Contacts of the helix formed by residues 5 - 29 (chain A) in PDB entry 1IME
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 TRP 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A GLN* 1.3 60.6 + - - +
7A GLU* 3.3 7.2 - - - +
8A CYS* 3.3 20.2 + - - +
9A MET* 3.0 26.9 + - - +
65A HIS* 4.9 5.4 - + - -
85A PRO* 4.0 21.8 - - + -
111A PHE* 3.8 31.2 - + + -
113A VAL* 3.7 24.8 - - + +
118A GLU* 3.6 34.0 - - + +
119A PHE* 3.8 6.8 - - + -
134A ARG* 3.7 21.4 - - - +
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Residues in contact with GLN 6 (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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5A TRP* 1.3 73.6 - - - +
7A GLU* 1.3 59.4 + - - +
9A MET* 4.0 21.6 - - - +
10A ASP* 2.8 44.5 + - - +
134A ARG* 3.0 38.3 + - - +
137A LYS* 5.8 0.5 - - - +
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Residues in contact with GLU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TRP* 5.0 3.8 - - - +
6A GLN* 1.3 76.5 - - - +
8A CYS* 1.3 74.5 + - - +
10A ASP* 3.3 7.4 + - - +
11A TYR* 3.0 23.6 + - - +
61A LYS* 5.4 4.2 + - - +
62A TYR* 3.2 27.7 + - - +
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Residues in contact with CYS 8 (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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5A TRP* 3.3 35.2 + - - +
7A GLU* 1.3 85.8 - - - +
9A MET* 1.3 54.3 + - - +
11A TYR* 2.9 6.1 + - - +
12A ALA* 2.8 33.1 + - - +
62A TYR* 3.5 35.0 - - - -
65A HIS* 4.1 14.8 - - - -
87A TRP* 3.8 18.7 - - + -
111A PHE* 4.3 2.9 - - - -
119A PHE* 3.9 11.0 - - + -
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Residues in contact with MET 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TRP 3.0 16.8 + - - +
6A GLN* 3.6 21.5 - - - +
7A GLU 3.3 0.2 - - - -
8A CYS* 1.3 75.6 - - - +
10A ASP* 1.3 63.2 + - - +
12A ALA* 3.3 1.2 + - - +
13A VAL* 3.1 26.7 + - + +
119A PHE* 3.6 30.4 - - + -
120A GLY 4.2 7.4 - - - +
121A VAL* 4.5 5.8 - - + -
132A THR* 3.9 29.8 - - + -
133A ALA 3.8 19.3 - - - +
134A ARG* 3.8 31.6 - - + +
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Residues in contact with ASP 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN* 2.8 35.1 + - - +
7A GLU* 3.8 7.3 - - - +
8A CYS 3.3 0.2 - - - -
9A MET* 1.3 73.4 - - - +
11A TYR* 1.3 59.9 + - - +
13A VAL* 3.3 7.9 + - - +
14A THR* 3.0 26.0 + - - -
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Residues in contact with TYR 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU 3.0 13.0 + - - +
8A CYS* 2.9 10.7 + - - +
10A ASP* 1.3 74.2 - - - +
12A ALA* 1.3 54.1 + - - +
14A THR* 2.9 18.4 + - + -
15A LEU* 2.8 68.9 + - + +
57A SER* 3.2 39.7 + - - -
58A ILE* 4.1 5.6 - - - -
60A GLU* 4.4 8.3 + - - -
61A LYS* 3.5 42.0 - - + +
62A TYR* 3.6 19.5 - + - +
87A TRP* 5.0 3.6 - + - -
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Residues in contact with ALA 12 (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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8A CYS 2.8 17.6 + - - +
9A MET 3.6 5.4 - - - +
11A TYR* 1.3 75.1 - - - +
13A VAL* 1.4 55.5 + - - +
15A LEU* 3.4 13.2 + - - +
16A ALA* 2.9 30.1 + - - +
87A TRP* 3.5 24.2 - - + -
109A ILE* 3.6 11.3 - - + +
119A PHE* 3.8 15.3 - - + -
121A VAL* 4.4 8.3 - - + -
