Contacts of the helix formed by residues 9 - 27 (chain E) in PDB entry 4QPQ
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 9 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ILE* 1.3 81.6 - - - +
10E ASN* 1.3 64.0 + - - +
11E ASP* 3.7 10.5 + - - +
12E ALA* 3.1 23.6 + - - +
13E TYR* 3.0 19.1 + - - +
2H ALA* 5.0 0.4 - - - -
44H GLU* 3.5 16.3 + - - -
13Q G 5.9 0.2 - - - -
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Residues in contact with ASN 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E SER* 1.3 70.4 - - - +
11E ASP* 1.3 67.3 + - - +
13E TYR* 3.5 8.7 + - + +
14E GLU* 3.0 39.3 + - + +
2H ALA* 4.1 19.5 + - - +
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Residues in contact with ASP 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E SER* 3.2 9.8 + - - +
10E ASN* 1.3 77.7 - - - +
12E ALA* 1.3 59.3 + - - +
14E GLU* 3.3 12.7 + - - +
15E LYS* 3.0 48.0 + - - +
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Residues in contact with ALA 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ILE* 4.2 17.9 - - + -
9E SER* 3.1 20.0 + - - +
11E ASP* 1.3 78.4 - - - +
13E TYR* 1.3 62.9 + - - +
15E LYS* 3.4 4.1 + - - +
16E ILE* 3.0 30.7 + - + +
43H LEU* 5.7 1.8 - - + -
44H GLU* 4.3 15.3 - - + -
47H LEU* 3.9 23.3 - - + +
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Residues in contact with TYR 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ILE* 3.8 11.4 - - + +
9E SER 3.0 16.6 + - - +
10E ASN* 3.6 9.4 - - + +
12E ALA* 1.3 76.7 - - - +
14E GLU* 1.3 71.4 + - + +
16E ILE* 3.4 6.0 + - - +
17E ASN* 3.2 44.4 + - - -
35E PHE* 3.6 32.8 - + - -
2H ALA* 4.3 14.6 - - + -
3H LYS 5.6 1.6 - - - -
4H VAL* 4.1 16.8 - - + -
11P G 5.0 7.9 + - - -
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Residues in contact with GLU 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ASN* 3.0 29.5 + - + +
11E ASP* 3.9 12.0 - - - +
13E TYR* 1.3 83.5 - - + +
15E LYS* 1.3 60.8 + - + +
17E ASN* 3.4 7.3 + - - +
18E ALA* 2.8 29.0 + - - +
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Residues in contact with LYS 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ASP* 3.0 34.0 + - - +
12E ALA* 3.7 8.5 - - - +
14E GLU* 1.3 75.7 - - + +
16E ILE* 1.3 63.2 - - - +
18E ALA* 3.3 9.5 + - - +
19E ILE* 3.1 28.3 + - - +
47H LEU* 4.3 20.2 - - + +
48H ARG* 6.3 1.4 - - - +
51H GLU* 3.7 24.3 + - - +
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Residues in contact with ILE 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ILE* 4.3 7.4 - - + -
12E ALA* 3.0 18.0 + - + +
13E TYR 3.7 4.5 - - - +
14E GLU 3.3 0.2 - - - -
15E LYS* 1.3 73.3 - - - +
17E ASN* 1.3 64.1 + - - +
19E ILE* 3.1 18.4 + - + +
20E ILE* 3.1 14.4 + - + +
35E PHE* 3.6 37.5 - - + -
38E THR* 3.7 22.7 - - - +
39E ALA* 4.0 15.5 - - + +
42E LEU* 4.1 16.2 - - + -
43H LEU* 3.7 30.5 - - + -
47H LEU* 4.5 4.0 - - + -
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Residues in contact with ASN 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E TYR* 3.2 48.3 + - - +
14E GLU* 3.7 9.7 - - - +
15E LYS 3.4 0.2 - - - -
16E ILE* 1.3 77.6 - - - +
18E ALA* 1.3 62.5 + - - +
20E ILE* 3.3 11.2 + - - +
21E GLU* 3.0 38.9 + - + +
35E PHE* 3.4 22.1 - - - -
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Residues in contact with ALA 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E GLU 2.8 18.5 + - - +
