Contacts of the helix formed by residues 1 - 28 (chain C) in PDB entry 1D7G
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 1 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ARG* 1.3 66.3 + - - +
3C LEU* 3.5 10.9 - - - +
4C ALA* 3.4 18.6 + - - +
5C ARG* 3.3 25.5 + - - +
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Residues in contact with ARG 2 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A T 4.9 3.0 + - - -
1C GLU* 1.3 77.4 - - - +
3C LEU* 1.3 58.4 + - - +
4C ALA 3.2 1.4 + - - -
5C ARG* 3.3 47.2 + - - +
6C GLU* 2.9 28.2 + - - +
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Residues in contact with LEU 3 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C GLU 4.8 8.1 - - - +
2C ARG* 1.3 73.8 - - - +
4C ALA* 1.3 62.7 + - + +
6C GLU* 2.8 25.0 - - - +
7C ASN* 4.0 9.9 - - - +
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Residues in contact with ALA 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C GLU* 3.4 21.3 + - - +
2C ARG 3.2 0.6 - - - -
3C LEU* 1.3 86.9 - - + +
5C ARG* 1.3 62.6 + - + +
6C GLU* 3.7 0.7 - - - -
7C ASN* 3.5 7.2 - - - +
8C HIS* 3.2 20.5 + - - +
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Residues in contact with ARG 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A G 3.1 21.8 + - - +
13A T 2.9 55.1 + - - +
14A G 6.0 0.9 - - - +
1C GLU 3.3 13.0 + - - +
2C ARG* 3.3 40.9 + - - +
4C ALA* 1.3 75.6 - - + +
6C GLU* 1.3 74.4 + - - +
8C HIS* 3.0 23.8 + - - +
9C SER* 2.8 40.5 + - - +
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Residues in contact with GLU 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ARG* 2.9 26.5 + - - +
3C LEU* 2.8 34.0 - - - +
5C ARG* 1.3 90.0 - - - +
7C ASN* 1.3 63.4 + - - +
9C SER* 3.2 4.4 + - - -
10C GLU* 3.0 45.9 + - + +
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Residues in contact with ASN 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B C 5.9 0.8 + - - -
3C LEU 4.0 11.6 - - - +
4C ALA* 3.5 12.1 - - - +
5C ARG 3.3 0.2 - - - -
6C GLU* 1.3 82.9 + - - +
8C HIS* 1.3 55.9 + - - +
10C GLU* 3.2 14.2 + - - +
11C ILE* 3.1 34.2 + - - +
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Residues in contact with HIS 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A T 3.3 56.3 + + + +
14A G 3.2 41.6 + - - -
15A C 4.6 4.2 + - - -
7B A 6.0 0.2 + - - -
8B G 4.4 6.5 + - - -
4C ALA 3.2 9.9 + - - +
5C ARG* 3.0 16.3 + - - +
7C ASN* 1.3 74.7 - - - +
9C SER* 1.3 60.6 + - - +
11C ILE* 3.3 25.5 - - + +
12C GLU* 3.5 7.7 + - + +
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Residues in contact with SER 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A G 3.0 39.0 + - - +
13A T 4.6 2.2 - - - -
5C ARG* 2.8 43.0 + - - +
6C GLU* 3.2 7.2 + - - -
8C HIS* 1.3 74.9 - - - +
10C GLU* 1.3 53.1 + - - +
12C GLU* 3.1 6.7 + - - +
13C ARG* 2.7 35.7 + - - +
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Residues in contact with GLU 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLU* 3.0 39.8 + - + +
7C ASN* 3.2 14.7 + - - +
9C SER* 1.3 74.8 - - - +
11C ILE* 1.3 61.5 + - - +
13C ARG* 3.2 21.8 - - - +
14C ARG* 3.3 10.0 + - - +
