Contacts of the helix formed by residues 9 - 31 (chain A) in PDB entry 6GA6
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 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ARG* 3.5 19.9 - - + +
8A PRO* 1.3 87.4 - - - +
10A TRP* 1.3 65.5 + - - +
11A ILE 3.1 3.4 - - - -
12A TRP* 3.1 23.4 + - - +
13A LEU* 3.2 18.2 + - + +
66A LEU* 5.4 0.5 - - - +
77A PRO* 5.7 0.3 - - - +
79A TYR* 2.5 37.2 + - + +
201A LEU* 3.6 20.8 - - - +
202A ASN* 3.9 13.7 + - - +
205A THR* 3.5 29.4 - - - +
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Residues in contact with TRP 10 (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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4A ILE* 3.4 33.0 - - + +
5A THR* 3.6 43.6 + - + +
7A ARG* 3.0 28.9 + - + +
8A PRO* 3.1 8.2 + - + -
9A GLU* 1.3 78.9 - - - +
11A ILE* 1.3 83.6 + - + +
13A LEU* 3.1 13.4 + - + +
14A ALA* 2.8 45.4 + - + +
61A LEU* 3.7 5.5 - - + +
304A D10 5.4 7.6 - - + -
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Residues in contact with ILE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO 3.7 15.9 - - - +
10A TRP* 1.3 115.8 - - + +
12A TRP* 1.3 97.8 + - + +
14A ALA* 3.4 3.0 + - + +
15A LEU* 2.9 34.0 + - + +
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Residues in contact with TRP 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 PRO 4.8 1.0 + - - -
9A GLU* 3.1 17.4 + - - +
11A ILE* 1.3 102.5 - - + +
13A LEU* 1.3 62.5 + - - +
15A LEU* 4.2 17.7 - - + -
16A GLY* 2.9 24.4 + - - -
57A TYR* 4.4 0.3 - - - -
202A ASN* 3.3 35.8 + - - +
203A ILE* 5.4 2.3 - - + +
205A THR* 3.9 13.9 - - + +
206A LEU* 3.7 48.8 - - + +
209A MET* 3.4 26.1 - - + +
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Residues in contact with LEU 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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7A ARG* 3.9 5.4 - - - +
9A GLU* 3.2 17.1 + - + +
10A TRP* 3.1 10.9 + - - +
12A TRP* 1.3 74.9 - - - +
14A ALA* 1.3 55.7 + - - +
16A GLY 3.4 0.2 + - - -
17A THR* 2.7 38.7 + - - -
57A TYR* 3.7 21.9 - - + +
60A MET* 3.8 44.2 - - + +
61A LEU* 4.0 16.6 - - + +
79A TYR* 3.6 28.3 - - + +
82A ARG* 4.6 2.5 - - - +
205A THR* 3.6 21.3 - - + -
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Residues in contact with ALA 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 TRP* 2.8 37.7 + - + +
11A ILE* 3.6 7.0 - - + +
13A LEU* 1.3 74.9 - - - +
15A LEU* 1.3 63.7 + - - +
17A THR* 3.3 3.7 + - - -
18A ALA* 3.0 25.1 + - - +
61A LEU* 3.9 17.2 - - + +
304A D10 4.0 19.1 - - + +
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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 ILE* 2.9 21.9 + - + +
12A TRP* 4.2 18.6 - - + -
14A ALA* 1.3 75.1 - - - +
16A GLY* 1.3 59.1 + - - +
18A ALA* 3.2 7.3 + - + +
19A LEU* 2.9 59.0 + - + +
209A MET* 3.6 22.9 - - + -
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Residues in contact with GLY 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 TRP 2.9 18.7 + - - -
13A LEU 3.8 1.3 - - - -
14A ALA 3.2 0.2 - - - -
15A LEU* 1.3 77.0 - - - +
17A THR* 1.3 62.0 + - - +
19A LEU* 3.3 3.2 + - - +
20A MET* 3.0 29.4 + - - +
57A TYR* 3.8 15.5 - - - -
209A MET* 3.6 19.9 - - - +
213A VAL* 4.9 2.9 - - - -
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Residues in contact with THR 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 LEU 2.7 25.4 + - - -
14A ALA* 3.5 6.7 - - - -
16A GLY* 1.3 77.3 - - - +
18A ALA* 1.3 57.5 + - - +
20A MET* 3.9 1.5 - - - -
21A GLY* 2.9 23.7 + - - -
54A PHE* 3.4 33.9 - - + +
57A TYR* 3.4 27.2 + - - +
58A LEU* 3.6 22.9 + - + -
61A LEU* 4.3 5.2 - - - +
304A D10 3.6 17.0 - - + -
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Residues in contact with ALA 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 ALA 3.0 17.0 + - - +
15A LEU* 3.6 9.9 - - + +
17A THR* 1.3 76.3 - - - +
19A LEU* 1.3 60.2 + - + +
21A GLY* 3.2 0.5 + - - -
22A LEU* 2.8 40.7 + - + +
304A D10 4.0 29.8 - - + +
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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 LEU* 2.9 44.0 + - + +
16A GLY 4.0 2.5 - - - +
18A ALA* 1.3 74.6 - - + +
20A MET* 1.3 62.6 + - - +
22A LEU* 3.9 8.1 - - + +
23A GLY* 2.9 25.3 + - - -
209A MET* 4.3 10.5 - - - -
213A VAL* 3.9 37.5 - - + -
217A VAL* 4.0 6.7 - - - +
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Residues in contact with MET 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 GLY 3.0 22.7 + - - +
17A THR 3.9 0.7 - - - +
19A LEU* 1.3 73.3 - - - +
