Contacts of the helix formed by residues 12 - 34 (chain A) in PDB entry 3ABD
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 GLY 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLN* 1.3 65.8 + - - +
14A VAL* 3.3 18.9 - - - +
15A VAL* 3.7 11.2 + - - +
16A ALA* 3.1 24.8 + - - +
75A LEU 4.6 0.9 - - - +
76A GLU* 3.6 26.5 - - - -
104A GLN* 4.8 7.9 + - - -
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Residues in contact with GLN 13 (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 GLY* 1.3 72.2 - - - +
14A VAL* 1.3 61.3 + - + +
16A ALA* 3.4 1.4 + - - +
17A ASP* 3.0 41.2 + - - +
76A GLU* 4.2 29.6 + - + +
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Residues in contact with VAL 14 (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 GLY 3.7 16.4 - - - +
13A GLN* 1.3 74.7 - - + +
15A VAL* 1.3 74.1 + - + +
17A ASP* 3.2 8.4 + - - +
18A VAL* 3.0 37.7 + - + +
116A LEU* 5.6 12.3 - - + -
196A ILE* 5.1 10.5 - - + -
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLY 3.7 11.0 + - - +
13A GLN 3.4 0.2 - - - -
14A VAL* 1.3 86.7 - - + +
16A ALA* 1.3 62.2 + - - +
18A VAL* 3.5 5.5 + - - +
19A LEU* 2.9 48.2 + - + +
104A GLN* 3.5 35.9 - - + +
196A ILE* 3.7 48.2 - - + +
197A LEU* 4.6 8.3 - - + -
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Residues in contact with ALA 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 GLY 3.1 11.6 + - - +
13A GLN 3.7 3.1 - - - +
14A VAL 3.3 0.2 - - - -
15A VAL* 1.3 77.5 - - - +
17A ASP* 1.3 57.7 + - - +
19A LEU* 3.4 0.7 + - - +
20A CYS* 2.8 36.2 + - - +
72A LYS* 3.9 9.0 - - + +
75A LEU* 3.9 16.8 - - + -
76A GLU* 3.3 44.6 - - + +
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Residues in contact with ASP 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 3.0 29.8 + - - +
14A VAL* 3.6 7.5 - - - +
15A VAL 3.2 0.2 - - - -
16A ALA* 1.3 74.2 - - - +
18A VAL* 1.3 70.2 + - + +
20A CYS* 4.0 1.4 - - - +
21A GLU* 3.0 27.2 + - - +
72A LYS* 2.2 42.2 + - - +
76A GLU* 5.1 1.7 - - - +
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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
----------------------------------------------------------
14A VAL* 3.0 19.2 + - + +
15A VAL* 3.9 5.4 - - - +
17A ASP* 1.3 82.7 - - + +
19A LEU* 1.3 58.6 + - + +
21A GLU* 3.7 8.3 - - - +
22A PHE* 2.9 27.0 + - - +
48A TYR* 4.3 2.1 + - + +
116A LEU* 4.1 27.6 - - + -
119A VAL* 4.3 14.4 - - + -
120A GLU* 5.3 9.6 - - + +
123A LEU* 3.7 26.0 - - + -
196A ILE* 5.8 6.7 - - + -
197A LEU* 6.0 2.5 - - + -
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Residues in contact with LEU 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 VAL* 2.9 27.1 + - + +
18A VAL* 1.3 79.3 - - + +
20A CYS* 1.3 57.7 + - - +
22A PHE* 3.6 13.6 - - + +
23A LEU* 2.8 40.7 + - + +
75A LEU* 3.8 29.6 - - + -
102A ILE* 4.1 22.9 - - + -
104A GLN* 5.3 0.2 - - - +
123A LEU* 5.3 2.7 - - + -
197A LEU* 4.1 33.7 - - + -
199A MET* 3.9 27.4 - - + -
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Residues in contact with CYS 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 ALA 2.8 21.8 + - - +
17A ASP 4.0 2.7 - - - +
19A LEU* 1.3 72.5 - - - +
21A GLU* 1.3 66.2 + - - +
23A LEU* 4.5 4.3 - - - -
24A GLU* 3.0 25.9 + - - +
68A LEU* 3.6 35.5 - - + +
