Contacts of the helix formed by residues 7 - 30 (chain A) in PDB entry 3EUP
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 SER 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU 5.0 4.0 - - - -
5A SER 3.4 2.3 + - - -
6A LYS* 1.3 78.8 - - - +
8A ASP* 1.3 59.9 + - - +
9A ARG* 3.5 14.7 + - - +
10A THR* 3.1 25.9 + - - -
11A ARG* 2.9 28.0 + - - +
49A ASN* 3.1 8.8 + - - +
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Residues in contact with ASP 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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7A SER* 1.3 73.6 - - - +
9A ARG* 1.3 60.6 + - + +
11A ARG* 3.5 13.7 + - - +
12A GLN* 2.9 29.5 + - - +
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Residues in contact with ARG 9 (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 SER* 3.2 11.8 + - - +
8A ASP* 1.3 76.9 - - + +
10A THR* 1.3 62.6 + - - +
12A GLN* 3.3 6.1 + - - +
13A PHE* 2.9 29.0 + - - +
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Residues in contact with THR 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 LEU 5.4 0.3 + - - -
5A SER* 3.2 37.0 + - - +
7A SER* 3.1 17.9 + - - -
9A ARG* 1.3 77.2 - - - +
11A ARG* 1.3 57.1 - - - +
13A PHE* 3.3 8.6 + - + +
14A ILE* 2.9 33.7 + - + +
41A LEU* 4.2 22.4 - - + -
45A SER 5.2 0.2 - - - +
49A ASN* 3.6 11.0 - - - +
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Residues in contact with ARG 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 SER 2.9 19.1 + - - +
8A ASP* 3.6 13.7 - - - +
10A THR* 1.3 77.7 - - - +
12A GLN* 1.3 59.5 + - - +
14A ILE* 3.2 7.1 + - - +
15A ILE* 3.0 48.0 + - - +
49A ASN* 3.7 28.6 + - + +
50A PHE* 3.7 30.5 - - + -
59A ALA* 4.2 12.3 - - - +
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Residues in contact with GLN 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 ASP 2.9 18.1 + - - +
9A ARG* 3.8 5.8 - - - +
10A THR 3.3 0.2 - - - -
11A ARG* 1.3 76.5 + - - +
13A PHE* 1.3 59.9 + - - +
15A ILE* 3.2 17.4 + - - +
16A GLU* 2.7 70.7 + - - +
63A TYR* 3.7 19.8 - - - -
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Residues in contact with PHE 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 ARG 2.9 17.8 + - - +
10A THR* 3.5 7.2 - - + +
12A GLN* 1.3 72.9 - - - +
14A ILE* 1.3 75.8 + - + +
16A GLU* 3.4 10.6 + - + +
17A SER* 2.8 50.4 + - - -
38A ALA 4.8 1.6 - - - -
39A THR* 3.2 37.5 - - - -
41A LEU* 4.2 12.1 - - + -
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Residues in contact with ILE 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 THR* 2.9 26.6 + - + +
11A ARG* 3.2 7.2 + - - +
13A PHE* 1.3 78.2 - - + +
15A ILE* 1.3 63.7 + - - +
18A THR* 2.9 43.4 + - + +
35A LEU* 6.5 0.2 - - + -
39A THR* 3.8 17.9 - - + -
41A LEU* 3.2 34.8 - - + -
46A ILE* 4.2 24.5 - - + -
49A ASN* 4.9 2.9 - - - +
50A PHE* 3.7 28.7 - - + -
56A VAL* 4.4 7.4 - - + -
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Residues in contact with ILE 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 ARG* 3.0 50.3 + - + +
12A GLN* 3.2 20.2 + - - +
14A ILE* 1.3 74.6 - - - +
16A GLU* 1.3 58.2 + - - +
18A THR* 3.7 4.2 + - - -
