Contacts of the helix formed by residues 124 - 130 (chain C) in PDB entry 1OVM
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 ARG 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B GLU* 3.6 24.8 + - - +
108C GLN* 4.7 8.9 + - - -
122C GLU* 3.7 1.6 - - - +
123C PHE* 1.3 87.3 - - + +
125C HIS* 1.3 67.7 + - - +
126C PHE 3.4 2.0 - - - -
127C TYR* 3.3 18.9 + - + +
128C HIS* 3.0 49.7 + - + -
139C VAL* 3.8 44.2 - - - +
141C THR* 6.1 1.6 - - - +
166C MET* 4.9 2.2 - - - -
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Residues in contact with HIS 125 (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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118C LEU* 3.4 23.3 - - + +
120C ASP* 2.8 30.5 + - - -
122C GLU* 3.4 30.0 + - + +
123C PHE 3.6 1.8 - - - -
124C ARG* 1.3 79.8 - - - +
126C PHE* 1.3 77.2 + - + +
128C HIS* 3.1 7.1 + - - +
129C MET* 2.9 30.4 + - - +
90D TYR* 6.3 0.4 - + - -
132D PRO* 4.1 28.0 - - + +
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Residues in contact with PHE 126 (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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75C PHE* 3.6 36.6 - + + -
76C GLY* 3.6 13.7 - - - -
79C GLU* 3.3 39.0 - - + +
80C LEU* 4.1 18.2 - - + -
83C MET* 4.9 1.9 - - - +
116C HIS 3.6 3.8 - - - -
117C THR* 4.5 3.8 - - - -
118C LEU* 3.7 42.8 - - + -
122C GLU 5.6 3.4 - - - -
123C PHE 6.1 0.2 - - - -
124C ARG 3.4 0.4 - - - -
125C HIS* 1.3 76.8 - - + +
127C TYR* 1.3 64.7 + - - +
129C MET* 3.2 23.5 + - - +
130C SER* 3.1 23.7 + - - -
133D ILE* 5.1 1.6 - - + -
407D TRP* 3.7 16.8 - + - -
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Residues in contact with TYR 127 (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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75C PHE* 6.2 0.6 - - - -
123C PHE 5.0 2.6 + - - +
124C ARG* 3.3 27.2 + - - +
125C HIS 3.2 0.4 - - - -
126C PHE* 1.3 77.3 - - - +
128C HIS* 1.3 86.4 + + - +
130C SER* 3.3 7.3 + - - -
131C GLU 3.6 0.5 + - - -
137C GLN* 3.1 70.1 + - + +
138C ALA* 3.7 21.1 - - - -
139C VAL* 3.6 31.8 + - + +
164C TYR* 3.5 32.4 + + - +
166C MET* 4.9 4.9 - - + -
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Residues in contact with HIS 128 (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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128B HIS* 6.2 4.5 - + - -
124C ARG* 3.0 43.8 + - + +
125C HIS* 3.5 7.0 - - - +
127C TYR* 1.3 95.0 - + - +
129C MET* 1.3 62.8 + - + +
130C SER 3.1 2.9 + - - -
131C GLU* 3.3 21.7 + - + +
132C PRO* 3.8 4.2 - - - +
137C GLN* 5.2 2.0 - - - -
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Residues in contact with MET 129 (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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80C LEU* 3.8 19.7 - - + -
83C MET* 4.1 7.8 - - + +
125C HIS 2.9 19.3 + - - +
126C PHE* 3.2 28.2 + - - +
128C HIS* 1.3 77.1 - - + +
130C SER* 1.3 58.0 + - - +
131C GLU 3.4 0.2 - - - -
132C PRO* 3.5 4.3 - - - +
83D MET* 3.6 24.9 - - - -
129D MET* 3.3 67.0 - - + +
132D PRO* 4.0 24.7 - - + -
133D ILE* 4.1 18.2 - - + -
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Residues in contact with SER 130 (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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83C MET* 3.3 22.4 - - - +
86C ILE* 5.1 1.9 - - - +
98C HIS* 5.0 3.1 + - - -
126C PHE 3.1 14.9 + - - -
127C TYR 3.6 6.3 - - - -
128C HIS 3.1 0.8 - - - -
129C MET* 1.3 77.1 - - - +
131C GLU* 1.3 61.2 + - - +
132C PRO* 3.4 2.2 - - - -
133C ILE* 3.3 22.8 + - - +
134C THR* 3.0 20.2 + - - +
137C GLN* 4.0 1.6 - - - -
164C TYR* 3.4 32.6 - - - -
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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