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Residues in contact with VAL 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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9A MET* 3.1 23.6 + - + +
10A ASP* 3.6 9.6 - - - +
11A TYR 3.2 0.2 - - - -
12A ALA* 1.4 70.5 - - - +
14A THR* 1.3 66.4 + - - +
16A ALA* 3.5 2.3 + - - +
17A ARG* 3.1 45.5 + - - +
121A VAL* 3.9 23.8 - - + -
130A MET* 3.8 15.3 - - + +
132A THR* 3.9 15.7 - - + -
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Residues in contact with THR 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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10A ASP 3.0 16.1 + - - -
11A TYR* 2.9 19.8 + - + -
13A VAL* 1.3 74.3 - - - +
15A LEU* 1.3 66.4 + - + +
17A ARG* 3.4 7.9 + - - +
18A GLN* 3.1 40.4 + - + +
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Residues in contact with LEU 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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11A TYR* 2.8 50.0 + - + +
12A ALA* 3.6 13.2 - - - +
13A VAL 3.3 0.2 - - - -
14A THR* 1.3 73.6 - - + +
16A ALA* 1.3 63.8 + - - +
18A GLN* 2.9 29.3 + - + +
19A ALA* 2.9 14.6 + - - +
54A LEU* 4.0 20.4 - - + +
57A SER* 3.7 26.2 - - - +
58A ILE* 3.5 37.0 - - + -
87A TRP* 5.2 0.2 - - + -
109A ILE* 4.6 3.1 - - + -
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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 ALA 2.9 18.4 + - - +
13A VAL 3.8 4.3 - - - +
15A LEU* 1.3 74.8 - - - +
17A ARG* 1.3 56.7 + - - +
19A ALA* 3.8 6.1 - - - +
20A GLY* 2.8 28.4 + - - -
107A VAL* 4.5 10.3 - - + +
109A ILE* 4.0 14.6 - - + +
121A VAL* 3.8 22.4 - - + -
123A TYR* 3.6 16.9 - - + +
130A MET* 4.3 4.9 - - + -
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Residues in contact with ARG 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 VAL* 3.1 26.8 + - - +
14A THR* 3.7 7.2 - - - +
15A LEU 3.3 0.2 - - - -
16A ALA* 1.3 75.5 - - - +
18A GLN* 1.3 57.7 + - + +
20A GLY* 3.4 1.2 + - - -
21A GLU* 3.0 43.5 + - + +
123A TYR* 4.2 27.6 + - + +
130A MET* 3.7 41.0 - - + +
142A ASN* 5.2 4.8 - - - +
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Residues in contact with GLN 18 (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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14A THR* 3.1 25.6 + - + +
15A LEU* 2.9 24.3 + - + +
17A ARG* 1.3 73.8 - - + +
19A ALA* 1.3 66.2 + - - +
21A GLU* 3.0 26.2 + - - +
22A VAL* 3.0 18.1 + - - +
53A MET* 5.3 5.6 - - - -
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Residues in contact with ALA 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 LEU 2.9 17.0 + - - +
16A ALA 3.8 3.8 - - - +
18A GLN* 1.3 71.6 - - - +
20A GLY* 1.3 56.4 + - - +
22A VAL* 2.8 28.0 + - - +
23A VAL* 2.9 18.8 + - - +
50A VAL* 3.7 26.9 - - + -
53A MET* 4.6 7.4 - - - -
54A LEU* 3.9 17.7 - - + -
107A VAL* 4.1 11.7 - - + -
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Residues in contact with GLY 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 22.7 + - - -
17A ARG 3.8 0.7 - - - -
18A GLN 3.1 0.4 - - - -
19A ALA* 1.3 71.4 - - - +
21A GLU* 1.3 55.8 + - - +
23A VAL* 3.5 2.3 + - - +
24A CYS* 3.0 33.3 + - - +
107A VAL* 3.9 3.5 - - - +
123A TYR* 3.6 24.0 - - - -
125A CYS* 3.8 13.1 - - - +