15E LYS* 3.3 12.1 - - - +
16E ILE 3.2 0.2 - - - -
17E ASN* 1.3 74.9 - - - +
19E ILE* 1.3 62.5 + - + +
21E GLU* 3.6 11.5 + - - +
22E LYS* 3.2 38.0 + - - +
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Residues in contact with ILE 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E LYS 3.1 15.3 + - - +
16E ILE* 3.1 9.8 + - + +
18E ALA* 1.3 76.3 - - + +
20E ILE* 1.3 62.1 + - + +
22E LYS* 3.0 19.0 + - + +
23E ARG* 2.9 56.1 + - + +
38E THR* 5.3 10.1 - - - -
41E MET* 5.6 2.9 - - + -
42E LEU* 4.1 26.0 - - + -
47H LEU* 4.2 9.9 - - + -
50H HIS* 3.7 35.7 - - + +
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Residues in contact with ILE 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE 3.1 14.3 + - - +
17E ASN* 3.3 13.0 + - - +
19E ILE* 1.3 75.2 - - - +
21E GLU* 1.3 58.7 + - + +
23E ARG* 3.2 8.4 + - - +
24E ARG* 2.9 45.5 + - + +
33E VAL* 3.3 21.1 - - + +
34E SER 3.9 2.7 - - - +
35E PHE* 3.7 37.0 - - + +
38E THR* 3.6 31.2 - - + +
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Residues in contact with GLU 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ASN* 3.0 30.0 + - + +
18E ALA* 3.9 9.2 - - - +
19E ILE 3.2 0.2 - - - -
20E ILE* 1.3 77.6 - - + +
22E LYS* 1.3 60.9 + - + +
24E ARG* 4.1 6.1 - - - +
25E GLN* 3.2 30.7 + - - +
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Residues in contact with LYS 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ALA* 3.2 26.8 + - - +
19E ILE* 3.0 19.1 + - + +
21E GLU* 1.3 76.9 - - + +
23E ARG* 1.3 60.9 + - + +
25E GLN* 3.1 8.1 + - - +
26E GLU* 2.8 45.1 + - - +
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Residues in contact with ARG 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ILE* 2.9 35.6 + - + +
20E ILE* 3.6 8.7 - - - +
22E LYS* 1.3 76.4 - - - +
24E ARG* 1.3 54.9 + - - +
25E GLN 3.0 0.2 - - - -
26E GLU* 4.1 16.7 + - - -
27E GLY 2.7 31.2 + - - -
28E ALA* 3.2 9.3 - - + +
33E VAL* 3.9 28.5 - - + +
38E THR* 5.3 5.3 - - + +
41E MET* 3.9 20.7 - - - +
50H HIS* 3.6 29.0 - - - -
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Residues in contact with ARG 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ILE* 2.9 29.0 + - + +
21E GLU* 4.1 5.6 - - - +
23E ARG* 1.3 74.9 - - - +
25E GLN* 1.3 56.5 + - - +
27E GLY 3.1 13.8 - - - +
28E ALA* 3.7 13.0 + - + +
30E GLU* 4.2 12.8 - - - +
31E LYS* 3.1 35.1 - - - +
33E VAL* 3.7 27.7 + - + +
34E SER* 5.8 1.2 - - - +
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Residues in contact with GLN 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E GLU* 3.2 22.2 + - - +
22E LYS* 3.1 9.1 + - - +
23E ARG 3.0 0.8 - - - -
24E ARG* 1.3 79.1 - - - +
26E GLU* 1.3 66.7 + - + +
27E GLY 3.6 2.5 - - - +
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Residues in contact with GLU 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E LYS* 2.8 27.5 + - - +
23E ARG* 3.9 21.7 + - - +
25E GLN* 1.3 76.0 - - + +
27E GLY* 1.3 64.1 + - - +
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Residues in contact with GLY 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E ARG 2.7 13.2 + - - -
24E ARG 3.1 13.8 - - - +
25E GLN 3.6 3.3 - - - +
26E GLU* 1.3 80.8 - - - +
28E ALA* 1.3 61.4 + - - -
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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