Contacts of the helix formed by residues 22 - 36 (chain E) in PDB entry 1QO0
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 22 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E PRO 3.5 2.7 + - - -
21E PRO* 1.3 75.1 - - - +
23E GLU* 1.3 60.6 + - - -
24E VAL 3.4 2.5 - - - -
25E SER* 3.3 3.9 + - - -
26E ASP* 2.9 39.9 + - - -
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Residues in contact with GLU 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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64B ARG* 5.2 13.8 + - - -
22E GLY* 1.3 68.1 - - - -
24E VAL* 1.3 70.6 + - + +
26E ASP* 3.3 8.9 + - - +
27E ALA* 3.1 24.4 + - - +
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Residues in contact with VAL 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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19E ASN* 3.6 20.9 - - - +
22E GLY 3.4 0.6 - - - -
23E GLU* 1.3 81.2 - - + +
25E SER* 1.3 65.8 + - - +
27E ALA* 3.3 3.5 + - - +
28E LEU* 3.1 24.2 + - + +
85E LEU* 4.6 5.2 - - + -
108E GLN* 3.5 30.1 - - - +
109E PRO* 6.0 2.2 - - + -
110E LEU* 3.5 27.5 - - + +
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Residues in contact with SER 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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17E VAL* 3.8 13.0 - - - +
19E ASN* 3.1 24.8 + - - +
20E PRO 2.8 26.7 + - - -
22E GLY 3.3 9.9 + - - -
23E GLU 3.3 0.6 - - - -
24E VAL* 1.3 81.4 - - - +
26E ASP* 1.3 57.5 + - - +
28E LEU* 3.8 1.6 - - - +
29E VAL* 2.9 35.6 + - - +
41E GLN* 3.7 20.9 - - - -
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Residues in contact with ASP 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E GLY* 2.9 31.4 + - - +
23E GLU* 3.3 8.8 + - - +
25E SER* 1.3 71.6 - - - +
27E ALA* 1.3 53.4 + - - +
29E VAL* 3.2 4.9 + - - +
30E LEU* 2.7 50.1 + - + +
41E GLN* 4.5 12.7 + - - +
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Residues in contact with ALA 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 GLU 3.1 14.5 + - - +
24E VAL* 3.8 3.6 - - - +
26E ASP* 1.3 79.4 - - - +
28E LEU* 1.3 57.9 + - - +
30E LEU* 3.4 7.5 + - - +
31E GLN* 2.9 32.1 + - - +
34E ARG* 4.6 1.9 + - - -
110E LEU* 4.5 15.2 - - + +
111E ASP* 6.2 1.6 - - - -
112E ALA* 5.9 1.0 - - - +
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Residues in contact with LEU 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E VAL* 3.9 19.1 - - + -
24E VAL* 3.1 18.4 + - + +
25E SER* 3.8 4.3 - - - +
27E ALA* 1.3 76.0 - - - +
29E VAL* 1.3 65.7 + - - +
31E GLN* 3.3 2.2 + - - -
32E LEU* 3.1 36.0 + - + +
57E PHE* 3.8 39.0 - - + -
85E LEU* 3.8 25.8 - - + -
106E ILE* 5.3 1.6 - - + -
110E LEU* 4.4 14.6 - - + +
115E VAL* 4.1 23.8 - - + -
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Residues in contact with VAL 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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17E VAL* 3.8 26.7 - - + -
25E SER 2.9 22.5 + - - +
26E ASP* 3.8 3.8 - - - +
28E LEU* 1.3 75.1 - - - +
30E LEU* 1.4 60.0 + - + +
32E LEU* 3.2 3.5 + - - +
33E ILE* 3.0 45.7 + - + +
39E VAL* 4.3 24.0 - - + +
40E ARG* 5.7 0.4 - - - -
41E GLN* 4.0 32.5 - - + +
