Contacts of the helix formed by residues 122 - 132 (chain A) in PDB entry 1IOU
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 MET 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.3 30.5 - - - -
20A SER* 4.0 4.9 - - - +
97A ILE* 2.8 46.4 - - + +
100A GLU* 3.3 31.2 - - + +
101A TYR* 3.4 31.0 - - + +
104A ALA* 5.8 3.1 - - + -
120A LEU 4.3 0.6 + - - -
121A LYS* 1.3 89.6 - - + +
123A LYS* 1.3 66.5 + - - +
124A GLN 2.9 7.8 + - - +
125A LEU* 3.0 23.3 + - + +
126A ASP* 2.9 13.0 + - - +
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Residues in contact with LYS 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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100A GLU* 5.0 1.8 + - - +
120A LEU* 4.0 42.9 + - + +
121A LYS* 5.9 4.4 - - - +
122A MET* 1.3 78.5 - - - +
124A GLN* 1.3 52.4 + - - +
126A ASP* 3.2 14.3 + - - +
127A THR* 2.7 38.7 + - - +
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Residues in contact with GLN 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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96A LYS* 4.0 10.1 + - - +
97A ILE* 5.4 0.6 - - - +
100A GLU* 3.1 53.5 + - + +
122A MET 2.9 0.6 + - - -
123A LYS* 1.3 74.8 - - - +
125A LEU* 1.3 65.2 + - - +
126A ASP 2.8 4.5 + - - -
127A THR* 2.9 6.2 + - - -
128A TYR* 2.7 80.8 + - + -
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Residues in contact with LEU 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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6A ILE* 3.3 11.1 - - + +
7A GLY* 3.2 17.0 - - - -
8A VAL* 3.0 30.3 - - + -
20A SER* 4.3 6.3 - - - +
22A VAL* 3.1 24.7 - - + +
97A ILE* 3.0 41.3 - - + +
122A MET* 3.0 17.8 + - - +
124A GLN* 1.3 78.6 - - - +
126A ASP* 1.3 79.4 + - - +
128A TYR* 3.7 8.1 - - - +
129A ILE* 3.2 20.6 + - - +
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Residues in contact with ASP 126 (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 GLU 4.8 3.1 + - - +
22A VAL* 3.3 26.2 + - + +
118A ASP 5.2 1.6 - - - +
120A LEU* 5.5 1.9 - - - -
121A LYS 3.8 9.4 + - - +
122A MET 2.9 17.1 - - - +
123A LYS* 3.2 17.8 - - - +
124A GLN 2.8 1.2 + - - -
125A LEU* 1.3 90.8 - - - +
127A THR* 1.3 64.2 + - - +
128A TYR 3.0 1.3 - - - -
129A ILE* 2.7 23.0 - - - +
130A SER* 3.1 9.1 + - - -
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Residues in contact with THR 127 (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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123A LYS* 2.7 19.5 + - - +
124A GLN* 2.9 8.6 + - - -
126A ASP* 1.3 73.6 - - - +
128A TYR* 1.3 67.8 + - + +
130A SER* 4.3 4.5 - - - -
131A LYS* 2.7 55.8 + - + +
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Residues in contact with TYR 128 (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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93A LEU* 4.0 18.4 - - + -
96A LYS* 3.1 51.3 - - + +
97A ILE* 5.3 1.6 - - + -
124A GLN* 2.7 57.6 + - + +
125A LEU* 3.7 8.5 - - - +
127A THR* 1.3 78.7 - - + +
129A ILE* 1.3 56.7 + - - +
130A SER 3.0 1.9 + - - -
131A LYS* 3.1 3.0 + - - +
132A TYR* 2.6 71.7 + + + +
139A ASP* 5.2 4.7 + - - -
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Residues in contact with ILE 129 (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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3A ILE* 3.2 28.6 - - + +
4A TYR 4.3 3.1 - - - +
6A ILE* 3.1 49.2 - - + +
22A VAL* 3.2 25.6 - - + -
23A LYS 4.2 8.5 - - - +
24A ASP* 3.2 39.2 - - + +
125A LEU 3.2 8.6 + - - +
126A ASP 2.7 24.2 - - - +
128A TYR* 1.3 78.7 - - - +
130A SER* 1.3 59.8 + - - +
132A TYR* 3.9 3.4 - - - -
133A GLN 3.8 1.0 + - - -
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Residues in contact with SER 130 (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* 4.4 6.7 - - - -
126A ASP 3.1 11.9 + - - -
127A THR* 3.6 11.7 - - - -
128A TYR 3.0 1.0 - - - -
129A ILE* 1.3 79.6 - - - +
131A LYS* 1.3 73.7 + - - +
133A GLN* 3.0 39.6 + - - +
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Residues in contact with LYS 131 (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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127A THR* 2.7 47.7 - - + +
128A TYR* 3.1 2.8 + - - +
130A SER* 1.3 87.1 - - - +
132A TYR* 1.3 62.9 + - - +
133A GLN* 3.0 7.8 + - - +
134A ASP* 3.8 5.0 + - - +
137A GLN* 3.1 42.8 + - - +
140A ALA* 4.4 5.8 - - - +
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Residues in contact with TYR 132 (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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3A ILE* 4.1 2.2 - - + -
85A TYR* 2.7 39.5 + + + +
89A PRO* 3.3 19.8 + - + -
92A THR* 3.2 17.5 - - + +
93A LEU* 3.0 38.7 + - + -
128A TYR* 2.6 50.4 + + + +
129A ILE* 4.1 7.9 - - - +
130A SER 3.4 0.2 - - - -
131A LYS* 1.3 67.6 - - - +
133A GLN* 1.3 51.0 + - - +
134A ASP* 2.4 36.7 + - - +
136A SER 3.6 23.5 - - - +
137A GLN* 3.8 12.3 - - + +
139A ASP* 3.2 26.8 + - - -
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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