Contacts of the helix formed by residues 11 - 22 (chain E) in PDB entry 4GTU
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 GLY 11 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E TYR* 3.8 13.0 - - - -
9E ILE* 3.4 6.0 + - - +
10E ARG* 1.3 92.4 + - - +
12E LEU* 1.3 60.2 + - - -
13E ALA 3.1 3.4 + - - -
14E HIS* 3.2 14.7 + - - +
161E ASP* 4.7 4.3 - - - +
207E LEU 3.3 19.7 + - - -
208E TYR* 5.5 0.4 - - - -
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Residues in contact with LEU 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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6E TYR* 3.2 23.8 - - + +
11E GLY* 1.3 70.3 - - - -
13E ALA* 1.3 58.6 + - - +
14E HIS 3.3 0.6 + - - -
15E ALA* 4.1 10.0 + - - +
16E ILE* 4.5 5.9 - - - +
59E LEU 4.4 2.5 - - - +
60E PRO* 3.3 32.1 - - + -
72E SER* 4.0 24.9 + - - +
76E LEU* 6.0 1.0 - - - +
104E MET* 4.8 19.1 - - + -
107E SER* 6.0 1.8 - - - +
108E ASN* 6.0 1.8 - - - +
158E LEU* 5.8 1.4 - - - +
161E ASP* 5.3 6.3 - - - +
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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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4E LEU* 4.7 4.9 - - + +
6E TYR* 3.5 22.4 - - + -
11E GLY 3.1 1.6 + - - -
12E LEU* 1.3 77.4 - - - +
14E HIS* 1.3 55.0 + - - +
15E ALA 3.2 3.4 - - - -
16E ILE* 2.7 46.0 + - + +
17E ARG* 3.1 31.3 + - - +
60E PRO* 3.9 15.0 - - + -
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Residues in contact with HIS 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 ARG* 3.4 43.0 + - + +
11E GLY 3.2 16.5 + - - +
12E LEU 3.3 0.2 - - - -
13E ALA* 1.3 76.5 - - - +
15E ALA* 1.3 61.1 + - - +
17E ARG* 3.1 33.3 + - + +
18E LEU* 3.5 32.7 + - + +
160E TYR* 5.0 6.9 - + - -
161E ASP* 4.1 13.2 - - + +
164E ASP* 5.3 0.2 + - - -
196E TYR* 5.5 0.4 - + - -
202E PHE* 3.9 24.9 - + - -
203E LEU 2.9 29.5 + - - -
204E PRO* 4.3 0.2 - - + -
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Residues in contact with ALA 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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12E LEU 4.1 7.0 + - - +
13E ALA 3.2 1.0 - - - -
14E HIS* 1.3 76.9 - - - +
16E ILE* 1.3 65.0 + - - +
18E LEU* 3.7 11.0 + - - +
19E LEU* 3.3 18.5 + - - +
76E LEU* 3.8 11.3 - - + +
157E PHE* 4.0 9.6 - - + +
158E LEU* 3.7 46.4 - - + +
161E ASP* 4.7 10.1 + - + +
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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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4E LEU* 3.6 26.0 - - + -
12E LEU 4.5 4.7 - - - +
13E ALA* 2.7 31.5 + - + +
15E ALA* 1.3 75.2 - - - +
17E ARG* 1.3 55.4 + - - +
18E LEU 3.0 3.1 - - - -
19E LEU* 2.8 25.9 + - - +
20E LEU* 3.1 20.6 + - + +
60E PRO* 4.0 8.7 - - + -
72E SER* 4.5 8.3 - - - +
75E ILE* 3.7 45.3 - - + -
76E LEU* 3.8 24.9 - - + -
79E ILE* 5.1 3.4 - - + -
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Residues in contact with ARG 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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4E LEU* 4.7 13.5 - - + +
6E TYR* 3.4 17.4 - - - +
7E TRP 4.7 1.2 + - - -
10E ARG* 2.8 36.5 + - - +
13E ALA* 3.1 23.9 + - - +
14E HIS* 3.1 43.0 + - + +
16E ILE* 1.3 78.2 - - - +
18E LEU* 1.3 59.1 + - - +
20E LEU* 3.6 19.8 - - + +
21E GLU* 3.4 27.9 + - - +
27E TYR* 5.2 5.5 + - + -
29E GLU* 5.3 8.5 + - - +
31E LYS* 5.9 0.6 - - - +
196E TYR* 3.4 28.8 - - + +
201E ARG 5.5 0.2 - - - -
203E LEU* 3.7 30.0 - - - +
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Residues in contact with LEU 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 HIS* 3.5 43.1 + - + +
15E ALA* 3.8 9.2 - - - +
16E ILE 3.0 0.6 - - - -
17E ARG* 1.3 75.7 - - - +
19E LEU* 1.3 64.0 + - - +
21E GLU* 3.7 2.3 + - - +
22E TYR* 3.2 19.2 + - - +
157E PHE* 3.5 23.9 - - + +
160E TYR* 4.1 13.5 - - + -
161E ASP* 5.8 0.4 - - + -
187E PHE* 4.1 17.5 - - + -
193E ILE* 3.9 30.8 - - + +
196E TYR* 3.7 28.3 - - + -
197E MET* 4.5 8.1 - - + -
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Residues in contact with LEU 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 ALA 3.3 9.9 + - - +
16E ILE* 2.8 10.3 + - - +
18E LEU* 1.3 78.2 - - - +
20E LEU* 1.3 60.5 + - - +
22E TYR* 3.6 0.3 + - - +
23E THR* 2.9 30.6 + - + -
76E LEU* 3.7 36.3 - - + +
79E ILE* 3.9 23.8 - - + -
80E ALA* 4.5 2.7 - - - +
85E LEU* 3.5 32.8 - - + -
154E PHE* 3.7 19.3 - - + -
157E PHE* 3.5 26.9 - - + -
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Residues in contact with LEU 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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2E MET* 5.1 3.1 - - + -
4E LEU* 3.8 25.1 - - + -
16E ILE* 3.1 16.8 + - + +
17E ARG* 3.6 22.2 - - - +
19E LEU* 1.3 78.1 - - - +
21E GLU* 1.3 62.1 + - - +
23E THR* 3.4 3.9 + - - -
24E ASP 3.3 2.9 + - - -
25E SER* 2.9 39.5 + - - +
27E TYR* 3.4 52.3 - - + -
62E LEU* 4.6 9.4 - - + -
79E ILE* 3.3 29.6 - - + +
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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 ARG 3.4 19.0 + - - +
18E LEU 3.8 4.5 - - - +
20E LEU* 1.3 80.8 - - - +
22E TYR* 1.3 64.1 + - - +
24E ASP* 3.1 20.9 + - - +
27E TYR* 2.7 34.3 + - + +
192E LYS* 4.4 9.6 - - - +
193E ILE* 5.6 1.6 - - + -
196E TYR* 3.5 44.5 + - + +
201E ARG* 3.6 25.3 + - - -
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Residues in contact with TYR 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 LEU 3.2 15.5 + - - +
19E LEU 4.1 1.1 - - - +
20E LEU 3.4 0.2 - - - -
21E GLU* 1.3 77.2 - - - +
23E THR* 1.3 66.6 + - + +
24E ASP 3.2 2.4 + - - -
85E LEU* 5.0 6.1 - - + -
152E ILE* 4.8 17.4 - - + +
157E PHE* 3.9 23.6 - + + -
190E LEU* 3.7 39.7 - - + +
191E GLU 5.6 0.2 - - - -
192E LYS* 3.0 63.5 + - + +
193E ILE* 3.9 20.6 - - + +
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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
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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