Contacts of the helix formed by residues 86 - 92 (chain B) in PDB entry 1O69
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 VAL 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ALA* 3.6 31.2 - - + -
78B SER 4.4 7.0 - - - +
81B THR* 4.5 5.8 - - + -
82B PHE 4.4 1.8 - - - +
83B ILE* 3.5 21.3 - - - +
85B SER* 1.3 83.7 - - - +
87B ALA* 1.3 65.2 - - - +
88B PRO* 3.2 3.1 - - - -
89B ILE* 2.9 33.3 + - + +
90B CYS* 3.8 3.8 + - - -
98B PHE* 3.9 12.1 - - + -
127B ILE* 5.0 4.0 - - + -
335B MET* 3.9 13.5 - - + -
341B PHE* 3.8 25.0 - - + -
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Residues in contact with ALA 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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211A GLN* 4.2 9.2 - - - +
224A TYR* 4.5 11.4 - - + -
225A GLY 3.8 10.5 - - - +
57B THR* 5.0 0.2 - - + -
83B ILE* 2.9 20.0 + - + +
84B ALA 4.6 2.0 - - - +
86B VAL* 1.3 77.5 - - - +
88B PRO* 1.3 61.0 - - + +
90B CYS* 2.9 30.2 + - - +
91B TYR* 3.0 36.6 + - + +
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Residues in contact with PRO 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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57B THR* 3.6 32.3 - - + +
60B LEU* 4.1 8.1 - - + -
61B HIS* 3.7 24.2 - - + +
64B LEU* 3.8 13.8 - - + +
84B ALA 3.6 15.0 - - - +
85B SER 4.0 3.8 - - - +
86B VAL* 3.3 7.4 - - - +
87B ALA* 1.3 91.1 - - + +
89B ILE* 1.3 59.9 + - - +
91B TYR* 3.2 25.1 + - + +
92B LEU* 3.2 19.2 + - - +
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Residues in contact with ILE 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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64B LEU* 3.8 7.6 - - + +
75B VAL* 3.7 29.4 - - + +
77B ALA* 4.1 15.7 - - + -
86B VAL* 2.9 20.5 + - + +
88B PRO* 1.3 76.7 - - - +
90B CYS* 1.3 62.1 + - - +
92B LEU* 3.4 1.3 + - - -
93B LYS 3.2 2.8 + - - -
94B ALA* 3.0 59.9 + - + +
95B LYS 4.1 1.1 - - - -
96B PRO* 3.8 36.6 - - + -
127B ILE* 3.9 22.9 - - + -
341B PHE* 6.0 0.2 - - + -
403B BME 4.8 0.7 - - - -
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Residues in contact with CYS 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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224A TYR* 3.8 38.4 + - + -
86B VAL 4.4 1.1 - - - -
87B ALA* 2.9 16.8 + - - +
89B ILE* 1.3 76.9 - - - +
91B TYR* 1.3 63.6 + - - +
93B LYS* 2.9 21.8 + - - +
341B PHE* 3.6 18.4 - - - -
403B BME 2.1 58.6 - - + +
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Residues in contact with TYR 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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61A HIS* 6.2 1.8 - + - -
91A TYR 4.4 13.2 - - - +
93A LYS* 5.1 3.3 - - - -
211A GLN* 4.4 0.2 + - - -
224A TYR* 3.8 19.5 - + - -
225A GLY 2.6 29.6 + - - -
226A TYR* 3.4 38.1 - + - -
57B THR* 3.5 28.1 - - + +
61B HIS* 3.6 39.9 - + + +
87B ALA* 3.0 25.6 + - + +
88B PRO* 3.2 19.7 + - + +
90B CYS* 1.3 75.9 - - - +
92B LEU* 1.3 62.8 + - - +
93B LYS* 3.4 6.6 + - - +
228B TYR* 4.8 4.5 - - - -
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Residues in contact with LEU 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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93A LYS* 4.4 11.5 + - - +
61B HIS* 3.9 24.9 - - + +
64B LEU* 3.7 31.2 - - + -
65B ARG* 3.9 24.2 - - + +
69B VAL* 3.9 35.0 - - + +
70B LYS* 5.2 0.7 - - - -
71B GLN* 3.3 19.2 + - - +
88B PRO 3.2 14.1 + - - +
89B ILE 3.4 3.1 + - - +
90B CYS 3.2 0.2 - - - -
91B TYR* 1.3 77.2 - - - +
93B LYS* 1.3 70.2 + - - +
94B ALA* 3.3 3.0 + - + +
224B TYR* 5.7 4.0 - - - +
226B TYR* 5.1 1.3 - - - +
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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