Contacts of the helix formed by residues 7 - 30 (chain B) in PDB entry 1CUN
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 MET 7 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B VAL* 1.3 66.4 + - + +
9B HIS* 3.5 4.7 - - - +
10B GLN* 3.5 10.2 + - - +
11B PHE* 3.1 27.9 + - - +
68B THR* 3.5 31.0 - - + +
71B LYS* 3.8 38.4 - - + -
72B LEU* 3.9 26.2 - - + +
75B ASP* 5.4 1.8 - - - +
120C ASN* 5.9 1.2 + - - -
170C ASP* 6.3 1.0 - - - +
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Residues in contact with VAL 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B MET* 1.3 76.7 - - + +
9B HIS* 1.3 67.1 + - + +
11B PHE* 3.4 5.5 + - - +
12B PHE* 3.2 49.5 + - + -
72B LEU* 4.1 28.3 - - + -
77B THR* 4.9 7.0 - - - +
78B ILE 5.9 1.1 - - - +
83B ILE* 4.2 11.4 - - + -
167C ARG* 4.0 26.2 - - - +
170C ASP* 3.7 25.8 - - + +
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Residues in contact with HIS 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B MET 3.5 3.2 - - - +
8B VAL* 1.3 79.2 - - + +
10B GLN* 1.3 63.1 + - - +
12B PHE* 3.4 7.0 + - - +
13B ARG* 3.1 30.4 + - - +
120C ASN* 3.2 44.4 + - - +
123C GLU* 3.2 21.6 + - + +
124C GLU* 2.6 38.3 + - + -
167C ARG* 3.8 26.9 + - + +
170C ASP* 5.6 4.0 - - + -
171C VAL* 3.6 20.3 - - + +
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Residues in contact with GLN 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B MET* 3.5 10.8 + - - +
8B VAL 3.3 0.2 - - - -
9B HIS* 1.3 76.7 - - - +
11B PHE* 1.3 56.8 + - - +
13B ARG* 2.9 44.2 + - - +
14B ASP* 2.8 62.6 + - - +
38C LEU* 3.9 5.5 - - - +
42C GLN* 3.8 16.1 + - - +
116C GLN* 3.1 34.8 - - - +
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Residues in contact with PHE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B MET 3.1 18.8 + - - +
8B VAL 3.4 7.4 - - - +
10B GLN* 1.3 77.0 - - - +
12B PHE* 1.3 74.7 + + - +
14B ASP* 3.8 6.0 - - - +
15B MET* 2.9 51.1 + - + +
65B VAL* 3.4 37.9 - - + -
68B THR* 3.8 22.4 - - + -
69B GLY* 3.6 13.5 - - - -
72B LEU* 3.6 20.2 - - + -
83B ILE* 4.1 17.3 - - + -
87B LEU* 3.8 24.0 - - + -
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Residues in contact with PHE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 3.2 38.3 + - + +
9B HIS* 4.0 5.8 - - - +
11B PHE* 1.3 84.0 - + - +
13B ARG* 1.3 66.8 + - + +
15B MET* 3.7 29.5 - - + +
16B ASP* 3.0 33.4 + - - +
82B GLU* 4.1 22.2 - - + -
83B ILE* 3.8 22.7 - - + -
86B ARG* 3.8 28.9 - - + -
167C ARG* 3.7 23.3 - - - -
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Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B HIS* 3.1 19.3 + - - +
10B GLN* 2.9 48.2 + - - +
12B PHE* 1.3 80.7 - - + +
14B ASP* 1.3 62.4 + - - +
16B ASP* 3.8 4.8 - - - +
17B ASP* 3.0 33.5 + - - +
38C LEU* 3.6 21.9 - - - +
116C GLN* 4.2 8.1 + - - +
119C ALA* 4.3 7.0 - - - +
120C ASN* 2.8 35.5 + - - +
123C GLU* 2.8 43.4 + - - +
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Residues in contact with ASP 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLN* 2.8 52.4 + - - +
11B PHE* 3.8 5.7 + - - +
13B ARG* 1.3 73.5 - - - +
15B MET* 1.3 57.7 + - - +
17B ASP* 3.2 9.9 + - - +
18B GLU* 2.9 36.0 + - + +
65B VAL* 4.1 16.9 - - + +
42C GLN* 5.4 0.7 + - - -
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Residues in contact with MET 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 2.9 36.7 + - + +
12B PHE* 3.7 22.9 - - + +
14B ASP* 1.3 76.7 - - - +
16B ASP* 1.3 57.7 + - - +
18B GLU* 3.3 4.3 + - - +
19B GLU* 2.9 42.4 + - - +
65B VAL* 4.1 15.4 - - + +
86B ARG* 3.3 68.9 - - + +
87B LEU* 4.3 3.4 - - - -
90B PHE* 3.9 20.4 - - + -
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Residues in contact with ASP 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 3.0 24.8 + - - +
13B ARG* 3.8 5.5 - - - +
15B MET* 1.3 77.3 - - - +
17B ASP* 1.3 66.6 + - - +
19B GLU* 3.4 8.1 + - - +
20B SER* 3.1 25.3 + - - -
86B ARG* 2.8 31.1 + - - -
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Residues in contact with ASP 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 3.0 26.9 + - - +
14B ASP* 3.2 10.5 + - - +