19A ALA* 2.9 36.9 + - - +
50A PHE* 3.7 14.4 - - + -
56A VAL* 5.5 1.6 - - + +
59A ALA* 3.8 30.5 - - + +
60A ALA* 4.3 3.9 - - - +
63A TYR* 3.4 37.2 - - + -
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Residues in contact with GLU 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 GLN* 2.7 54.2 + - - +
13A PHE* 3.8 11.3 - - + +
15A ILE* 1.3 76.6 - - - +
17A SER* 1.3 60.4 + - - +
19A ALA* 4.4 1.0 - - - +
20A PRO* 3.4 17.8 - - - +
63A TYR* 3.6 33.0 + - + +
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Residues in contact with SER 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 PHE* 2.8 45.4 + - - -
14A ILE 3.8 3.1 - - - -
16A GLU* 1.3 77.5 - - - +
18A THR* 1.3 61.6 + - - +
20A PRO* 3.6 9.5 - - - +
21A VAL* 4.2 3.6 - - - +
38A ALA* 3.7 31.8 + - - +
39A THR* 4.0 13.0 - - - -
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Residues in contact with THR 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 ILE* 2.9 27.6 + - + +
15A ILE* 3.7 3.1 + - - -
17A SER* 1.3 78.3 - - - +
19A ALA* 1.3 61.2 + - - +
20A PRO* 3.3 2.9 - - - -
21A VAL* 3.0 10.2 + - - +
22A PHE* 3.0 32.0 + - - -
35A LEU* 3.6 34.8 - - + +
38A ALA* 4.3 4.3 - - + -
39A THR* 3.5 26.2 - - + -
56A VAL* 3.6 18.2 - - + +
60A ALA* 4.9 1.2 - - - +
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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 ILE 2.9 18.8 + - - +
16A GLU 4.4 0.2 - - - +
18A THR* 1.3 77.7 + - - +
20A PRO* 1.3 62.4 - - + +
22A PHE* 3.5 1.2 + - - +
23A ASN* 3.0 23.6 + - - +
60A ALA* 3.9 20.0 - - + +
63A TYR* 3.8 18.2 - - + -
64A ASN* 3.0 37.5 - - - +
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Residues in contact with PRO 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 GLU 3.4 18.6 - - - +
17A SER 3.6 9.6 - - - +
18A THR 3.4 4.3 - - - -
19A ALA* 1.3 89.7 - - + +
21A VAL* 1.3 64.3 + - + +
23A ASN* 3.6 1.3 + - + +
24A VAL* 3.3 29.8 + - - +
63A TYR* 6.0 0.9 - - + -
64A ASN* 4.8 2.7 - - - +
102A PRO* 6.3 0.2 - - + -
103A VAL* 3.9 37.9 - - + +
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Residues in contact with VAL 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 SER 4.2 5.4 - - - +
18A THR* 3.0 12.5 + - - +
20A PRO* 1.3 76.6 - - + +
22A PHE* 1.3 66.4 + - - +
24A VAL* 3.3 2.8 + - - -
25A LYS* 2.8 45.3 + - + +
30A THR* 3.8 24.2 - - + +
34A ASP* 4.1 13.9 - - + +
35A LEU* 5.4 0.4 - - + -
38A ALA* 4.0 27.4 - - + -
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Residues in contact with PHE 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 THR* 3.0 31.1 + - - -
19A ALA 3.5 4.9 + - - +
21A VAL* 1.3 76.9 - - - +
23A ASN* 1.3 59.5 + - - +
26A GLY* 2.8 34.9 + - - -
27A LEU* 4.2 7.2 - - + -
30A THR* 3.6 26.9 - - + -
35A LEU* 3.8 22.2 - - + -
53A LYS* 4.0 21.3 - - + -
56A VAL* 3.4 27.8 - - + -
57A ALA* 3.9 33.0 - - + +
60A ALA* 3.7 24.0 - - + -
64A ASN* 5.4 0.2 - - - +
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Residues in contact with ASN 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 3.0 19.8 + - - +
20A PRO* 4.0 1.6 - - + +
21A VAL 3.2 0.2 - - - -
22A PHE* 1.3 76.4 - - - +
24A VAL* 1.3 57.1 + - - +
