASN 2 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 1.3 79.3 - - - +
3B GLU* 1.3 68.6 + - - +
4B ASN* 3.0 22.2 + - - +
5B LEU* 3.1 44.2 - - + +
6B TRP* 3.5 6.4 - - - -
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Residues in contact with GLU 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET 3.2 6.0 + - - +
2B ASN* 1.3 69.2 + - - +
4B ASN* 1.3 67.6 + - - +
5B LEU 2.9 3.2 + - - -
6B TRP* 3.2 16.1 + - - +
7B LYS* 3.5 26.5 + - + +
70B ASN* 5.2 11.3 + - - +
78B ARG* 3.0 39.5 + - - -
143B LEU* 4.4 7.1 - - - +
144B SER 5.6 0.2 - - - +
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Residues in contact with ASN 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASN* 3.0 13.7 + - - +
3B GLU* 1.3 78.5 - - - +
5B LEU* 1.3 65.0 + - + +
7B LYS* 3.5 31.1 + - - +
8B ILE* 3.3 29.5 + - - +
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Residues in contact with LEU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 4.5 9.2 - - - +
2B ASN* 3.1 44.3 + - + +
3B GLU 2.9 0.8 + - - -
4B ASN* 1.3 77.3 - - + +
6B TRP* 1.3 60.3 + - + +
8B ILE* 2.5 34.2 + - + +
9B CYS* 2.9 10.3 + - - +
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Residues in contact with TRP 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 4.1 11.3 + - - +
2B ASN 3.5 21.3 + - - -
3B GLU* 3.2 13.9 + - - +
5B LEU* 1.3 79.4 - - + +
7B LYS* 1.3 64.5 + - - +
9B CYS* 2.9 10.3 + - + +
10B PHE* 2.8 25.6 + - - +
75B ASP* 3.3 35.5 + - + -
78B ARG* 3.5 72.6 - - + +
79B LEU* 4.0 16.6 - - + -
82B LEU* 4.4 23.8 - - + -
142B ILE* 4.6 20.3 - - + +
143B LEU* 5.4 3.8 - - + -
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Residues in contact with LYS 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLU* 3.5 23.6 + - + +
4B ASN* 3.5 38.5 + - - +
5B LEU 2.9 0.6 + - - -
6B TRP* 1.3 78.6 - - - +
8B ILE* 1.3 66.8 + - + +
10B PHE* 3.3 2.7 + - - +
11B ILE* 2.9 28.2 + - - +
60B ALA 3.6 9.7 + - - +
61B VAL* 3.3 56.1 + - + +
63B SER 4.9 5.3 + - - -
64B SER* 5.8 4.0 - - - +
143B LEU* 5.1 6.7 - - + +
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Residues in contact with ILE 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ASN* 3.3 25.1 - - - +
5B LEU* 2.5 17.6 + - + +
7B LYS* 1.3 76.5 - - + +
9B CYS* 1.3 64.2 + - - +
11B ILE* 3.2 22.6 - - + +
12B VAL* 3.4 13.4 + - + +
61B VAL* 5.8 2.5 - - + -
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Residues in contact with CYS 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU 2.9 8.2 + - - +
6B TRP* 2.9 19.7 + - + +
8B ILE* 1.3 75.7 - - - +
10B PHE* 1.3 66.7 + - - +
12B VAL* 2.7 24.2 + - - +
13B MET* 3.1 21.3 + - - +
82B LEU* 3.3 34.8 - - + -
142B ILE* 6.1 1.8 - - + -
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Residues in contact with PHE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TRP 2.8 17.9 + - - +
7B LYS 3.9 2.0 - - - +
9B CYS* 1.3 72.0 - - - +
11B ILE* 1.3 60.3 + - + +
12B VAL 2.7 10.4 + - - -
13B MET* 2.9 13.2 + - + -
14B PHE* 2.7 61.3 + + + +
57B PRO* 4.5 12.3 - - + -
58B LEU* 5.3 1.6 - - + -
61B VAL* 4.0 19.7 - - + -
82B LEU* 6.3 0.2 - - - -
85B THR* 6.5 0.4 - - + -
135B TRP* 4.5 11.9 - + - -
139B GLN* 3.8 32.5 - - + -
142B ILE* 4.2 23.5 - - + +
143B LEU* 3.7 39.7 - - + -
