Contacts of the helix formed by residues 18 - 31 (chain E) in PDB entry 1O9I
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 ASP 18 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ARG* 3.8 4.1 + - + +
17E SER* 1.3 77.6 - - - +
19E PRO* 1.3 64.4 - - - +
20E ILE* 3.2 13.7 + - - +
21E MET* 3.0 34.1 + - + +
22E ALA 3.0 22.0 + - - -
24E ARG* 4.9 3.3 + - - -
80E LEU* 2.9 25.2 + - + +
161E MET 5.2 1.4 - - - +
162E THR* 4.7 9.4 + - - -
164E ASP* 6.0 1.8 - - + +
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Residues in contact with PRO 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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17E SER* 4.3 4.9 - - - +
18E ASP* 1.3 85.3 - - - +
20E ILE* 1.3 64.4 + - + +
22E ALA* 3.5 9.0 + - + +
23E ARG* 3.1 21.0 + - - +
80E LEU 3.5 7.4 - - - +
81E LEU* 3.9 9.9 - - + +
84E ALA* 3.8 27.1 - - + -
85E PRO* 4.2 3.4 - - + -
100E THR* 3.7 29.4 - - + -
104E MET* 3.8 23.6 - - + +
108E HIS* 4.8 1.6 + - - -
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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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18E ASP* 3.2 8.9 + - - +
19E PRO* 1.3 76.2 - - + +
21E MET* 1.3 64.8 + - - +
23E ARG* 3.2 8.8 + - + +
24E ARG* 3.0 49.5 + - + +
99E THR 5.2 0.2 - - - +
100E THR* 3.5 30.7 - - + +
103E GLY* 3.5 38.4 - - - +
104E MET* 3.8 3.1 - - + +
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Residues in contact with MET 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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18E ASP* 3.0 33.1 + - + +
20E ILE* 1.3 74.0 - - - +
22E ALA* 1.3 66.2 + - - +
24E ARG* 3.1 28.6 + - - +
25E LEU* 2.9 32.7 + - + +
80E LEU* 4.1 15.3 - - + -
158E LEU* 3.6 46.4 - - + +
161E MET 3.8 11.7 - - - +
162E THR* 3.9 19.5 - - + +
167E VAL* 4.0 15.5 - - + -
171E LEU* 4.6 1.1 - - + -
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Residues in contact with ALA 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 ASP 3.0 12.6 + - - +
19E PRO 3.5 9.9 - - - +
21E MET* 1.3 78.2 - - - +
23E ARG* 1.3 62.6 + - - +
25E LEU 3.3 1.4 + - - -
26E GLN* 3.2 22.7 + - - +
77E ILE* 3.7 18.4 - - + +
80E LEU* 3.8 19.9 - - + +
81E LEU* 3.7 31.0 - - + -
108E HIS* 4.1 3.3 - - + -
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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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23B ARG* 5.4 9.1 - - - +
122B ASN* 5.6 2.9 + - - -
19E PRO 3.1 11.4 + - - +
20E ILE* 3.4 10.5 - - - +
22E ALA* 1.3 75.3 - - - +
24E ARG* 1.3 65.7 + - + +
26E GLN* 3.1 19.4 + - + +
102E ALA 5.0 1.6 + - - -
103E GLY* 2.9 34.2 + - - +
104E MET 4.0 6.3 + - - -
105E ASP* 3.7 23.1 - - + +
108E HIS* 4.0 14.1 - - + -
121E PRO* 2.7 43.0 + - + +
122E ASN* 3.2 19.2 + - - +
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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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18E ASP* 4.9 2.6 + - - -
20E ILE* 3.0 38.5 + - + +
21E MET* 3.1 31.8 + - - +
23E ARG* 1.3 75.8 - - + +
25E LEU* 1.3 58.7 + - - +
27E GLU* 3.0 29.1 + - - +
28E SER 4.4 0.2 + - - -
121E PRO* 3.8 6.5 - - - +
158E LEU* 3.7 16.8 - - + +
161E MET* 3.4 60.2 + - - +
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Residues in contact with LEU 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 MET* 2.9 31.1 + - + +
22E ALA 3.7 5.2 - - - +
24E ARG* 1.3 72.5 - - - +
