Contacts of the helix formed by residues 112 - 125 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 4.1 15.3 - - + -
28A GLN* 4.0 16.8 - - + +
29A SER* 3.9 28.7 - - - +
32A TYR* 3.8 46.9 - - + -
34A GLN* 3.9 8.5 - - - +
110A SER* 2.8 10.7 - - - +
111A GLN* 1.3 83.5 - - - +
113A LYS* 1.3 63.7 + - - +
114A GLN 3.2 2.9 - - - -
115A GLN* 3.1 21.7 + - + +
116A ILE* 2.9 32.0 + - + +
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLU* 2.7 34.4 + - - +
106A ILE* 4.3 13.7 - - - +
107A LYS 4.0 19.3 - - - -
108A GLU* 5.4 1.8 - - - +
109A GLY* 5.3 5.8 - - - +
110A SER* 3.1 26.0 + - - +
111A GLN 3.6 1.0 - - - -
112A LEU* 1.3 75.6 - - - +
114A GLN* 1.3 63.0 + - + +
116A ILE* 3.4 4.6 + - + +
117A GLN* 2.8 49.5 + - - +
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Residues in contact with GLN 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLN 4.9 9.6 + - - +
112A LEU 3.2 0.8 - - - -
113A LYS* 1.3 82.6 - - + +
115A GLN* 1.3 59.9 + - + +
117A GLN* 3.6 8.6 + - - +
118A SER* 3.1 26.7 + - - -
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Residues in contact with GLN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASP* 5.9 0.7 - - - +
25A LEU* 3.5 35.8 - - + +
28A GLN* 4.9 9.5 - - - +
111A GLN 6.1 0.2 - - - +
112A LEU* 3.1 23.2 + - + +
114A GLN* 1.3 77.2 - - + +
116A ILE* 1.3 59.3 + - - +
118A SER* 3.2 6.8 + - - -
119A ILE* 2.9 25.1 + - - +
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Residues in contact with ILE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 4.0 14.6 - - + -
34A GLN* 3.7 24.7 - - - +
52A GLU* 3.6 42.6 - - + +
53A PHE* 4.0 16.8 - - + -
104A VAL* 4.1 11.4 - - + -
110A SER* 4.2 1.8 - - - +
112A LEU* 2.9 40.2 + - + +
113A LYS* 3.7 7.0 - - + +
115A GLN* 1.3 74.7 - - - +
117A GLN* 1.3 66.5 + - - +
119A ILE* 3.1 3.3 + - - +
120A GLN* 2.9 30.8 + - - +
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Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS* 2.8 36.1 + - - +
114A GLN* 3.8 9.7 - - - +
116A ILE* 1.3 76.6 - - - +
118A SER* 1.3 63.6 + - - +
120A GLN* 3.4 17.7 + - - +
121A GLN* 3.1 34.3 + - + +
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 4.3 14.7 + - - -
114A GLN 3.1 17.6 + - - -
115A GLN* 3.5 9.0 - - - -
116A ILE 3.1 0.2 - - - -
117A GLN* 1.3 77.6 - - - +
119A ILE* 1.3 62.5 + - - +
121A GLN* 3.3 13.5 + - - +
122A SER* 3.0 22.1 + - - -
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.0 11.9 - - + -
21A LYS* 4.0 35.0 - - + +
22A LEU* 3.6 36.6 - - + +
25A LEU* 3.4 27.4 - - + -
53A PHE* 4.1 16.8 - - + -
115A GLN 2.9 13.3 + - - +
116A ILE 3.8 3.6 - - - +
118A SER* 1.3 72.4 - - - +
120A GLN* 1.3 61.9 + - - +
122A SER* 3.1 3.5 + - - -
123A ILE* 2.8 40.1 + - + +
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Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLU* 2.8 49.0 + - - +
53A PHE* 4.3 8.7 - - + -
79A PRO* 4.0 17.4 - - + +
116A ILE* 2.9 19.8 + - - +
117A GLN* 3.4 32.0 + - - +
118A SER 3.3 0.2 - - - -
119A ILE* 1.3 77.7 - - - +
121A GLN* 1.3 58.6 + - + +
123A ILE* 3.2 7.0 + - - +
124A GLU* 2.8 33.4 + - - +
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Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLN* 3.1 23.6 + - + +
118A SER* 3.6 9.9 - - - +
119A ILE 3.2 0.2 - - - -
120A GLN* 1.3 76.7 - - + +
122A SER* 1.3 64.8 + - - +
124A GLU* 3.1 17.6 + - - +
125A ARG* 3.2 39.7 + - - +
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Residues in contact with SER 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.9 27.3 - - - +
21A LYS* 4.0 19.9 + - - -
118A SER* 3.0 16.2 + - - -
119A ILE* 3.1 11.3 + - - -
121A GLN* 1.3 75.7 - - - +
123A ILE* 1.3 63.4 + - - +
125A ARG* 3.4 30.7 + - - +
126A LEU* 3.6 11.1 - - - +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PRO* 5.1 0.2 - - + -
18A LEU* 5.1 3.1 - - + -
22A LEU* 4.2 3.1 - - + -
53A PHE* 4.0 25.4 - - + -
54A ILE 5.0 0.2 - - - +
79A PRO* 3.9 11.0 - - + -
80A TYR 3.3 33.9 - - - +
81A VAL* 3.4 34.8 - - + -
119A ILE* 2.8 39.6 + - + +
120A GLN 3.6 5.6 - - - +
122A SER* 1.3 72.9 - - - +
124A GLU* 1.3 65.4 - - - +
126A LEU* 2.9 22.7 + - - +
127A LEU* 3.3 15.0 + - + +
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Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASN* 4.7 3.3 - - - +
79A PRO* 3.7 25.0 - - - +
120A GLN* 2.8 20.2 + - - +
121A GLN* 3.1 8.9 + - - +
123A ILE* 1.3 73.3 - - - +
125A ARG* 1.3 59.2 + - - +
126A LEU 3.2 0.4 - - - -
127A LEU* 3.4 17.1 + - - +
128A VAL 3.1 32.7 + - - +
503A CA 3.4 22.3 - - - -
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLN* 3.2 40.7 + - - +
122A SER* 3.4 23.3 + - - +
123A ILE 3.0 1.2 - - - -
124A GLU* 1.3 75.7 - - - +
126A LEU* 1.3 67.1 + - + +
128A VAL* 3.9 10.4 + - - +
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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