Contacts of the strand formed by residues 83 - 95 (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 MET 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B SER* 1.3 72.1 + - - +
84B THR* 1.3 63.1 + - - +
85B MET* 4.0 28.2 + - + -
123B LEU* 4.6 19.1 - - + -
127B PHE* 4.1 26.4 - - + -
237B ILE 3.9 0.7 - - - +
238B VAL* 3.3 2.7 - - - -
239B LEU* 2.7 53.7 + - + +
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Residues in contact with THR 84 (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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82B SER* 4.2 3.9 + - - -
83B MET* 1.3 75.4 - - - +
85B MET* 1.3 77.1 + - - +
86B SER* 5.4 0.9 - - - +
133B THR* 5.9 0.2 - - - +
236B THR* 4.1 19.5 - - + -
237B ILE 3.6 7.9 - - - +
238B VAL* 3.9 23.4 - - + +
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Residues in contact with MET 85 (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* 4.0 23.3 + - + +
84B THR* 1.3 95.1 - - - +
86B SER* 1.3 64.8 + - - +
87B LYS* 4.2 10.5 - - - -
119B GLN* 5.7 3.8 - - - -
120B LEU* 4.3 20.6 - - + -
123B LEU* 4.3 26.5 - - + -
235B TYR* 3.7 10.3 - - + +
236B THR* 2.9 26.3 - - - +
237B ILE* 2.9 17.6 + - + +
239B LEU* 5.3 4.5 - - + -
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Residues in contact with SER 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 4.3 1.7 + - - +
85B MET* 1.3 74.4 - - - +
87B LYS* 1.3 66.6 + - - +
235B TYR 3.1 6.7 - - - -
236B THR* 2.7 32.1 + - - +
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Residues in contact with LYS 87 (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* 5.6 8.6 - - + -
86B SER* 1.3 77.9 - - - +
88B THR* 1.3 66.6 + - - +
89B GLU* 4.0 13.2 - - + -
119B GLN* 2.8 39.9 + - - +
233B ILE 3.6 1.6 - - - +
234B GLN* 3.5 2.6 - - - +
235B TYR* 2.9 61.4 + - + +
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Residues in contact with THR 88 (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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87B LYS* 1.3 79.9 - - - +
89B GLU* 1.3 62.6 + - - +
138B LYS* 5.0 4.5 - - + -
232B PHE* 3.9 28.4 - - + -
233B ILE 3.1 11.7 - - - +
234B GLN* 3.3 34.6 + - + +
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Residues in contact with GLU 89 (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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87B LYS* 4.0 14.1 - - + -
88B THR* 1.3 78.6 - - - +
90B LEU* 1.3 62.4 + - - +
117B PHE* 4.2 1.2 - - - -
118B PRO* 3.4 22.0 - - + +
119B GLN* 2.9 36.1 + - - +
120B LEU* 3.4 14.9 + - - +
232B PHE* 3.3 8.2 - - - +
233B ILE* 2.8 44.0 + - + +
235B TYR* 2.6 33.9 + - + +
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Residues in contact with LEU 90 (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* 1.3 73.3 - - - +
91B LEU* 1.3 66.5 + - - +
92B SER* 3.8 20.0 - - - +
93B THR* 5.7 2.5 - - - +
118B PRO* 3.8 23.0 - - + +
230B GLU* 3.9 29.2 - - + +
231B LEU 3.6 11.0 - - - +
232B PHE* 3.7 22.7 - - + -
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Residues in contact with LEU 91 (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 2.0 + - - -
90B LEU* 1.3 76.4 - - - +
92B SER* 1.3 62.8 + - - +
107B TRP* 3.8 35.7 - - + +
115B ALA 3.7 24.0 - - - +
116B VAL* 4.3 19.5 - - + +
137B VAL* 4.5 16.8 - - + -
214B ILE* 4.9 13.0 - - + -
231B LEU* 2.8 35.2 + - + +
233B ILE* 4.3 25.4 - - + +
326B GLU* 4.4 6.8 - - - +
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Residues in contact with SER 92 (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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90B LEU* 3.8 9.0 - - - +
91B LEU* 1.3 84.0 - - - +
93B THR* 1.3 70.4 + - - +
94B VAL* 5.0 0.5 - - - +
105B GLU* 4.8 2.2 + - - -
107B TRP* 3.7 25.7 - - - -
216B LEU* 5.0 1.7 - - - +
230B GLU* 3.2 6.6 - - - +
231B LEU* 2.8 45.9 + - - +
326B GLU* 3.7 21.1 - - - -
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Residues in contact with THR 93 (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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90B LEU* 5.7 2.3 - - - +
92B SER* 1.3 84.5 + - - +
94B VAL* 1.3 68.0 + - - +
95B LYS* 3.9 10.8 + - + +
105B GLU* 4.7 7.4 - - - +
216B LEU* 5.3 1.4 - - - +
227B VAL* 3.5 37.2 - - + -
229B GLY 3.9 5.4 - - - +
230B GLU* 4.3 12.5 + - + +
325B MET* 3.8 18.8 - - + +
326B GLU* 2.9 28.9 + - - +
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Residues in contact with VAL 94 (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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93B THR* 1.3 75.6 - - - +
95B LYS* 1.3 64.2 + - - +
139B TYR* 4.0 15.7 - - + -
151B VAL* 4.6 9.2 - - + -
216B LEU* 4.5 16.8 - - + -
218B THR* 4.1 19.3 - - + +
221B PHE* 5.9 0.2 - - + -
227B VAL* 3.4 2.6 - - - -
228B VAL* 2.9 41.5 + - + +
229B GLY 2.8 28.7 + - - +
230B GLU* 3.9 9.6 - - - +
231B LEU* 4.0 23.6 - - + -
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Residues in contact with LYS 95 (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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93B THR* 3.9 16.7 + - + +
94B VAL* 1.3 80.1 - - - +
96B GLY* 1.3 68.2 + - - +
97B THR* 4.2 1.4 + - - -
218B THR* 3.4 18.8 + - - +
225B ASP* 4.2 27.8 - - + +
226B THR 3.0 21.5 - - - +
227B VAL* 4.6 4.5 - - + -
228B VAL* 4.8 1.3 - - - -
302B PRO* 6.3 1.2 - - - +
325B MET* 3.6 32.1 - - - +
326B GLU* 6.0 1.1 - - - -
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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