Contacts of the helix formed by residues 124 - 130 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B GLN* 4.5 9.6 + - - -
122B GLU* 3.7 1.4 - - - +
123B PHE* 1.3 88.3 - - + +
125B HIS* 1.3 66.1 + - - +
126B PHE 3.4 2.0 - - - -
127B TYR* 3.4 16.8 + - + +
128B HIS* 3.0 49.8 + - + +
139B VAL* 3.9 45.0 - - - +
141B THR* 6.1 1.6 - - - +
166B MET* 4.9 3.1 - - - -
122C GLU* 3.6 24.6 + - - +
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Residues in contact with HIS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PRO* 4.0 29.1 - - + +
118B LEU* 3.5 21.6 - - + +
120B ASP* 2.9 30.2 + - - -
122B GLU* 3.4 29.7 + - + +
123B PHE 3.6 1.8 - - - -
124B ARG* 1.3 79.9 - - - +
126B PHE* 1.3 75.0 + - + +
128B HIS* 3.2 7.5 + - - +
129B MET* 2.9 32.3 + - - +
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Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ILE* 5.0 1.3 - - + -
407A TRP* 3.6 17.7 - + - -
75B PHE* 3.6 33.2 - + + -
76B GLY* 3.6 15.5 - - - -
79B GLU* 3.3 40.0 - - + +
80B LEU* 4.0 25.4 - - + -
83B MET* 4.9 2.6 - - - +
116B HIS 3.6 3.1 - - - -
117B THR* 4.6 4.3 - - - -
118B LEU* 3.7 30.5 - - + -
122B GLU 5.6 3.6 - - - -
123B PHE 5.2 0.4 + - - -
124B ARG 3.4 0.2 - - - -
125B HIS* 1.3 83.1 - - + +
127B TYR* 1.3 66.2 + - - +
129B MET* 3.3 23.5 + - - +
130B SER* 3.1 23.4 + - - -
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Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PHE* 6.3 0.2 - - - -
123B PHE 5.1 2.1 + - - +
124B ARG* 3.5 26.1 - - - +
125B HIS 3.2 0.2 - - - -
126B PHE* 1.3 78.5 - - - +
128B HIS* 1.3 86.8 + + - +
130B SER* 3.2 8.0 + - - -
131B GLU 3.5 0.5 + - - -
137B GLN* 3.1 73.7 + - + +
138B ALA* 3.7 17.8 - - - -
139B VAL* 3.6 32.3 + - + +
164B TYR* 3.5 32.3 + + - +
166B MET* 4.9 5.8 - - + -
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Residues in contact with HIS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PRO* 6.4 1.3 - - + -
124B ARG* 3.0 41.5 + - + +
125B HIS* 3.6 7.5 + - - +
127B TYR* 1.3 95.8 - + - +
129B MET* 1.3 64.2 + - + +
130B SER 3.1 3.5 + - - -
131B GLU* 3.2 22.0 + - + +
132B PRO* 3.7 4.3 - - - +
137B GLN* 5.3 1.8 - - - -
128C HIS* 6.2 4.5 - + - -
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Residues in contact with MET 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A MET* 3.6 25.1 - - - -
129A MET* 3.3 66.7 - - + +
132A PRO* 4.1 22.2 - - + -
133A ILE* 4.0 18.6 - - + -
80B LEU* 3.7 17.3 - - + -
83B MET* 4.4 8.1 - - + -
125B HIS 2.9 20.9 + - - +
126B PHE* 3.3 31.6 + - - +
128B HIS* 1.3 76.9 - - + +
130B SER* 1.3 57.5 + - - +
131B GLU 3.4 0.2 - - - -
132B PRO* 3.4 3.9 - - - +
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Residues in contact with SER 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B MET* 3.3 21.9 - - - +
86B ILE* 5.1 2.3 - - - +
98B HIS* 4.9 2.6 + - - -
126B PHE 3.1 14.9 + - - -
127B TYR 3.6 7.2 - - - -
128B HIS 3.1 1.2 - - - -
129B MET* 1.3 76.9 - - - +
131B GLU* 1.3 60.1 + - - +
132B PRO* 3.4 2.5 - - - -
133B ILE* 3.4 19.4 + - - +
134B THR* 3.0 20.9 + - - +
137B GLN* 4.1 1.8 - - - -
164B TYR* 3.4 32.1 - - - -
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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