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Residues in contact with ILE 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B C 4.2 29.8 - - + +
7B A 4.6 5.4 - - - +
7C ASN* 3.1 23.6 + - - +
8C HIS* 3.3 31.9 - - + +
10C GLU* 1.3 73.5 - - - +
12C GLU* 1.3 60.2 + - + +
14C ARG* 3.3 27.8 + - - +
15C ARG* 2.9 51.4 + - - +
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Residues in contact with GLU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A G 3.3 11.4 - - + +
13A T 2.8 35.9 - - + +
9B C 2.9 26.6 + - - +
10B A 3.5 1.0 + - - -
8C HIS* 3.5 14.4 - - - +
9C SER* 3.1 6.0 + - - +
11C ILE* 1.3 80.3 - - + +
13C ARG* 1.3 57.6 + - - +
15C ARG* 3.6 19.9 - - - +
16C ARG* 2.9 75.8 + - - +
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Residues in contact with ARG 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A C 2.8 46.0 + - - -
12A G 5.7 4.4 + - - +
9C SER 2.7 15.9 + - - +
10C GLU* 3.2 17.3 - - - +
12C GLU* 1.3 71.9 - - - +
14C ARG* 1.3 57.4 + - - +
15C ARG 3.2 0.5 + - - -
16C ARG* 3.5 21.6 - - - +
17C ASN* 3.0 49.2 + - - +
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Residues in contact with ARG 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B C 4.9 3.4 - - - -
7B A 2.9 37.1 + - - -
10C GLU 3.3 7.5 + - - +
11C ILE* 3.3 26.7 + - - +
13C ARG* 1.3 77.4 - - - +
15C ARG* 1.3 58.3 + - - +
17C ASN* 2.8 28.4 - - - +
18C LYS* 3.6 27.3 - - - +
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Residues in contact with ARG 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B A 3.3 39.2 + - - +
8B G 3.3 42.0 + - + -
9B C 4.1 8.5 - - - -
11C ILE* 2.9 45.8 + - - +
12C GLU* 3.7 32.8 + - - +
13C ARG 3.1 0.4 - - - -
14C ARG* 1.3 77.5 - - - +
16C ARG* 1.3 66.5 + - - +
18C LYS* 3.3 51.3 - - - +
19C MET* 3.5 18.7 + - + +
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Residues in contact with ARG 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A A 6.0 3.1 - - + -
11A C 3.2 38.2 - - + +
12A G 2.7 31.5 + - - -
9B C 5.4 1.6 - - - -
10B A 3.2 16.0 + - - +
11B C 3.2 17.2 - - - +
12C GLU* 2.9 57.3 + - - +
13C ARG* 3.5 15.9 - - - +
15C ARG* 1.3 76.6 - - - +
17C ASN* 1.3 62.8 + - - +
19C MET* 3.4 16.7 - - + +
20C THR* 3.4 25.1 + - - +
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Residues in contact with ASN 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ARG* 3.0 41.8 + - - +
14C ARG* 2.8 36.5 - - - +
16C ARG* 1.3 75.9 - - - +
18C LYS* 1.3 64.5 + - - +
20C THR* 2.8 23.4 + - - +
21C ALA* 3.1 13.7 + - - +
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Residues in contact with LYS 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B A 4.9 1.0 - - - -
8B G 3.0 28.2 + - - -
14C ARG* 3.6 31.8 + - - +
15C ARG* 3.3 44.7 + - - +
17C ASN* 1.3 79.0 + - - +
19C MET* 1.3 74.2 + - + +
21C ALA* 3.4 9.3 + - + +
22C TYR* 3.0 56.7 + - + +
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Residues in contact with MET 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B G 5.9 1.8 - - + -
9B C 4.1 19.1 - - - +
15C ARG* 3.5 28.0 - - + +
16C ARG* 3.4 20.6 + - + +
18C LYS* 1.3 95.2 - - + +
20C THR* 1.3 59.1 + - + +
22C TYR* 3.1 15.4 + - + +
23C ILE* 3.1 30.3 + - + +
23D PHE* 5.4 5.2 - - - -
