Contacts of the helix formed by residues 125 - 133 (chain A) in PDB entry 1O0C
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 THR 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLU 3.3 4.9 + - - +
124A LEU* 1.3 78.1 - - - +
126A PRO* 1.3 76.4 - - + +
127A GLU* 3.1 16.7 + - - +
128A GLN* 3.0 42.5 + - - +
129A ILE* 3.0 18.4 + - - +
168A GLY 4.3 2.7 - - - +
169A LYS* 5.9 6.1 - - + +
974B C 3.7 2.2 - - - +
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Residues in contact with PRO 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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125A THR* 1.3 89.6 - - + +
127A GLU* 1.3 73.5 + - - +
129A ILE* 3.2 17.2 - - + +
130A ARG* 4.0 9.0 + - - +
168A GLY* 3.6 23.3 - - - +
974B C 3.7 38.6 + - + +
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Residues in contact with GLU 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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125A THR* 3.0 17.4 + - - +
126A PRO* 1.3 94.8 - - - +
128A GLN* 1.3 65.3 - - + +
130A ARG* 3.3 26.7 + - - +
131A GLU* 3.3 31.4 + - - +
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Residues in contact with GLN 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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123A GLU 4.5 1.6 + - - -
124A LEU* 3.5 33.1 - - + +
125A THR* 3.0 47.1 + - - +
127A GLU* 1.3 74.4 - - + +
129A ILE* 1.3 65.2 + - - +
131A GLU* 3.0 18.3 + - - +
132A TYR* 2.9 37.3 + - + -
145A TYR* 5.6 1.2 + - - -
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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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124A LEU* 4.2 15.6 - - + +
125A THR 3.0 12.0 + - - +
126A PRO* 3.2 24.2 - - + +
128A GLN* 1.3 76.2 - - - +
130A ARG* 1.3 64.7 + - - +
132A TYR* 3.3 1.7 + - - +
133A ARG* 3.0 34.3 + - - +
171A CYS* 5.1 1.3 - - - -
173A ARG* 3.7 39.0 + - - +
178A MET* 5.6 0.2 - - - +
189A VAL* 3.9 25.4 - - + -
974B C 3.8 37.5 - - + +
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Residues in contact with ARG 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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126A PRO 4.4 8.8 + - - +
127A GLU* 3.3 31.6 + - - +
128A GLN 3.2 0.4 - - - -
129A ILE* 1.3 80.5 - - - +
131A GLU* 1.3 66.0 + - - +
133A ARG* 3.0 32.8 + - - +
134A GLY 4.1 5.2 + - - +
972B A 4.1 13.2 + - + +
973B G 3.3 32.5 + - - +
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Residues in contact with GLU 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 GLU* 3.4 20.9 - - - +
128A GLN* 3.0 24.0 + - - +
130A ARG* 1.3 86.8 + - - +
132A TYR* 1.3 64.7 + - + +
134A GLY* 4.6 3.0 + - - -
141A LYS* 4.2 9.8 + - - -
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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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124A LEU* 3.8 24.5 - - + +
128A GLN* 2.9 33.4 + - + +
129A ILE* 3.9 4.0 - - - +
131A GLU* 1.3 81.6 - - + +
133A ARG* 1.3 61.5 + - - +
134A GLY 3.2 2.4 + - - -
140A GLY* 3.2 0.3 - - - -
141A LYS* 2.8 84.0 + - + +
142A ASN 3.3 20.4 - - - -
143A SER* 4.0 11.2 - - - -
144A PRO* 3.9 19.2 - - + +
173A ARG* 5.2 0.7 - - - +
178A MET* 3.6 6.3 - - + +
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Residues in contact with ARG 133 (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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129A ILE* 3.0 24.7 + - + +
130A ARG* 3.0 28.3 + - - +
132A TYR* 1.3 78.2 - - - +
134A GLY* 1.3 55.4 + - - +
140A GLY* 3.4 4.0 - - - -
173A ARG* 5.1 3.4 - - - +
178A MET* 4.2 7.9 - - + -
183A ILE* 3.9 24.9 - - + -
186A ARG* 2.7 51.7 + - + +
972B A 2.9 32.9 + - - +
973B G 2.9 27.1 + - - -
974B C 2.8 40.4 + - - -
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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