Contacts of the helix formed by residues 4 - 26 (chain A) in PDB entry 1PVI
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 PRO 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER 4.4 3.4 - - - +
3A HIS* 1.4 102.6 - - + +
5A ASP* 1.3 64.1 + - - +
6A LEU 3.1 1.0 + - - -
7A ASN* 3.2 26.5 + - - +
8A LYS* 4.4 3.8 + - - -
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Residues in contact with ASP 5 (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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3A HIS* 3.1 21.4 + - - +
4A PRO* 1.3 78.0 - - - +
6A LEU* 1.3 55.1 + - - +
7A ASN 3.1 0.4 - - - -
8A LYS* 2.6 63.1 + - - +
9A LEU 3.1 8.7 + - - -
22B LEU* 3.6 14.9 - - + +
25B LYS* 3.6 20.2 + - - +
26B HIS* 2.8 32.8 - - + -
44B LEU* 3.9 9.7 - - + +
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Residues in contact with LEU 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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2A SER* 4.0 18.6 - - - +
3A HIS 2.9 16.6 + - - +
5A ASP* 1.3 77.4 - - - +
7A ASN* 1.3 66.2 - - - +
8A LYS 3.2 0.2 + - - -
9A LEU* 3.2 17.0 + - + -
10A LEU* 3.2 42.1 + - + +
41B GLN* 5.4 1.1 - - + +
44B LEU* 3.9 35.2 - - + +
45B ILE* 4.4 23.3 - - + -
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Residues in contact with ASN 7 (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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3A HIS 5.3 0.9 - - - +
4A PRO* 3.2 16.7 + - - +
5A ASP 3.1 0.8 - - - -
6A LEU* 1.3 81.1 - - - +
8A LYS* 1.3 63.7 + - - +
10A LEU* 3.7 8.6 + - - +
11A GLU* 3.4 33.0 + - - +
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Residues in contact with LYS 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO 4.7 3.3 + - - -
5A ASP* 2.6 50.3 + - - +
7A ASN* 1.3 79.3 - - - +
9A LEU* 1.3 64.3 + - - +
11A GLU* 3.0 24.9 + - - +
12A LEU* 3.4 17.2 + - + +
22B LEU* 3.9 19.9 - - + +
25B LYS* 4.4 9.1 - - - +
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASP 3.1 5.7 + - - -
6A LEU* 3.2 18.8 + - + +
8A LYS* 1.3 78.7 - - - +
10A LEU* 1.3 68.3 + - + +
12A LEU* 3.2 3.7 + - - +
13A TRP* 3.1 35.3 + - + +
16A ILE* 4.4 0.2 - - + -
19B TYR* 3.2 37.2 - - + +
22B LEU* 4.1 8.8 - - + +
40B LEU* 4.6 2.9 - - + -
41B GLN* 3.7 37.5 - - + +
44B LEU* 3.9 28.0 - - + -
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Residues in contact with LEU 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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6A LEU* 3.2 35.2 + - + +
7A ASN* 4.2 7.2 - - - +
9A LEU* 1.3 81.8 - - + +
11A GLU* 1.3 62.5 + - - +
13A TRP* 3.6 12.9 + - + +
14A PRO* 3.5 15.8 - - - +
41B GLN* 6.1 3.1 - - - +
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Residues in contact with GLU 11 (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 ASN* 3.4 22.9 + - - +
8A LYS* 3.0 18.9 + - - +
10A LEU* 1.3 78.4 - - + +
12A LEU* 1.3 64.8 + - + +
14A PRO* 3.4 13.9 - - - +
15A HIS* 4.0 9.0 + - - -
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Residues in contact with LEU 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 LYS* 3.6 16.4 - - + +