44D SER* 5.9 0.4 - - - +
46D MET* 3.9 26.5 - - + -
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Residues in contact with THR 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A A 3.2 34.8 - - - +
16C ARG 3.4 10.5 + - - +
17C ASN* 2.8 26.9 + - - +
19C MET* 1.3 73.0 - - + +
21C ALA* 1.3 63.4 + - - +
23C ILE* 3.3 13.1 + - + +
24C THR* 3.1 25.3 + - - +
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ASN 3.1 15.7 + - - +
18C LYS* 3.4 15.5 - - + +
19C MET 3.3 0.2 - - - -
20C THR* 1.3 75.5 - - - +
22C TYR* 1.3 64.2 + - + +
24C THR* 3.2 11.0 - - - +
25C GLU* 3.0 38.8 + - - +
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Residues in contact with TYR 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LYS* 3.0 52.8 + - + +
19C MET* 3.1 15.3 + - + +
21C ALA* 1.3 75.4 - - + +
23C ILE* 1.3 56.6 + - + +
25C GLU* 3.6 20.5 + - - +
26C LEU* 2.9 31.7 + - - +
46D MET* 3.4 51.4 - - + -
50D ILE* 5.6 10.1 - - + -
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Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C MET* 3.1 16.4 + - + +
20C THR* 3.5 18.2 - - + +
21C ALA 3.3 0.2 - - - -
22C TYR* 1.3 76.0 - - + +
24C THR* 1.3 57.9 + - - +
26C LEU* 3.4 8.9 + - + +
27C SER* 2.9 27.4 + - - -
45C ILE* 3.6 32.3 - - + +
46C LEU* 4.0 30.7 - - + -
19D GLU* 5.6 5.2 - - - +
23D PHE* 6.1 5.2 - - + -
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Residues in contact with THR 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C THR 3.1 15.7 + - - +
21C ALA* 3.2 21.1 - - - +
23C ILE* 1.3 73.4 - - - +
25C GLU* 1.3 66.8 + - + +
27C SER* 3.3 9.2 + - - -
28C ASP* 2.9 37.9 + - - +
45C ILE* 6.1 0.2 - - - -
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Residues in contact with GLU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA* 3.0 37.6 + - - +
22C TYR* 3.7 21.6 + - - +
24C THR* 1.3 77.6 - - + +
26C LEU* 1.3 60.7 + - - +
28C ASP* 3.1 23.3 + - - +
29C MET* 3.5 14.1 + - - +
50D ILE* 5.2 9.0 - - - +
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Residues in contact with LEU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C TYR 2.9 19.7 + - - +
23C ILE* 3.4 8.5 + - + +
25C GLU* 1.3 73.7 - - - +
27C SER* 1.3 57.0 + - - +
29C MET* 3.0 35.0 + - + -
44C THR 4.9 0.7 - - - +
45C ILE* 4.2 18.6 - - + +
46C LEU* 4.3 15.9 - - + -
49C ALA* 4.1 30.7 - - + -
22D VAL* 6.3 0.7 - - + -
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Residues in contact with SER 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE 2.9 17.4 + - - -
24C THR* 3.3 11.2 + - - -
26C LEU* 1.3 71.3 - - - +
28C ASP* 1.3 59.7 + - - +
29C MET 3.1 8.7 + - - -
30C VAL* 3.5 16.3 - - - +
32C THR* 3.4 12.2 + - - +
40C PRO* 4.8 6.9 - - - +
44C THR* 3.2 33.8 + - - +
45C ILE* 3.9 13.5 - - - +
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Residues in contact with ASP 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C THR* 2.9 30.1 + - - +
25C GLU* 3.1 12.2 + - - +
27C SER* 1.3 74.2 + - - +
29C MET* 1.3 70.4 + - - +
30C VAL 3.1 7.8 - - - +
31C PRO* 5.2 0.2 - - - +
32C THR* 3.5 30.8 + - - +
33C CYS* 6.1 0.2 - - - -
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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