16B ASP* 1.3 78.0 - - - +
18B GLU* 1.3 66.6 + - + +
20B SER* 3.3 9.1 + - - -
21B TRP* 3.1 20.4 + - - +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASP* 2.9 22.4 + - + +
15B MET 3.8 0.4 - - - +
17B ASP* 1.3 75.2 - - - +
19B GLU* 1.3 61.7 + - - +
21B TRP* 3.1 5.8 + - - +
22B ILE* 2.8 33.6 + - - +
58B HIS* 2.7 37.8 + - - -
61B ALA* 3.8 14.9 - - - +
62B ILE* 3.8 13.0 - - + +
65B VAL* 4.1 18.2 - - + -
90B PHE* 3.6 21.3 - - + -
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B MET* 2.9 22.0 + - - +
16B ASP* 3.8 7.7 - - - +
17B ASP 3.3 0.2 - - - -
18B GLU* 1.3 76.5 - - - +
20B SER* 1.3 56.9 + - - +
22B ILE* 3.7 8.3 - - + +
23B LYS* 2.9 30.8 + - - +
86B ARG* 3.0 30.2 + - - +
89B GLN* 4.1 8.5 + - - +
90B PHE* 3.4 36.0 + - + +
93B HIS* 3.1 34.2 + - + +
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ASP 3.1 14.5 + - - -
17B ASP* 3.5 11.5 - - - -
18B GLU 3.1 0.2 - - - -
19B GLU* 1.3 74.0 - - - +
21B TRP* 1.3 66.6 + - - +
23B LYS* 3.5 6.8 + - - +
24B GLU* 3.1 23.6 + - - +
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Residues in contact with TRP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASP 3.1 11.7 + - - +
18B GLU* 3.1 13.6 + - - +
20B SER* 1.3 76.7 - - - +
22B ILE* 1.3 73.7 + - + +
24B GLU* 3.2 8.4 + - - +
25B LYS* 3.0 55.7 + - + +
54B GLU* 4.3 15.0 + - + -
55B LEU* 3.7 21.8 - - + -
58B HIS* 3.5 57.1 + + + -
62B ILE* 5.2 0.2 - - + -
94B TRP* 3.7 24.2 - + - -
97B LEU* 4.2 2.9 - - + -
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU 2.8 18.8 + - - +
19B GLU* 3.7 6.5 - - - +
21B TRP* 1.3 86.8 - - + +
23B LYS* 1.3 58.2 + - - +
25B LYS* 3.2 2.9 + - - +
26B LYS* 2.8 31.1 + - + +
62B ILE* 4.2 5.8 - - + -
90B PHE* 3.8 30.7 - - + -
93B HIS* 3.7 32.1 - - + +
94B TRP* 3.9 42.2 - - + +
97B LEU* 4.0 15.4 - - + +
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU 2.9 18.8 + - - +
20B SER* 3.9 7.6 - - - +
21B TRP 3.3 0.2 - - - -
22B ILE* 1.3 78.0 - - - +
24B GLU* 1.3 60.5 + - - +
26B LYS* 3.4 10.2 + - + +
27B LEU* 2.9 54.6 + - + +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B SER 3.1 15.2 + - - +
21B TRP* 3.5 9.9 - - - +
22B ILE 3.1 0.2 - - - -
23B LYS* 1.3 75.0 - - - +
25B LYS* 1.3 78.1 + - + +
27B LEU* 3.3 10.6 + - + +
28B LEU* 3.0 31.2 + - + +
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TRP* 3.0 53.4 + - + +
22B ILE 3.8 5.4 - - - +
24B GLU* 1.3 88.0 + - + +
26B LYS* 1.3 57.1 + - - +
28B LEU* 3.3 23.9 + - + +
29B VAL* 2.9 32.1 + - - +
51B LEU* 4.1 21.6 - - + +
54B GLU* 3.5 29.0 + - - -
55B LEU* 4.8 3.6 - - + -
97B LEU* 3.8 19.7 - - + +
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE* 2.8 20.6 + - + +
23B LYS* 3.5 11.7 - - + +
25B LYS* 1.3 74.9 - - - +
27B LEU* 1.3 81.7 + - + +
29B VAL* 3.3 6.5 + - - +
30B SER* 2.9 32.7 + - - +
93B HIS* 6.1 1.8 - - + -
96B GLU* 3.3 38.6 - - + +
97B LEU* 3.7 17.9 - - + +
100B LEU* 4.1 18.1 - - + +
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LYS* 2.9 45.4 + - + +
24B GLU* 3.3 9.4 + - + +
26B LYS* 1.3 100.0 - - + +
28B LEU* 1.3 61.6 + - - +
30B SER* 3.3 20.4 + - - +
31B SER 4.2 1.6 + - - -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU* 3.0 20.6 + - + +
25B LYS* 3.5 39.0 - - + +
27B LEU* 1.3 73.3 - - - +
29B VAL* 1.3 57.8 + - - +
30B SER 3.0 8.2 + - - -
31B SER* 3.4 19.8 + - - -
47B LYS* 6.1 5.4 - - - +
51B LEU* 4.8 11.7 - - + -
104B ARG* 5.1 1.0 + - - -
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LYS 2.9 14.8 + - - +
26B LYS 3.3 8.0 + - - +
28B LEU* 1.3 74.3 - - - +
30B SER* 1.3 59.1 + - - +
31B SER 3.2 5.5 + - - +
48B HIS* 4.1 12.1 - - + +
51B LEU* 3.8 27.6 - - + -
97B LEU* 4.6 6.3 - - + -
100B LEU* 3.4 41.1 - - + +
101B ALA* 3.7 22.2 - - + +
104B ARG* 3.5 26.3 - - - +
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Residues in contact with SER 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LYS* 2.9 26.3 + - - +
27B LEU* 3.3 16.5 - - - +
28B LEU 3.0 1.4 - - - -
29B VAL* 1.3 78.0 - - - +
31B SER* 1.3 66.0 + - - +
32B GLU* 3.4 12.4 + - - +
100B LEU* 5.0 8.0 - - - +
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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