9A LEU* 3.2 5.5 + - - +
11A GLU* 1.3 80.4 - - + +
13A TRP* 1.3 53.4 + - - +
15A HIS* 2.7 42.9 + - + +
16A ILE* 3.3 14.8 + - + +
15B HIS* 4.0 19.3 - - + +
18B GLU* 4.0 33.9 - - + +
19B TYR* 4.0 37.2 - - + +
22B LEU* 4.2 14.8 - - + -
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Residues in contact with TRP 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 LEU* 3.1 40.5 + - + +
10A LEU* 3.9 15.3 - - + +
12A LEU* 1.3 73.8 - - - +
14A PRO* 1.3 61.7 - - + +
15A HIS 2.6 2.3 + - - -
16A ILE* 2.5 51.1 + - + +
17A GLN* 2.9 28.9 + - + +
32A PHE* 4.6 15.0 - + - -
19B TYR* 3.8 12.3 - + - -
37B GLY 5.3 0.7 - - - -
38B LYS* 5.8 0.7 - - + -
41B GLN* 3.2 42.8 - - - -
107B ILE* 3.1 38.1 + - + +
108B ALA* 4.9 3.6 - - - +
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Residues in contact with PRO 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 LEU 3.5 8.3 - - - +
11A GLU 3.4 18.2 - - - +
12A LEU 3.4 0.2 - - - -
13A TRP* 1.3 92.4 - - + +
15A HIS* 1.3 69.2 + - + +
17A GLN* 4.1 18.2 - - - +
18A GLU* 3.5 24.8 + - - +
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Residues in contact with HIS 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 GLU 4.0 14.0 + - - -
12A LEU* 2.7 24.6 + - + +
13A TRP 2.6 4.4 + - - -
14A PRO* 1.3 80.2 - - + +
16A ILE* 1.3 63.5 + - + +
17A GLN 3.3 0.2 - - - -
18A GLU* 3.2 17.6 + - - +
19A TYR* 3.0 20.4 + - - +
12B LEU* 4.2 16.5 - - + +
15B HIS* 3.9 52.8 + + + -
16B ILE* 4.6 4.6 - - + +
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Residues in contact with ILE 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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9A LEU* 4.4 0.2 - - + -
12A LEU* 4.0 8.5 - - + +
13A TRP* 2.5 44.7 + - + +
15A HIS* 1.3 70.2 - - + +
17A GLN* 1.3 67.0 + - - +
19A TYR* 2.9 9.5 + - - +
20A GLN* 2.9 20.8 + - - +
31A ILE* 4.6 6.5 - - + +
32A PHE* 4.0 15.7 - - + -
15B HIS 5.9 1.1 - - - +
16B ILE* 4.7 12.1 - - + -
19B TYR* 3.3 46.7 - - + -
107B ILE* 3.8 22.2 - - + -
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Residues in contact with GLN 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 TRP* 2.9 28.1 + - + +
14A PRO* 4.3 14.4 - - - +
16A ILE* 1.3 78.7 - - - +
18A GLU* 1.3 57.4 + - - +
20A GLN* 3.3 8.4 + - + +
21A ASP* 3.0 49.5 + - - +
107B ILE* 4.5 8.1 - - + -
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Residues in contact with GLU 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 PRO 3.5 17.6 + - - +
15A HIS* 3.2 19.8 + - - +
16A ILE 3.1 1.0 - - - -
17A GLN* 1.3 80.1 - - - +
19A TYR* 1.3 59.5 + - - +
21A ASP* 3.4 13.4 + - + +
22A LEU* 3.4 17.0 + - - +
12B LEU* 3.8 26.8 - - + +
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Residues in contact with TYR 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 HIS 3.0 11.3 + - - +
16A ILE* 2.9 10.4 + - - +
18A GLU* 1.3 73.4 - - - +
20A GLN* 1.3 64.3 + - - +
21A ASP 3.1 1.8 - - - -
22A LEU* 3.0 19.0 + - + +
23A ALA* 3.2 12.6 + - - +
31A ILE* 3.6 26.2 - - + -
37A GLY* 2.9 28.7 + - - -