71A VAL* 5.1 0.4 - - - -
72A LYS* 3.5 34.3 - - - -
75A LEU* 3.9 15.9 - - - -
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Residues in contact with GLU 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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17A ASP 3.0 19.6 + - - +
18A VAL* 3.7 7.0 - - - +
20A CYS* 1.3 81.0 - - - +
22A PHE* 1.3 61.7 + - - +
24A GLU* 3.3 14.3 + - - +
25A VAL* 3.3 21.1 + - + +
47A LYS* 5.4 10.7 + - + +
48A TYR* 4.1 12.2 - - + +
120A GLU* 5.3 5.7 - - - +
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Residues in contact with PHE 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 17.8 + - - +
19A LEU* 3.6 13.9 - - + +
21A GLU* 1.3 77.1 - - - +
23A LEU* 1.3 64.2 + - + +
24A GLU 3.3 0.2 + - - -
25A VAL* 3.3 2.8 + - - +
26A ALA* 2.8 33.2 + - + +
48A TYR* 3.0 24.3 + + - +
100A PHE* 3.7 28.3 - + - -
123A LEU* 3.8 38.6 - - + -
126A PHE* 3.7 20.0 - - + -
127A ILE* 3.8 23.8 - - + -
130A ILE* 5.5 0.9 - - + -
199A MET* 3.6 28.7 - - + -
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Residues in contact with LEU 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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19A LEU* 2.8 33.0 + - + +
20A CYS* 3.9 1.1 - - - +
22A PHE* 1.3 79.3 - - + +
24A GLU* 1.3 57.4 + - - +
26A ALA* 3.8 1.9 - - - +
27A VAL* 2.8 39.7 + - + +
68A LEU* 3.7 29.2 - - + -
71A VAL* 5.1 1.1 - - + -
75A LEU* 4.8 12.3 - - + -
83A VAL* 4.1 31.4 - - + -
100A PHE* 3.9 44.9 - - + -
102A ILE* 5.0 6.3 - - + -
199A MET* 5.7 0.4 - - - -
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Residues in contact with GLU 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 CYS 3.0 14.5 + - - +
21A GLU* 3.7 10.1 - - - +
22A PHE 3.1 0.4 - - - -
23A LEU* 1.3 78.6 - - - +
25A VAL* 1.3 63.6 + - + +
27A VAL* 3.4 1.2 + - - +
28A HIS* 3.0 48.7 + - + -
54A MET* 4.5 9.7 - - + +
61A ASN* 5.0 3.8 - - - +
64A ILE* 4.2 8.1 - - + -
65A GLN* 3.7 30.3 + - - +
68A LEU* 3.4 21.8 - - + +
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Residues in contact with VAL 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 GLU* 3.3 16.6 + - + +
22A PHE 3.3 7.0 + - - +
24A GLU* 1.3 78.5 - - + +
26A ALA* 1.3 57.2 + - - +
28A HIS* 3.3 4.0 + - - +
29A LEU* 3.0 27.1 + - + +
47A LYS* 3.9 38.6 - - + +
48A TYR* 4.4 10.3 - - + -
52A VAL* 4.1 26.0 - - + -
53A GLN 4.9 0.3 - - - +
54A MET* 4.2 15.5 - - + +
127A ILE* 4.0 19.1 - - + -
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Residues in contact with ALA 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 PHE* 2.8 29.0 + - + +
23A LEU* 3.8 5.6 - - + +
25A VAL* 1.3 73.6 - - - +
27A VAL* 1.3 55.9 + - - +
29A LEU* 3.2 3.1 + - - +
30A ILE* 2.9 36.7 + - - +
100A PHE* 3.9 22.7 - - + -
127A ILE* 4.4 6.5 - - + +
130A ILE* 3.9 23.7 - - + +
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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 LEU* 2.8 31.6 + - + +
24A GLU 3.9 3.1 - - - +
26A ALA* 1.3 68.3 - - + +
28A HIS* 1.3 69.2 + - - +
30A ILE* 3.3 9.2 + - - +
31A LEU* 3.0 38.5 + - + +
64A ILE* 3.8 35.4 - - + -
68A LEU* 5.2 6.3 - - + -
83A VAL* 6.3 1.3 - - + -
85A VAL* 3.8 26.2 - - + -
100A PHE* 6.1 0.2 - - + -
146A PHE* 4.4 11.7 - - + -
148A VAL* 5.1 9.2 - - + -
