Contacts of the helix formed by residues 117 - 122 (chain C) in PDB entry 1OJ7
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 TRP 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C TYR* 3.7 26.1 - + + -
115C ASP* 3.0 14.1 + - - +
116C PRO* 1.3 76.5 - - - +
118C HIS* 1.3 57.1 + - - +
119C ILE 3.1 0.2 - - - -
120C LEU* 2.9 50.7 + - + +
121C GLN* 3.0 36.1 + - + +
152C ILE* 3.7 19.7 - - + -
153C SER 3.9 11.4 - - - -
154C ARG* 3.5 55.5 - - + +
157C THR* 5.6 0.2 + - - -
159C ASP* 3.6 32.8 + - + -
161C GLN* 3.8 16.7 - - + +
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Residues in contact with HIS 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C TYR* 2.7 30.6 + + + -
114C ILE* 3.6 25.7 - - + +
115C ASP* 2.9 18.6 + - - +
117C TRP* 1.3 75.2 - - - +
119C ILE* 1.3 53.6 + - - +
121C GLN* 3.2 24.4 + - - +
122C THR* 2.7 55.4 + - + +
126C GLU* 3.4 23.1 + - - -
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Residues in contact with ILE 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C PHE* 4.1 11.0 - - + -
106C ALA* 4.0 8.3 - - + -
107C ALA* 3.8 34.8 - - + +
110C TYR* 3.5 38.1 - - + -
116C PRO* 3.0 16.9 + - + +
118C HIS* 1.3 76.1 - - - +
120C LEU* 1.3 62.3 + - + +
122C THR* 3.3 5.1 + - - -
123C GLY 3.0 7.4 + - - -
124C GLY* 2.8 29.3 + - - +
127C ILE* 3.9 9.6 - - + -
163C PHE* 3.7 38.8 - - + -
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C PHE* 3.6 35.4 - - + -
117C TRP* 2.9 51.1 + - + +
119C ILE* 1.3 80.8 - - + +
121C GLN* 1.3 63.9 + - - +
122C THR 3.3 0.3 + - - -
123C GLY* 3.4 8.0 + - - +
152C ILE* 4.0 10.8 - - + -
161C GLN* 3.4 43.7 - - + +
162C ALA 3.7 26.0 - - - +
163C PHE* 3.7 15.5 - - + -
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Residues in contact with GLN 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C TRP* 3.0 38.0 + - + +
118C HIS* 3.2 32.2 + - - +
120C LEU* 1.3 76.5 - - - +
122C THR* 1.3 63.8 + - + +
123C GLY 3.5 0.2 - - - -
161C GLN* 6.0 1.8 - - - -
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Residues in contact with THR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C TYR* 4.0 4.7 + - - -
118C HIS* 2.7 42.6 + - + +
119C ILE* 3.3 8.1 + - - -
121C GLN* 1.3 81.4 - - + +
123C GLY* 1.3 61.6 + - - +
124C GLY* 3.2 4.2 + - - -
125C LYS* 3.3 36.0 + - - +
126C GLU* 3.4 28.4 + - - +
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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