40A LEU* 4.1 16.6 - - + +
41A GLN* 4.7 1.4 + - - +
9B LEU* 3.7 35.8 - - + +
12B LEU* 3.6 23.7 - - + +
13B TRP* 3.7 21.9 - + - -
16B ILE* 4.2 18.2 - - + -
32B PHE* 4.0 21.1 - + - -
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Residues in contact with GLN 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 ILE 2.9 14.3 + - - +
17A GLN* 3.6 5.6 - - + +
19A TYR* 1.3 77.8 - - - +
21A ASP* 1.3 63.2 + - - +
22A LEU 3.2 0.2 - - - -
23A ALA* 4.0 0.4 - - - +
24A LEU* 3.3 29.7 + - - +
28A ILE 4.3 5.5 + - - -
29A ASN 3.1 31.2 + - - +
31A ILE* 3.5 39.3 - - + +
106B GLY* 6.0 0.9 - - - -
107B ILE* 3.4 39.3 + - + +
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Residues in contact with ASP 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 GLN* 3.0 42.1 + - - +
18A GLU* 3.6 15.6 - - + +
19A TYR 3.1 0.6 - - - -
20A GLN* 1.3 81.1 - - - +
22A LEU* 1.3 62.0 + - - +
24A LEU* 3.5 12.6 - - - +
25A LYS* 3.3 19.9 + - - +
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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 GLU 3.4 9.2 + - - +
19A TYR* 3.0 15.6 + - + +
21A ASP* 1.3 78.6 - - - +
23A ALA* 1.3 64.9 + - - +
25A LYS* 3.1 18.7 + - + +
26A HIS* 3.1 26.3 + - - +
40A LEU* 4.1 9.4 - - + -
44A LEU* 4.3 14.4 - - + -
5B ASP* 4.0 40.2 - - - +
8B LYS* 4.6 14.4 - - + -
9B LEU* 4.5 19.1 - - + +
12B LEU* 5.5 3.6 - - + -
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Residues in contact with ALA 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 TYR 3.2 6.1 + - - +
20A GLN* 4.1 2.7 - - - +
22A LEU* 1.3 75.7 - - - +
24A LEU* 1.3 58.7 + - - +
26A HIS 2.7 22.3 + - - -
28A ILE* 3.0 35.9 + - + +
31A ILE* 3.7 28.9 - - + -
36A GLY 5.7 0.2 - - - +
40A LEU* 3.3 30.8 - - + +
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Residues in contact with LEU 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 GLN* 3.3 29.8 + - - +
21A ASP* 3.5 13.5 - - - +
23A ALA* 1.3 79.0 - - - +
25A LYS* 1.3 61.3 + - - +
26A HIS 3.1 0.9 + - - -
27A GLY* 3.1 13.9 + - - -
28A ILE 3.1 18.1 + - - +
29A ASN* 4.4 20.7 + - - +
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Residues in contact with LYS 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 ASP 3.3 11.0 + - - +
22A LEU* 3.1 20.9 + - + +
23A ALA 3.1 0.2 - - - -
24A LEU* 1.3 80.0 - - - +
26A HIS* 1.3 65.8 + - + +
27A GLY 3.5 1.2 + - - -
5B ASP* 3.4 25.9 + - - +
8B LYS* 4.0 17.4 - - - +
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Residues in contact with HIS 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* 3.1 20.9 + - + +
23A ALA 2.7 7.8 + - - -
25A LYS* 1.3 92.6 - - + +
27A GLY* 1.3 55.5 + - - +
28A ILE* 2.9 16.2 - - + +
40A LEU* 3.7 26.3 - - + +
43A LEU* 4.0 7.3 - - + +
44A LEU* 3.7 16.9 - - + +
49A THR* 5.9 1.9 - - - +
50A VAL* 3.3 13.2 - - - +
3B HIS* 3.3 29.2 + + - -
5B ASP* 2.8 36.6 - - + -
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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
------------------------------------------------------------
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