Contacts of the helix formed by residues 112 - 127 (chain D) in PDB entry 2OZB
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 LEU 112 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D LEU* 4.1 13.0 - - + -
28D GLN* 3.9 11.2 - - - +
29D SER* 3.8 27.8 - - - +
32D TYR* 3.6 56.5 - - + -
34D GLN* 3.8 8.3 - - - +
110D SER* 3.0 10.1 + - - +
111D GLN* 1.3 82.8 - - + +
113D LYS* 1.3 52.5 - - - +
114D GLN 3.4 2.0 - - - -
115D GLN* 3.2 23.7 + - - +
116D ILE* 2.8 46.5 + - + +
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Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D GLU* 3.3 38.0 + - - -
106D ILE* 5.7 3.1 - - - +
107D LYS 5.5 5.2 - - - +
109D GLY* 5.8 0.9 - - - +
110D SER* 3.4 26.6 + - - +
111D GLN 3.3 2.0 - - - -
112D LEU* 1.3 76.2 - - - +
114D GLN* 1.3 62.5 + - + +
116D ILE* 3.2 7.5 + - - +
117D GLN* 2.8 68.1 + - - +
120D GLN* 4.9 1.4 + - - -
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Residues in contact with GLN 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D GLN 4.8 5.8 + - - +
112D LEU 3.4 0.6 - - - -
113D LYS* 1.3 78.1 - - + +
115D GLN* 1.3 71.4 + - + +
117D GLN* 3.3 9.5 + - - +
118D SER* 3.0 29.3 + - - -
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Residues in contact with GLN 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LEU* 3.6 20.2 - - + +
28D GLN* 3.5 23.3 + - - +
111D GLN 3.5 20.2 + - - +
112D LEU* 3.2 18.0 + - - +
114D GLN* 1.3 90.1 - - + +
116D ILE* 1.3 62.5 + - - +
118D SER* 3.5 7.2 - - - -
119D ILE* 3.1 27.8 + - + +
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Residues in contact with ILE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 4.0 16.2 - - + -
34D GLN* 3.3 29.6 - - - +
52D GLU* 3.6 40.2 - - + +
53D PHE* 4.1 5.7 - - + -
104D VAL* 4.1 18.6 - - + -
112D LEU* 2.8 41.8 + - + +
113D LYS* 3.6 11.0 - - - +
115D GLN* 1.3 73.3 - - - +
117D GLN* 1.3 57.0 + - - +
119D ILE* 3.7 2.8 - - - +
120D GLN* 2.8 40.2 + - - +
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Residues in contact with GLN 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LYS* 2.8 54.5 + - - +
114D GLN* 3.8 6.5 - - - +
116D ILE* 1.3 72.7 - - - +
118D SER* 1.3 58.2 + - - +
120D GLN* 3.3 19.7 - - - +
121D GLN* 3.1 35.2 + - - +
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Residues in contact with SER 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D GLN 3.0 17.2 + - - -
115D GLN* 3.5 9.6 - - - -
117D GLN* 1.3 75.1 - - - +
119D ILE* 1.3 60.5 + - - +
121D GLN* 3.3 8.1 + - - +
122D SER* 3.0 30.2 + - - -
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Residues in contact with ILE 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.9 13.5 - - + -
21D LYS* 3.6 34.3 - - + +
22D LEU* 3.5 33.4 - - + +
25D LEU* 3.7 18.4 - - + -
53D PHE* 4.0 20.6 - - + -
115D GLN* 3.1 18.2 + - + +
116D ILE 3.8 2.2 - - - +
118D SER* 1.3 74.7 - - - +
120D GLN* 1.3 67.0 - - - +
122D SER* 3.1 6.5 + - - +
123D ILE* 3.0 33.1 + - + +
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Residues in contact with GLN 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D GLU* 3.0 49.5 + - - +
53D PHE* 4.3 7.0 - - + -
79D PRO* 4.0 22.2 - - + +
113D LYS* 4.9 1.2 + - - -
116D ILE* 2.8 20.7 + - - +
117D GLN* 3.3 31.2 + - - +
119D ILE* 1.3 79.5 - - - +
121D GLN* 1.3 58.8 + - + +
123D ILE* 3.4 5.7 + - - +
124D GLU* 2.8 33.3 + - - +
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Residues in contact with GLN 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D GLN* 3.1 23.6 + - - +
118D SER* 3.8 6.5 - - - +
119D ILE 3.2 0.4 - - - -
120D GLN* 1.3 74.1 - - + +
122D SER* 1.3 65.9 + - - +
124D GLU* 3.5 13.1 + - + +
125D ARG* 3.2 37.9 + - + +
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Residues in contact with SER 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.8 27.1 - - - +
21D LYS* 4.9 7.8 + - - -
118D SER* 3.0 16.2 + - - -
119D ILE* 3.1 15.1 + - - +
121D GLN* 1.3 77.7 - - - +
123D ILE* 1.3 62.5 + - - +
125D ARG* 3.4 21.2 + - - +
126D LEU* 3.6 14.5 - - - +
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PRO* 4.9 2.7 - - + +
18D LEU* 5.1 2.5 - - + -
22D LEU* 4.5 4.3 - - + -
53D PHE* 4.2 24.5 - - + -
79D PRO* 3.5 22.0 - - + +
80D TYR 3.4 24.9 - - - +
81D VAL* 3.5 32.3 - - + -
119D ILE* 3.0 37.3 + - + +
120D GLN* 3.7 5.4 - - - +
121D GLN 3.2 0.2 - - - -
122D SER* 1.3 74.1 - - - +
124D GLU* 1.3 64.9 + - - +
126D LEU* 3.2 24.7 + - - +
127D LEU* 4.0 2.6 + - - +
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Residues in contact with GLU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ASN* 4.8 9.9 + - - -
79D PRO* 3.6 25.5 - - - +
120D GLN* 2.8 25.4 - - - +
121D GLN* 3.9 14.8 - - + +
123D ILE* 1.3 76.2 - - - +
125D ARG* 1.3 62.6 + - - +
127D LEU* 3.1 18.9 + - - +
128D VAL* 3.4 11.1 + - - +
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Residues in contact with ARG 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D GLN* 3.2 27.7 + - + +
122D SER* 3.5 14.4 - - - +
123D ILE 3.3 0.4 - - - -
124D GLU* 1.3 77.7 - - - +
126D LEU* 1.3 58.6 + - + +
128D VAL* 2.8 28.2 + - - +
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Residues in contact with LEU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PRO* 3.9 23.2 - - + +
13D LEU 5.1 7.0 - - - +
14D ALA* 5.0 5.2 - - - -
15D ASP 6.0 1.1 - - - +
18D LEU* 3.7 22.4 - - + -
81D VAL* 3.5 31.4 - - + -
122D SER 3.6 11.9 - - - +
123D ILE* 3.4 12.8 - - - +
124D GLU 3.1 0.8 - - - -
125D ARG* 1.3 75.5 - - + +
127D LEU* 1.3 63.0 + - - +
128D VAL* 3.1 10.0 + - - +
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Residues in contact with LEU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D TYR* 4.4 23.3 - - + +
12D PRO* 3.7 37.5 - - + -
80D TYR* 5.6 4.9 - - + +
123D ILE 4.0 2.1 + - - +
124D GLU* 3.1 11.7 + - - +
126D LEU* 1.3 77.4 - - - +
128D VAL* 1.3 72.8 + - - +
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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