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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 ARG* 3.0 29.4 + - + +
18A GLN* 3.0 21.8 + - - +
20A GLY* 1.3 73.4 - - - +
22A VAL* 1.3 67.8 + - + +
24A CYS* 3.3 5.9 + - - +
25A GLU* 3.1 24.6 + - - +
123A TYR* 5.5 3.8 - - - +
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Residues in contact with VAL 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 GLN 3.0 13.8 + - - +
19A ALA 2.8 8.1 + - - +
21A GLU* 1.3 79.4 - - + +
23A VAL* 1.3 63.0 + - - +
25A GLU* 3.3 4.7 + - - +
26A ALA* 3.1 21.7 + - + +
46A THR* 4.5 4.9 - - + -
49A LYS* 4.3 20.4 - - + +
50A VAL* 3.7 21.8 - - + -
53A MET* 3.8 26.5 - - + -
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Residues in contact with VAL 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 ALA 2.9 15.9 + - - +
20A GLY 3.8 6.7 - - - +
22A VAL* 1.3 75.1 - - - +
24A CYS* 1.3 56.7 + - - +
26A ALA* 3.1 8.2 + - - +
27A ILE* 3.0 27.9 + - + +
46A THR* 4.4 2.2 - - + -
50A VAL* 3.9 17.0 - - + -
91A PRO 4.3 7.4 - - - +
92A ILE* 3.9 24.5 - - + -
98A PHE* 3.6 24.8 - - + -
105A VAL* 4.0 13.7 - - + -
107A VAL* 4.3 7.6 - - + -
125A CYS* 3.9 18.8 - - + -
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Residues in contact with CYS 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 GLY 3.0 13.6 + - - +
21A GLU* 4.0 6.1 - - - +
22A VAL 3.3 0.6 - - - -
23A VAL* 1.3 75.2 - - - +
25A GLU* 1.3 63.1 + - - +
27A ILE* 3.3 16.4 - - - +
28A LYS* 3.2 23.1 - - - +
125A CYS* 3.2 48.9 - - - -
126A VAL* 3.7 15.5 - - - -
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Residues in contact with GLU 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 3.1 16.0 + - - +
22A VAL* 3.9 5.0 - - - +
24A CYS* 1.3 76.5 - - - +
26A ALA* 1.3 66.5 + - - +
28A LYS* 3.1 31.3 + - + +
29A ASN* 3.9 12.5 + - - +
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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 VAL* 3.1 17.3 + - + +
23A VAL 3.1 4.7 + - - +
25A GLU* 1.3 79.0 - - - +
27A ILE* 1.3 60.2 + - - +
28A LYS 3.2 1.2 + - - -
29A ASN* 3.2 21.8 + - - +
31A MET* 3.5 12.5 - - - +
46A THR* 3.8 28.3 - - + +
98A PHE* 3.8 8.9 - - + -
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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 VAL* 3.0 13.6 + - + +
24A CYS* 3.3 28.5 - - - +
26A ALA* 1.3 75.8 - - - +
28A LYS* 1.3 67.7 + - + +
29A ASN 3.2 3.3 + - - +
31A MET* 3.7 12.9 - - - +
98A PHE* 3.9 37.5 - - + +
101A ARG* 3.6 43.7 - - + +
102A PHE 5.0 1.1 - - - +
103A PRO* 5.7 0.4 - - + -
105A VAL* 4.4 6.5 - - + -
126A VAL* 4.2 26.0 - - + -
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A CYS* 3.2 23.7 + - - +
25A GLU* 3.6 18.4 - - + +
26A ALA 3.1 1.6 - - - -
27A ILE* 1.3 84.8 - - + +
29A ASN* 1.3 68.1 + - - +
101A ARG* 5.5 3.8 - - - +
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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
----------------------------------------------------------
25A GLU* 3.9 16.9 + - - +
26A ALA* 3.2 12.9 + - - +
27A ILE 3.2 2.6 - - - +
28A LYS* 1.3 98.9 + - - +
30A GLU* 1.3 71.2 + - + +
31A MET* 3.6 18.2 + - - +
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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) + - + + + + + -
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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