Contacts of the helix formed by residues 117 - 125 (chain B) in PDB entry 1OPO
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 PHE 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B GLU* 4.2 2.0 - - - +
109B VAL* 4.6 12.1 - - + -
110B SER 3.3 39.5 - - - -
111B PRO* 3.6 13.7 - - + +
113B ASN 2.9 6.5 + - - +
114B VAL 3.4 3.3 - - - +
116B VAL* 1.3 96.5 - - + +
118B PRO* 1.3 71.3 - - - +
119B GLN 3.5 1.1 - - - -
120B LEU* 3.4 30.3 - - + -
121B SER* 2.8 21.6 + - - +
132B ILE* 5.4 6.7 - - + -
135B LEU* 5.1 3.8 - - + -
233B ILE* 3.8 22.7 - - + -
235B TYR* 3.7 35.2 - + + -
237B ILE* 5.3 4.7 - - + -
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Residues in contact with PRO 118 (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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89B GLU* 3.4 22.7 - - + +
90B LEU* 3.8 21.8 - - + +
91B LEU 5.9 0.2 - - - +
114B VAL* 3.4 17.4 - - + +
115B ALA 5.2 2.9 - - - +
116B VAL 3.3 11.0 - - - +
117B PHE* 1.3 79.2 - - - +
119B GLN* 1.3 57.5 + - - +
121B SER* 2.7 23.7 + - - +
278B ALA* 5.6 4.5 - - + -
279B ALA 5.4 7.2 - - - +
347B ARG* 2.8 17.0 + - - +
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Residues in contact with GLN 119 (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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85B MET* 5.7 4.0 - - - -
87B LYS* 2.8 42.1 + - - +
89B GLU* 2.9 16.4 + - - +
118B PRO* 1.3 77.0 - - + +
120B LEU* 1.3 70.3 + - - +
122B LEU* 2.8 26.9 + - + +
123B LEU* 3.4 23.9 + - + +
235B TYR* 5.5 0.4 + - - +
347B ARG* 4.5 2.9 - - - +
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Residues in contact with LEU 120 (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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85B MET* 4.3 22.0 - - + -
89B GLU* 3.4 3.8 + - - -
111B PRO* 3.9 15.0 - - + -
117B PHE* 3.4 35.4 - - + -
118B PRO 3.6 0.4 - - - -
119B GLN* 1.3 80.0 - - - +
121B SER* 1.3 63.8 + - - +
123B LEU* 3.0 12.1 + - + +
124B ALA* 2.9 20.1 + - - +
235B TYR* 3.6 31.1 + - + +
237B ILE* 3.3 33.4 - - + -
239B LEU* 4.4 12.8 - - + -
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Residues in contact with SER 121 (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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111B PRO 3.1 24.5 + - - -
112B ARG* 4.0 12.8 - - - -
113B ASN 4.3 0.2 - - - -
114B VAL* 3.7 21.4 - - - +
117B PHE* 2.8 14.7 + - - +
118B PRO 2.7 23.4 + - - -
120B LEU* 1.3 76.1 - - - +
122B LEU* 1.3 63.4 + - - +
124B ALA* 3.2 13.2 + - - +
125B THR* 3.4 9.0 + - - +
347B ARG* 3.7 12.3 + - - -
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Residues in contact with LEU 122 (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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119B GLN* 2.8 17.0 + - + +
121B SER* 1.3 81.8 + - - +
123B LEU* 1.3 66.6 + - + +
125B THR* 2.3 30.9 + - - +
126B ASN* 3.8 4.3 + - - -
248B ILE* 4.5 20.6 - - + -
347B ARG* 4.0 38.6 - - - +
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Residues in contact with LEU 123 (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* 4.6 19.1 - - + -
85B MET* 4.3 30.7 - - + -
119B GLN* 4.0 31.6 - - + +
120B LEU* 3.0 13.4 + - + +
122B LEU* 1.3 86.8 - - + +
124B ALA* 1.3 61.9 + - - +
125B THR 3.0 1.6 + - - -
126B ASN* 3.2 19.4 + - - +
127B PHE* 3.5 15.7 - - + -
239B LEU* 4.3 10.8 - - + -
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Residues in contact with ALA 124 (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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111B PRO* 3.9 33.2 - - + +
112B ARG* 3.1 22.4 + - - +
120B LEU 2.9 12.2 + - - +
121B SER 3.4 10.1 - - - +
122B LEU 3.2 0.2 - - - -
123B LEU* 1.3 72.7 - - - +
125B THR* 1.3 55.8 + - - +
126B ASN 2.9 12.1 + - - -
127B PHE* 3.2 13.2 + - - +
198B ILE* 3.9 10.8 - - + +
239B LEU* 4.3 14.1 - - + +
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Residues in contact with THR 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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112B ARG* 4.2 10.9 + - - +
121B SER 3.4 6.4 + - - +
122B LEU* 2.3 38.8 + - - +
123B LEU 3.0 0.4 + - - -
124B ALA* 1.3 73.7 - - - +
126B ASN* 1.3 63.0 + - - +
127B PHE 3.6 0.7 - - - -
243B THR* 5.0 1.0 - - - +
244B LYS 3.7 2.6 - - - +
245B THR* 3.2 12.3 - - + -
246B ALA* 2.8 67.1 + - + +
247B LYS 4.4 3.4 - - - +
248B ILE* 4.4 12.3 - - + -
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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