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Residues in contact with LEU 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 ASP* 2.7 35.3 + - + +
27E ALA* 4.0 5.6 - - - +
29E VAL* 1.4 73.5 - - + +
31E GLN* 1.3 56.2 + - - +
33E ILE* 3.3 20.6 + - + +
34E ARG* 2.9 55.0 + - - +
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Residues in contact with GLN 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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113A TYR* 3.6 6.7 - - - +
366A TYR* 3.0 39.0 + - - -
89D GLU* 4.1 1.8 + - - -
27E ALA 2.9 18.6 + - - +
28E LEU 3.9 2.9 - - - +
30E LEU* 1.3 75.2 - - - +
32E LEU* 1.4 57.1 + - - +
34E ARG* 2.8 41.7 + - - +
35E ILE* 2.9 34.0 + - + +
110E LEU* 6.5 0.2 - - + -
112E ALA* 3.4 40.4 + - + +
115E VAL* 3.9 21.3 - - + -
116E LEU 5.5 0.2 - - - +
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Residues in contact with LEU 32 (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 VAL* 3.5 27.4 - - + -
17E VAL* 4.0 8.7 - - + -
28E LEU* 3.1 35.1 + - + +
29E VAL 3.7 2.9 - - - +
31E GLN* 1.4 74.9 - - - +
33E ILE* 1.3 57.3 + - - +
35E ILE* 3.5 6.5 + - + +
36E GLY 2.8 21.5 + - - -
37E CYS* 2.9 22.2 + - + +
39E VAL* 3.6 28.3 - - + -
57E PHE* 4.0 14.6 - - + -
115E VAL* 3.9 18.6 - - + -
119E LEU* 4.2 19.7 - - + -
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Residues in contact with ILE 33 (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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332A GLN* 6.0 3.6 - - - +
29E VAL* 3.0 35.2 + - + +
30E LEU* 3.5 22.4 - - + +
31E GLN 3.2 0.2 - - - -
32E LEU* 1.3 75.5 - - - +
34E ARG* 1.3 58.6 + - + +
36E GLY* 3.0 18.4 + - - +
37E CYS 4.2 6.5 - - - +
39E VAL* 3.6 16.6 - - + +
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Residues in contact with ARG 34 (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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113A TYR* 3.4 52.9 + - - -
331A ARG 5.5 0.4 + - - -
332A GLN* 2.8 29.8 + - + +
333A ASN* 4.2 11.9 - - + -
364A ASP* 4.5 3.1 - - - +
365A PRO* 6.0 0.8 - - + +
366A TYR* 3.3 26.8 + - + +
11E ARG* 3.6 7.3 + - - -
27E ALA 4.6 1.8 + - - -
30E LEU* 2.9 39.2 + - - +
31E GLN* 2.8 59.5 + - - +
33E ILE* 1.3 75.4 - - + +
35E ILE* 1.3 64.4 + - - +
36E GLY 3.2 0.5 + - - -
112E ALA* 4.7 1.2 - - - +
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Residues in contact with ILE 35 (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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366A TYR* 3.8 34.3 - - + +
10E LEU* 4.7 11.3 - - + +
11E ARG* 3.1 22.5 + - - +
31E GLN* 2.9 29.3 + - - +
32E LEU* 3.6 11.9 - - + +
34E ARG* 1.3 74.3 - - - +
36E GLY* 1.3 56.9 + - - +
37E CYS* 3.8 21.1 - - - +
115E VAL* 3.7 29.2 - - + -
116E LEU* 4.0 35.4 - - + +
119E LEU* 4.5 3.4 - - + -
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Residues in contact with GLY 36 (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 ARG* 3.4 43.0 - - - +
32E LEU 2.8 4.8 + - - -
33E ILE 3.0 14.7 + - - -
34E ARG 4.1 0.7 - - - -
35E ILE* 1.3 78.9 - - - +
37E CYS* 1.3 68.0 + - - +
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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