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Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LYS 2.9 19.0 + - - +
8B ILE* 3.2 30.7 - - + +
10B PHE* 1.3 79.1 - - + +
12B VAL* 1.3 60.3 + - + +
14B PHE* 4.1 11.4 - - + -
15B ILE* 3.0 29.1 + - + +
58B LEU* 3.4 23.6 - - + -
61B VAL* 4.4 10.3 - - + -
62B PHE* 3.3 37.7 - - + -
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Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.5 16.4 - - + +
9B CYS* 2.7 11.7 + - - +
10B PHE 2.7 0.2 + - - -
11B ILE* 1.3 81.5 - - + +
13B MET* 1.3 81.5 + - + +
14B PHE 2.9 0.9 - - - -
15B ILE* 2.6 23.6 + - + +
16B ILE* 2.7 26.0 + - + +
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Residues in contact with MET 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B CYS* 3.4 34.8 - - - +
10B PHE* 2.9 16.7 + - + +
12B VAL* 1.3 82.2 - - + +
14B PHE* 1.3 52.0 + - - +
16B ILE* 3.2 13.8 + - + +
17B TRP* 2.5 38.0 + - - +
82B LEU* 4.2 23.8 - - + -
85B THR* 5.6 6.3 - - + -
86B PHE* 5.1 21.8 - - + +
89B ILE* 3.5 16.1 - - + +
135B TRP* 4.7 8.1 - - + -
142B ILE* 5.7 2.9 - - + -
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Residues in contact with PHE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PHE* 2.7 47.2 + + + +
11B ILE* 3.9 15.9 - - + +
13B MET* 1.3 73.9 - - - +
15B ILE* 1.3 74.0 + - - +
17B TRP* 2.8 38.9 + + - +
18B VAL* 2.7 45.1 + - + +
53B MET 4.0 13.9 - - - -
54B VAL* 3.8 22.7 - - + -
57B PRO* 5.4 0.2 - - + -
58B LEU* 4.0 23.1 - - + -
135B TRP* 4.7 3.3 - - - -
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Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.0 13.4 + - + +
12B VAL* 2.6 43.5 + - + +
14B PHE* 1.3 84.0 - - + +
16B ILE* 1.3 62.0 + - + +
18B VAL* 3.6 5.4 + - - +
19B PHE* 3.1 25.6 + - + +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 2.7 36.7 + - + +
13B MET* 3.4 14.6 - - + +
15B ILE* 1.3 75.3 - - + +
17B TRP* 1.3 66.4 + - - +
18B VAL 3.0 1.3 - - - -
19B PHE* 2.9 14.7 + - + +
20B VAL* 2.9 27.4 + - + +
89B ILE* 3.8 30.5 - - + -
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Residues in contact with TRP 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B MET 2.5 22.5 + - - +
14B PHE* 2.8 34.2 + + - +
16B ILE* 1.3 71.4 - - - +
18B VAL* 1.3 72.1 + - + +
20B VAL* 3.6 12.2 + - - +
21B ARG* 3.6 8.4 + - - +
53B MET* 3.8 25.1 - - + -
89B ILE* 3.8 13.5 - - + -
92B PHE* 3.7 28.3 - + - -
131B HIS* 3.4 21.7 + + - -
132B LEU* 4.3 15.3 - - + -
135B TRP* 3.2 69.5 - + + -
1194B PLM 4.0 28.0 - - + +
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PHE* 2.7 54.8 + - + +
15B ILE* 3.7 6.3 - - - +
17B TRP* 1.3 81.5 - - + +
19B PHE* 1.3 66.4 + - - +
21B ARG* 2.9 8.5 + - - +
22B LYS* 2.8 29.4 + - + +
1194B PLM 4.3 25.4 - - + -
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Residues in contact with PHE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.1 20.2 + - + +
16B ILE* 2.9 16.7 + - + +
18B VAL* 1.3 77.4 - - - +
20B VAL* 1.3 71.2 + - + +
22B LYS* 3.2 7.2 + - + -
23B VAL* 3.0 53.0 + - + +
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 2.9 23.3 + - + +
17B TRP 3.6 8.1 - - - +
19B PHE* 1.3 85.0 - - + +
21B ARG* 1.3 60.3 + - - +
23B VAL* 3.7 2.4 + - - +
24B TYR* 3.3 33.5 + - + +