26E GLN* 1.3 63.9 + - - +
27E GLU 3.0 1.8 - - - -
28E SER* 3.0 25.8 + - - +
29E LEU 3.2 7.6 + - - -
73E ILE* 3.6 12.8 - - + +
76E MET* 3.7 18.2 - - + -
77E ILE* 3.9 13.2 - - + -
80E LEU* 3.5 31.4 - - + -
158E LEU* 3.8 23.6 - - + -
167E VAL* 4.7 5.2 - - + -
170E MET* 4.5 8.7 - - + -
171E LEU* 4.5 14.6 - - + -
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Residues in contact with GLN 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 ALA 3.2 13.0 + - - +
23E ARG* 3.1 14.8 + - - +
24E ARG 3.0 1.2 - - - -
25E LEU* 1.3 77.9 - - - +
27E GLU* 1.3 55.0 + - - +
29E LEU* 3.9 9.2 - - - +
30E GLY 2.8 27.4 + - - -
31E GLY 3.5 1.7 + - - -
77E ILE* 3.6 10.7 - - - +
105E ASP* 5.4 2.2 - - - +
108E HIS* 2.8 30.3 + - + +
116E ALA* 3.5 6.2 - - - -
117E SER* 2.8 46.3 + - - +
119E ASN 2.9 26.3 + - - +
120E ASN* 3.7 12.5 - - - +
121E PRO* 4.0 2.5 - - + -
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Residues in contact with GLU 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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24E ARG 3.0 15.8 + - - +
26E GLN* 1.3 78.1 - - - +
28E SER* 1.3 60.1 + - - +
31E GLY* 2.9 44.5 + - - +
32E GLN* 3.8 9.2 + - - +
34E GLY* 3.8 7.3 + - - -
120E ASN* 4.2 6.8 + - - +
121E PRO* 3.0 29.3 - - + +
154E GLN* 3.5 34.5 + - + +
158E LEU* 5.9 2.9 - - + -
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Residues in contact with SER 28 (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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24E ARG 4.4 0.2 + - - -
25E LEU* 3.0 13.7 + - - +
27E GLU* 1.3 78.8 - - - +
29E LEU* 1.3 57.4 + - - +
34E GLY* 4.0 6.5 - - - -
35E GLU* 2.8 38.9 + - - +
73E ILE* 4.2 23.5 - - - +
154E GLN* 5.2 6.3 + - - +
155E VAL* 4.7 10.5 - - - +
158E LEU* 3.6 25.1 - - - +
174E LEU* 6.3 0.2 - - - -
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Residues in contact with LEU 29 (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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25E LEU 3.2 4.8 + - - +
26E GLN* 3.2 11.9 + - - +
28E SER* 1.3 82.0 - - - +
30E GLY* 1.3 60.8 + - - +
31E GLY 3.6 0.6 + - - -
34E GLY 4.8 0.3 - - - -
35E GLU* 4.4 1.0 + - - -
36E THR* 2.8 35.9 + - - +
70E VAL* 3.8 31.4 - - + +
73E ILE* 3.8 13.9 - - + -
74E SER* 3.4 31.4 - - - +
77E ILE* 4.1 6.7 - - + -
116E ALA* 3.9 16.2 - - + -
117E SER 3.2 25.6 - - - +
118E LEU* 4.1 13.2 - - + +
126E TRP* 4.5 0.5 - - - -
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Residues in contact with GLY 30 (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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26E GLN 2.8 13.1 + - - -
29E LEU* 1.3 75.7 - - - +
31E GLY* 1.3 60.2 + - - -
118E LEU* 3.8 16.6 - - - -
119E ASN 3.6 14.0 + - - -
120E ASN* 4.0 10.1 + - - +
124E ALA 4.4 0.9 - - - +
126E TRP* 3.4 32.0 + - - +
130E TYR* 3.9 2.4 - - - -
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Residues in contact with GLY 31 (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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26E GLN 3.5 2.2 + - - -
27E GLU* 2.9 32.5 + - - -
29E LEU 3.6 1.0 - - - +
30E GLY* 1.3 80.6 - - - +
32E GLN* 1.3 67.7 + - - +
33E TRP 3.2 2.9 - - - -
34E GLY* 3.1 13.3 + - - -
37E THR* 3.4 7.8 + - - -
120E ASN* 4.0 11.0 - - - -
126E TRP* 3.7 4.3 - - - -
130E TYR* 3.8 2.2 - - - -
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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