21A GLY* 1.3 57.1 + - - +
23A GLY* 3.7 0.5 - - - -
24A THR* 2.8 39.4 + - - -
50A PRO* 3.7 21.5 - - - +
53A ALA* 3.8 22.7 - - + -
54A PHE* 3.7 14.4 - - - +
57A TYR* 4.2 10.1 - - + -
212A ASP* 3.6 45.5 - - + +
213A VAL* 3.8 11.2 - - + +
216A LYS* 3.7 15.5 - - + -
217A VAL* 4.1 17.7 - - - -
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Residues in contact with GLY 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 THR 2.9 15.5 + - - -
18A ALA* 3.6 3.4 - - - -
20A MET* 1.3 76.5 - - - +
22A LEU* 1.3 59.5 + - - +
24A THR* 3.2 6.7 + - - -
25A LEU* 3.0 36.1 + - - +
54A PHE* 3.7 20.8 - - - -
304A D10 5.4 4.5 - - - -
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Residues in contact with LEU 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 ALA* 2.8 33.9 + - + +
19A LEU* 4.0 9.9 - - + +
21A GLY* 1.3 73.2 - - - +
23A GLY* 1.3 59.0 + - - +
25A LEU* 3.3 10.9 + - + +
26A TYR* 2.9 31.6 + - - +
304A D10 3.6 37.2 - - + -
314A OCT 4.8 13.7 - - + +
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Residues in contact with GLY 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 2.9 19.5 + - - -
20A MET 3.7 1.3 - - - -
22A LEU* 1.3 76.3 - - - +
24A THR* 1.3 61.3 + - - +
26A TYR* 3.3 6.3 + - - +
27A PHE* 3.0 33.5 + - - -
50A PRO* 4.4 1.8 - - - -
217A VAL* 4.2 24.0 - - - -
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Residues in contact with THR 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 MET 2.8 27.0 + - - -
21A GLY* 3.2 8.3 + - - -
23A GLY* 1.3 73.8 - - - +
25A LEU* 1.3 68.7 + - + +
27A PHE* 3.3 1.1 + - - -
28A LEU* 2.9 26.4 + - + +
47A THR* 3.9 14.3 - - + +
50A PRO* 3.1 11.1 + - - +
51A ALA* 3.1 43.0 + - + -
54A PHE* 4.6 2.0 - - + +
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Residues in contact with LEU 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 GLY 3.0 21.2 + - - +
22A LEU* 3.7 11.4 - - + +
24A THR* 1.3 80.5 - - + +
26A TYR* 1.3 63.7 + - - +
28A LEU* 3.3 16.3 + - + +
29A VAL* 3.0 32.7 + - + +
304A D10 4.5 21.3 - - + -
314A OCT 4.4 12.6 - - + -
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Residues in contact with TYR 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 LEU 2.9 18.0 + - - +
23A GLY* 3.7 6.1 - - - +
25A LEU* 1.3 78.6 - - - +
27A PHE* 1.3 73.1 + + - +
29A VAL* 3.3 1.4 + - - +
30A LYS* 2.9 61.4 + - + +
221A LEU* 3.6 26.2 - - + +
225A ARG* 5.7 3.3 - - - +
314A OCT 3.9 53.2 - - + +
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Residues in contact with PHE 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 GLY 3.0 20.6 + - - +
24A THR 3.9 2.7 - - - +
26A TYR* 1.3 88.7 - + - +
28A LEU* 1.3 62.9 + - - +
30A LYS* 3.8 6.2 - - + +
31A GLY* 3.0 20.8 + - - -
43A TYR* 3.8 3.6 - - - -
46A THR* 3.6 31.4 - - + -
47A THR* 3.4 21.6 + - + +
50A PRO* 3.9 16.6 - - + -
216A LYS 4.3 1.6 - - - -
217A VAL* 3.7 38.4 - - + -
220A GLY* 3.7 18.2 - - - -
221A LEU* 3.8 24.2 - - + -
224A LEU* 3.6 18.4 - - + -
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Residues in contact with LEU 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 THR* 2.9 21.2 + - + +
25A LEU* 3.6 18.6 - - + +
26A TYR 3.2 0.2 - - - -
27A PHE* 1.3 77.4 - - - +
29A VAL* 1.3 64.3 + - + +
31A GLY* 3.4 8.3 + - - -
32A MET* 3.3 19.9 + - + +
47A THR* 4.0 17.0 - - + +
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Residues in contact with VAL 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 LEU* 3.0 22.9 + - + +
26A TYR 3.8 2.7 - - - +
28A LEU* 1.3 79.7 - - + +
30A LYS* 1.3 64.0 + - - +
32A MET* 3.1 37.5 + - - +
33A GLY 4.5 0.7 + - - -
314A OCT 3.8 50.4 - - + +
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Residues in contact with LYS 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 TYR* 2.9 51.3 + - + +
27A PHE* 3.8 7.9 - - + +
29A VAL* 1.3 79.3 - - - +
31A GLY* 1.3 60.3 + - - +
32A MET 3.5 0.9 + - - -
33A GLY* 4.1 6.1 + - - -
34A VAL* 4.2 4.3 - - - +
43A TYR* 2.7 36.6 + - + +
221A LEU* 6.1 0.2 - - + -
224A LEU* 2.9 28.2 + - + -
225A ARG* 4.4 18.9 - - - +
314A OCT 4.6 13.5 - - + -
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Residues in contact with GLY 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 PHE 3.0 12.3 + - - -
28A LEU 3.4 4.0 + - - -
29A VAL 3.2 0.6 - - - -
30A LYS* 1.3 75.3 - - - +
32A MET* 1.3 63.5 + - - +
33A GLY 3.3 2.0 + - - -
34A VAL* 3.4 20.2 + - - +
43A TYR* 3.5 30.1 - - - +
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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