Contacts of the strand formed by residues 84 - 95 (chain A) 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 THR 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A MET* 1.3 95.0 - - - +
85A MET* 1.3 69.0 + - - +
86A SER* 5.3 0.3 + - - -
236A THR* 4.6 11.1 - - - +
237A ILE 3.4 11.9 - - - -
238A VAL* 3.8 22.4 - - + +
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Residues in contact with MET 85 (chain A).
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 5.3 0.9 - - - +
84A THR* 1.3 81.3 + - - +
86A SER* 1.3 67.2 + - - +
87A LYS* 4.1 21.1 - - + +
119A GLN* 3.8 24.7 - - - +
120A LEU* 4.9 10.1 - - + -
123A LEU* 3.9 26.5 - - + -
235A TYR* 3.9 19.6 - - + +
236A THR* 3.2 3.1 - - - -
237A ILE* 2.9 34.5 + - + +
239A LEU* 5.9 5.2 - - + -
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A THR* 5.3 0.5 + - - -
85A MET* 1.3 74.2 - - - +
87A LYS* 1.3 69.7 + - - +
235A TYR* 3.1 6.7 - - - -
236A THR* 2.7 36.4 + - - +
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Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A MET* 4.1 15.2 - - + +
86A SER* 1.3 78.2 - - - +
88A THR* 1.3 65.7 + - - +
89A GLU* 4.0 10.8 - - + -
119A GLN* 3.0 40.0 + - - +
234A GLN* 4.5 0.8 - - - +
235A TYR* 3.0 59.8 + - + +
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LYS* 1.3 76.3 - - - +
89A GLU* 1.3 62.4 + - - +
138A LYS* 4.7 7.6 - - + -
232A PHE* 4.0 26.5 - - + -
233A ILE 3.2 13.9 - - - +
234A GLN* 3.2 35.6 + - + +
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Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LYS* 4.0 11.2 - - + -
88A THR* 1.3 76.8 - - - +
90A LEU* 1.3 65.1 + - - +
117A PHE* 4.4 2.4 - - - -
118A PRO* 3.3 16.6 - - + +
119A GLN* 2.8 36.4 + - - +
120A LEU* 3.2 19.9 + - - +
232A PHE* 3.4 8.4 - - - +
233A ILE* 2.8 44.4 + - + +
235A TYR* 2.8 34.1 + - + +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLU* 1.3 74.5 - - - +
91A LEU* 1.3 69.4 + - - +
92A SER* 4.1 11.4 - - - +
93A THR* 5.7 5.4 - - + -
116A VAL 5.2 0.3 - - - +
118A PRO* 4.2 20.3 - - - +
230A GLU* 4.1 24.9 - - + +
231A LEU 3.9 8.5 - - - +
232A PHE* 3.6 35.1 - - + -
233A ILE* 5.1 0.4 - - - -
279A ALA* 5.5 11.9 - - + -
324A GLN 5.9 2.9 - - - +
326A GLU* 5.9 1.8 - - - +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLU 3.6 1.0 + - - -
90A LEU* 1.3 78.2 - - - +
92A SER* 1.3 61.2 + - - +
107A TRP* 3.7 37.9 + - + +
115A ALA 3.5 26.5 - - - +
116A VAL* 4.3 12.6 - - + +
137A VAL* 4.9 11.0 - - + -
214A ILE* 5.3 10.1 - - + -
231A LEU* 2.9 40.6 + - + +
232A PHE* 4.4 4.0 - - - -
233A ILE* 4.4 25.4 - - + -
326A GLU* 4.7 5.9 - - - +
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 4.0 7.0 - - - +
91A LEU* 1.3 84.1 - - - +
93A THR* 1.3 72.5 + - - +
94A VAL* 4.7 0.5 - - - +
105A GLU* 5.2 2.3 + - - -
107A TRP* 3.7 26.6 - - - -
216A LEU* 5.0 1.6 - - - +
230A GLU* 3.3 4.0 - - - +
231A LEU* 2.8 41.8 + - - +
326A GLU* 3.6 21.5 - - - -
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Residues in contact with THR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 5.7 5.8 - - + -
92A SER* 1.3 85.7 + - - +
94A VAL* 1.3 61.9 + - - +
95A LYS* 4.2 22.0 + - - +
105A GLU* 5.6 1.7 - - - +
216A LEU* 5.3 2.1 - - - +
227A VAL* 4.7 11.3 - - + +
229A GLY 3.7 7.2 - - - -
230A GLU* 4.1 16.6 - - + +
324A GLN 5.7 0.9 - - - +
325A MET* 3.9 23.1 - - + +
326A GLU* 2.8 35.5 + - - +
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR* 1.3 80.8 - - - +
95A LYS* 1.3 68.1 + - - +
139A TYR* 4.2 15.3 - - + -
151A VAL* 4.8 4.9 - - + -
216A LEU* 4.3 20.6 - - + -
218A THR* 4.4 12.6 - - + -
227A VAL* 3.5 1.6 - - - -
228A VAL* 2.8 42.7 + - + +
229A GLY 2.7 26.5 + - - +
230A GLU* 4.0 4.0 - - - -
231A LEU* 3.9 30.7 - - + -
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Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR* 4.2 11.9 + - - +
94A VAL* 1.3 83.0 - - - +
96A GLY* 1.3 67.1 + - - +
97A THR* 4.6 0.3 + - - -
218A THR* 4.1 12.6 + - - +
225A ASP* 4.1 30.7 + - + +
226A THR 3.2 16.4 - - - +
227A VAL* 4.1 20.2 - - + +
228A VAL* 4.6 3.1 - - - -
325A MET* 3.8 29.3 - - - +
326A GLU* 5.5 2.0 - - - +
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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