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Residues in contact with HIS 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 GLU* 3.0 37.9 + - + +
25A VAL 3.5 7.6 - - - +
27A VAL* 1.3 81.6 - - - +
29A LEU* 1.3 62.9 + - - +
31A LEU* 3.4 6.9 + - - +
32A TYR* 3.1 18.2 + - - +
42A PHE* 3.5 11.5 - - - -
53A GLN 3.6 13.7 - - - +
54A MET* 3.6 27.7 - - + +
55A SER* 2.9 32.7 + - - -
61A ASN* 3.1 34.4 + - - +
64A ILE* 3.7 24.8 - - + +
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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 VAL* 3.0 18.8 + - + +
26A ALA* 3.6 5.8 - - - +
28A HIS* 1.3 77.1 - - - +
30A ILE* 1.3 57.6 + - - +
32A TYR* 3.2 13.8 + - + +
33A VAL* 2.9 42.4 + - + +
51A PRO 5.4 0.2 - - - +
52A VAL* 4.6 7.4 - - + -
53A GLN* 3.9 27.3 + - + +
127A ILE* 3.6 39.9 - - + +
130A ILE* 3.6 26.0 - - + -
131A SER* 4.0 12.1 - - - +
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Residues in contact with ILE 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 ALA 2.9 21.9 + - - +
27A VAL* 3.3 4.9 + - - +
29A LEU* 1.3 75.5 - - - +
31A LEU* 1.3 59.4 + - + +
33A VAL* 4.1 6.5 - - - -
34A ARG* 2.8 35.0 + - + +
85A VAL* 4.1 27.4 - - + -
87A ILE* 4.2 7.0 - - + -
98A PHE* 3.7 59.5 - - + -
100A PHE* 4.0 20.2 - - + -
130A ILE* 4.0 18.2 - - + -
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Residues in contact with LEU 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* 3.0 28.0 + - + +
28A HIS* 3.6 6.1 - - - +
30A ILE* 1.3 77.9 - - + +
32A TYR* 1.3 59.3 + - - +
35A GLU* 3.3 1.6 + - - -
36A VAL* 2.9 47.1 + - + -
37A TYR* 3.9 18.6 + - + -
42A PHE* 3.9 11.9 - - + -
60A LEU* 4.2 6.7 - - + -
64A ILE* 3.9 20.4 - - + -
85A VAL* 5.2 5.6 - - + -
87A ILE* 5.7 0.2 - - + -
146A PHE* 3.5 57.7 - - + -
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Residues in contact with TYR 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 HIS 3.1 13.0 + - - +
29A LEU* 3.2 10.3 + - + +
31A LEU* 1.3 75.0 - - - +
33A VAL* 1.3 77.0 + - + +
35A GLU* 2.9 20.6 + - - +
37A TYR 5.2 1.1 - - - +
39A VAL* 4.1 32.3 - - + +
42A PHE* 3.6 41.9 - + + -
53A GLN* 3.6 45.2 + - + -
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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
----------------------------------------------------------
29A LEU* 2.9 37.5 + - + +
30A ILE* 3.8 8.3 - - + +
32A TYR* 1.3 91.4 - - + +
34A ARG* 1.3 90.9 + - + +
35A GLU* 3.3 1.8 + - - +
130A ILE* 3.7 29.4 - - + +
131A SER* 4.0 14.1 - - - +
133A CYS* 3.8 8.7 - - - -
134A ASP* 4.5 12.5 - - + +
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Residues in contact with ARG 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 ILE 2.8 21.2 + - - +
31A LEU 4.0 0.2 - - - -
33A VAL* 1.3 104.5 + - + +
35A GLU* 1.3 68.9 + - - +
36A VAL* 3.2 6.6 + - + +
87A ILE* 3.7 23.3 - - + -
96A GLU* 2.7 41.3 + - - +
98A PHE* 3.9 18.6 - - + -
133A CYS* 4.2 1.1 - - - -
134A ASP* 3.7 25.7 + - - +
137A LEU* 3.6 15.0 + - - +
138A ASP 2.9 23.0 + - - -
139A HIS* 4.4 3.6 + - - +
140A ASN* 3.7 30.2 + - - +
144A CYS* 6.0 0.7 - - - +
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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
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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