89B ILE* 4.1 16.6 - - + -
92B PHE* 3.5 18.8 - - + -
93B THR* 3.0 42.8 - - + -
96B HIS* 4.8 4.3 - - + -
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TRP 3.6 3.7 + - - +
18B VAL* 2.9 9.2 + - - +
20B VAL* 1.3 75.7 - - - +
22B LYS* 1.3 69.3 + - - +
23B VAL 2.9 2.3 + - - -
24B TYR 3.0 0.3 + - - -
25B GLY* 2.8 27.4 + - - +
50B PHE* 6.0 0.2 - - - -
92B PHE* 4.2 18.3 - - + -
96B HIS* 3.2 21.1 + - + +
103B TRP* 3.1 36.1 - - + -
128B MET* 3.1 26.4 - - - +
132B LEU* 5.1 4.8 - - - +
1194B PLM 2.9 80.1 - - + +
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL* 2.8 23.7 + - + +
19B PHE* 3.2 9.6 + - + +
21B ARG* 1.3 76.6 - - - +
23B VAL* 1.3 58.7 + - + +
26B THR* 2.9 33.6 + - + +
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 3.0 53.6 + - + +
20B VAL* 3.8 5.6 - - - +
21B ARG 2.9 1.6 + - - -
22B LYS* 1.3 81.1 - - + +
24B TYR* 1.3 76.9 + - + +
25B GLY 3.4 0.2 + - - -
26B THR* 3.6 10.4 + - - -
27B ARG* 3.6 11.6 + - - +
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Residues in contact with TYR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL* 3.3 25.9 + - + +
21B ARG 3.0 1.8 + - - -
23B VAL* 1.3 94.3 - - + +
25B GLY* 1.3 60.4 + - - +
27B ARG* 3.5 8.6 - - + +
28B ALA* 3.4 19.6 + - - +
93B THR* 4.4 8.5 + - + -
96B HIS* 2.9 44.3 - + + +
97B LYS* 3.0 54.4 - - + +
100B GLY* 5.0 10.5 - - - +
103B TRP* 5.3 0.2 - - - -
1195B CDL 5.2 0.2 + - - -
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Residues in contact with GLY 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 2.8 21.4 + - - -
24B TYR* 1.3 68.7 - - - +
26B THR* 1.3 63.4 + - - +
27B ARG 2.8 4.3 - - - -
28B ALA* 2.7 15.4 + - - +
29B MET* 2.9 18.0 + - - +
96B HIS* 4.5 2.6 - - - -
103B TRP* 3.8 28.2 - - - -
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Residues in contact with THR 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 2.9 24.1 + - + +
23B VAL* 3.6 5.7 + - - -
25B GLY* 1.3 72.7 - - - +
27B ARG* 1.3 60.2 + - - +
29B MET* 3.6 26.7 + - + +
30B LYS* 3.6 13.7 + - - +
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Residues in contact with ARG 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 3.6 10.3 + - + +
24B TYR* 3.5 14.3 + - - +
25B GLY 2.8 1.2 + - - -
26B THR* 1.3 83.3 + - - +
28B ALA* 1.3 58.4 + - - +
30B LYS* 3.9 14.4 - - - +
31B ASN* 4.7 2.1 + - - +
101B ASN* 3.5 13.6 - - - +
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Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR 3.4 7.9 + - - +
25B GLY 2.7 12.6 + - - +
27B ARG* 1.3 71.9 - - - +
29B MET* 1.3 56.7 + - - +
30B LYS 3.2 4.7 - - - -
31B ASN* 3.8 8.6 + - - +
100B GLY 3.3 27.8 - - - +
101B ASN* 3.7 18.6 - - - +
103B TRP* 4.1 16.8 - - + +
110B LYS* 3.3 24.8 + - - +
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Residues in contact with MET 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLY 2.9 19.1 + - - +
26B THR* 4.1 18.4 - - + +
27B ARG 3.4 0.2 - - - -
28B ALA* 1.3 77.2 - - - +
30B LYS* 1.3 55.8 + - - +
31B ASN 3.1 12.8 + - - +
103B TRP* 4.6 16.4 - - + -
104B SER* 5.9 1.8 - - - +
108B GLU* 5.6 6.3 - - - +
110B LYS* 5.4 2.2 - - - +
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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