Contacts of the helix formed by residues 7 - 21 (chain E) in PDB entry 3AG2
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 THR 7 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5E HIS 5.8 0.4 - - - +
6E GLU* 1.3 79.3 - - - +
8E ASP* 1.3 64.6 + - - +
9E GLU* 3.0 18.5 + - - +
10E GLU* 3.0 42.1 + - - +
11E PHE* 2.9 22.2 + - - +
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Residues in contact with ASP 8 (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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6E GLU 5.2 0.7 - - - +
7E THR* 1.3 74.6 - - - +
9E GLU* 1.3 69.8 + - - +
11E PHE* 3.3 6.9 + - - +
12E ASP* 2.9 39.7 + - - +
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Residues in contact with GLU 9 (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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7E THR* 3.0 15.5 + - - +
8E ASP* 1.3 87.2 + - - +
10E GLU* 1.3 64.4 + - + +
12E ASP* 3.4 9.2 + - - +
13E ALA* 3.0 25.9 + - - +
46E LYS* 5.4 9.7 + - - +
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Residues in contact with GLU 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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6E GLU* 3.5 22.9 - - - +
7E THR* 3.0 41.4 + - - +
9E GLU* 1.3 75.4 - - + +
11E PHE* 1.3 64.0 + - - +
13E ALA* 3.4 5.3 + - - +
14E ARG* 3.1 27.8 + - + +
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Residues in contact with PHE 11 (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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6E GLU* 3.9 17.8 + - + +
7E THR 2.9 13.0 + - - +
8E ASP* 3.3 10.3 + - - +
10E GLU* 1.3 77.5 - - - +
12E ASP* 1.3 79.0 + - - +
13E ALA 3.2 0.9 + - - -
14E ARG* 3.4 21.8 + - - +
15E TRP* 3.2 54.3 + + - -
36E LEU* 4.0 9.2 - - + -
39E TYR* 3.7 35.4 - + - -
41E LEU* 3.7 29.8 - - + -
47E ILE* 4.4 4.9 - - + -
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Residues in contact with ASP 12 (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 ASP* 2.9 26.6 + - - +
9E GLU* 3.8 7.0 - - - +
11E PHE* 1.3 91.3 - - - +
13E ALA* 1.3 58.1 + - - +
15E TRP* 3.1 3.8 + - - +
16E VAL* 2.9 32.7 + - - +
44E GLU* 3.2 32.6 + - - +
46E LYS* 3.9 24.3 + - - +
47E ILE* 3.7 19.0 - - + +
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Residues in contact with ALA 13 (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 GLU 3.0 19.2 + - - +
10E GLU* 3.9 5.6 - - - +
11E PHE 3.1 0.2 - - - -
12E ASP* 1.3 75.5 - - - +
14E ARG* 1.3 65.8 + - - +
16E VAL* 3.4 7.3 + - - +
17E THR* 2.9 31.7 + - - +
46E LYS* 6.3 0.9 - - - -
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Residues in contact with ARG 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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6E GLU* 3.1 36.2 + - - +
10E GLU* 3.1 15.5 + - + +
11E PHE* 3.6 26.6 - - - +
13E ALA* 1.3 76.9 - - - +
15E TRP* 1.3 78.4 + - - +
17E THR* 3.5 6.4 + - - -
18E TYR* 3.0 25.8 + - - +
39E TYR* 5.0 5.5 + - - -
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Residues in contact with TRP 15 (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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11E PHE* 3.2 53.9 + + - -
12E ASP 3.1 8.9 + - - +
14E ARG* 1.3 95.1 - - - +
16E VAL* 1.3 67.0 + - - +
18E TYR* 3.1 29.2 + + + +
19E PHE* 3.1 42.8 + + - -
32E GLY* 3.4 42.6 - - - -
35E THR* 4.1 11.0 - - + -
36E LEU* 3.9 19.3 - - + -
39E TYR* 3.9 24.4 - + - -
47E ILE* 3.8 19.5 - - + -
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Residues in contact with VAL 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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12E ASP 2.9 19.5 + - - +
13E ALA* 3.7 7.0 - - - +
15E TRP* 1.3 76.6 - - - +
17E THR* 1.3 65.0 + - - +
18E TYR 3.2 0.2 + - - -
19E PHE 3.3 0.2 + - - -
20E ASN* 2.9 49.8 + - - +
46E LYS* 3.5 47.6 - - + +
47E ILE* 4.0 4.9 - - - +
50E ALA* 3.9 9.6 - - + +
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Residues in contact with THR 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 ALA* 2.9 19.2 + - - +
14E ARG* 3.7 7.4 - - - -
16E VAL* 1.3 79.8 - - - +
18E TYR* 1.3 64.3 + - - +
20E ASN* 3.4 6.9 + - - +
21E LYS* 3.4 17.2 + - - +
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Residues in contact with TYR 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 ARG 3.0 14.4 + - - +
15E TRP* 3.1 28.2 + + + +
17E THR* 1.3 79.0 - - - +
19E PHE* 1.3 84.4 + + - +
21E LYS* 3.5 15.9 + - - +
24E ILE* 3.9 12.2 - - + +
27E TRP* 5.1 0.9 - - - -
28E GLU* 2.6 46.8 + - + +
31E LYS* 4.0 9.1 - - + +
32E GLY* 3.5 21.5 + - - -
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Residues in contact with PHE 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 TRP* 3.1 39.6 + + - -
18E TYR* 1.3 98.8 - + - +
20E ASN* 1.3 57.8 + - - +
21E LYS 3.4 0.9 + - - +
24E ILE* 4.1 8.4 - - + +
29E LEU* 4.0 30.3 - - + -
32E GLY* 3.8 18.4 - - - -
33E MET* 3.7 20.0 - - - -
36E LEU* 4.1 4.7 - - + -
47E ILE* 4.0 22.7 - - + -
50E ALA* 3.5 26.9 - - + +
51E ALA* 3.7 25.1 - - + -
54E ALA* 3.5 10.5 - - + +
57E ARG* 2.8 20.1 + - - -
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Residues in contact with ASN 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 VAL* 2.9 40.5 + - - +
17E THR* 3.9 7.1 - - - +
18E TYR 3.3 0.6 - - - -
19E PHE* 1.3 76.0 - - - +
21E LYS* 1.3 64.8 + - - +
22E PRO* 3.0 10.6 - - - +
50E ALA* 3.4 21.8 - - - +
53E ARG* 5.3 5.7 - - - +
57E ARG* 3.4 13.5 + - - +
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Residues in contact with LYS 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 THR 3.4 9.4 + - - +
18E TYR* 3.8 13.2 - - - +
19E PHE 3.2 2.8 - - - -
20E ASN* 1.3 73.0 - - - +
22E PRO* 1.3 73.3 - - + +
23E ASP* 3.4 24.3 + - - +
24E ILE* 3.0 30.4 + - + +
28E GLU* 3.2 36.6 + - - -
57E ARG* 2.9 13.7 + - - -
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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