26A GLY 5.0 0.2 + - - -
64A ASN* 3.6 13.1 + - - +
102A PRO* 3.9 7.1 - - - +
103A VAL 2.7 26.6 + - - +
104A GLY 3.3 8.3 - - - -
105A GLY 3.0 24.0 + - - -
107A PRO* 3.3 21.8 - - - +
110A ASN* 2.9 32.7 + - - +
111A THR* 5.5 0.9 + - - -
203B SO4 2.9 19.9 + - - -
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Residues in contact with VAL 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 PRO 3.3 17.2 + - - +
21A VAL* 3.3 3.5 + - - +
22A PHE 3.1 0.2 - - - -
23A ASN* 1.3 78.1 - - - +
25A LYS* 1.3 71.9 + - + +
26A GLY 3.5 0.4 + - - -
103A VAL* 4.0 10.5 - - + -
104A GLY* 3.7 28.0 - - - +
113B ILE 4.9 0.2 - - - +
114B GLU* 4.5 3.1 - - - +
117B ASP* 3.7 35.4 - - + +
118B THR* 3.6 17.1 - - + +
203B SO4 3.5 19.0 + - - -
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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 VAL* 2.8 31.9 + - + +
24A VAL* 1.3 87.5 - - + +
26A GLY* 1.3 62.3 + - - +
29A GLY* 3.3 35.9 + - - +
30A THR* 3.5 8.5 - - - +
34A ASP* 2.9 33.6 + - - +
28B ALA* 4.7 4.5 - - - +
114B GLU* 5.5 3.2 - - - +
118B THR* 4.6 10.5 - - + -
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Residues in contact with GLY 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 PHE* 2.8 23.0 + - - -
23A ASN 4.7 0.2 - - - -
24A VAL 3.5 1.6 + - - -
25A LYS* 1.3 80.8 - - - +
27A LEU* 1.3 65.0 + - - -
28A ALA 3.3 0.4 - - - -
30A THR* 2.7 25.1 + - - -
114A GLU* 3.1 15.9 - - - -
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Residues in contact with LEU 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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22A PHE* 4.2 7.9 - - + -
26A GLY* 1.3 74.4 - - - +
28A ALA* 1.3 59.8 + - - +
30A THR* 3.3 4.9 + - - +
53A LYS* 2.9 54.0 + - + +
54A GLU* 4.2 11.4 - - + -
57A ALA* 3.8 27.6 - - + -
114A GLU* 2.8 18.7 + - - +
119A HIS* 3.6 35.2 - - + +
122A LEU* 4.6 11.4 - - + -
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Residues in contact with ALA 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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27A LEU* 1.3 77.8 - - - +
29A GLY* 1.3 60.6 + - - +
30A THR 3.5 3.1 + - - +
53A LYS* 4.5 4.0 + - - +
114A GLU* 2.8 16.1 + - - +
25B LYS 4.9 3.8 - - - +
28B ALA* 4.2 9.6 - - + +
29B GLY* 3.7 30.7 - - - +
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Residues in contact with GLY 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 LYS* 3.3 37.1 + - - +
28A ALA* 1.3 77.0 - - - +
30A THR* 1.3 61.0 + - - +
31A SER* 3.6 1.4 + - - -
34A ASP* 3.3 11.8 - - - +
28B ALA* 3.6 18.2 - - - +
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Residues in contact with THR 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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21A VAL* 3.6 24.6 + - + +
22A PHE* 3.6 23.3 - - + -
25A LYS* 3.5 14.5 - - - +
26A GLY 2.7 22.2 + - - -
27A LEU 3.3 1.3 + - - -
28A ALA 3.3 1.8 - - - +
29A GLY* 1.3 76.9 - - - +
31A SER* 1.3 60.4 + - - +
34A ASP* 3.4 4.5 - - + -
35A LEU* 3.6 31.6 - - + -
53A LYS* 2.6 36.7 + - + +
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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