Contacts of the helix formed by residues 83 - 91 (chain X) in PDB entry 2OU0
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 LYS 83 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81X ASN* 2.9 10.0 + - - +
82X ALA* 1.3 79.5 - - + +
84X LEU* 1.3 65.4 + - + +
85X LYS 3.6 0.2 - - - -
86X PRO* 3.7 9.0 - - - +
87X VAL* 3.8 16.6 - - - +
112X ALA* 4.0 32.8 - - + +
115X THR* 5.4 7.2 - - + +
118X LEU* 4.6 7.4 - - + +
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Residues in contact with LEU 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78X ILE* 3.8 20.6 - - + +
81X ASN* 3.1 18.9 + - + +
83X LYS* 1.3 77.7 - - - +
85X LYS* 1.3 60.0 + - - +
87X VAL* 3.2 5.4 + - - +
88X TYR* 2.9 28.4 + - - +
103X VAL* 4.1 19.1 - - + -
108X GLU* 3.8 35.7 - - + +
111X VAL* 4.0 6.1 - - + -
112X ALA* 3.8 26.5 - - + +
118X LEU* 3.9 16.2 - - + -
303X MR3 3.7 22.1 - - + -
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Residues in contact with LYS 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78X ILE 3.4 11.5 + - - +
79X LEU* 3.4 35.6 - - + +
81X ASN 2.9 18.6 + - - +
82X ALA* 5.1 1.3 - - - -
84X LEU* 1.3 76.2 - - - +
86X PRO* 1.4 62.7 - - + +
88X TYR* 3.3 6.2 + - - +
89X ASP* 2.6 59.6 + - - +
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Residues in contact with PRO 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82X ALA 3.3 24.0 - - - +
83X LYS* 3.8 6.7 - - - +
84X LEU 3.6 2.5 - - - -
85X LYS* 1.4 95.0 - - + +
87X VAL* 1.3 61.4 + - + +
89X ASP* 3.6 7.2 + - + +
90X SER* 3.2 23.4 + - - -
122X GLN* 3.6 21.0 + - - +
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Residues in contact with VAL 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83X LYS 3.8 16.6 - - - +
84X LEU 3.2 6.8 + - - +
86X PRO* 1.3 74.3 - - + +
88X TYR* 1.3 66.5 + - - +
90X SER* 2.7 22.9 + - - +
91X LEU* 3.3 13.1 - - + +
118X LEU* 3.8 41.3 - - + +
119X ARG* 5.6 0.4 - - - -
121X LEU* 4.1 15.0 - - + -
122X GLN* 3.4 22.4 - - + +
303X MR3 3.7 23.1 - - + -
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Residues in contact with TYR 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X VAL* 4.1 15.0 - - + +
78X ILE* 3.5 24.2 - - + -
79X LEU* 3.7 29.4 - - + -
84X LEU 2.9 16.8 + - - +
85X LYS* 3.6 3.4 - - - +
87X VAL* 1.3 76.0 - - - +
89X ASP* 1.3 66.5 + - - +
91X LEU* 3.1 15.7 + - - +
96X ARG* 3.0 75.4 + - + +
99X ALA* 4.1 15.9 - - + -
100X ILE* 3.6 24.9 - - + +
303X MR3 3.8 7.5 - - + -
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Residues in contact with ASP 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79X LEU* 4.2 6.6 - - - +
85X LYS* 2.6 54.9 + - - +
86X PRO* 4.0 7.4 - - + +
88X TYR* 1.3 87.2 - - - +
90X SER* 1.3 60.7 + - - +
91X LEU 3.7 0.5 - - - +
96X ARG* 2.9 26.1 + - - +
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Residues in contact with SER 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86X PRO 3.2 14.8 + - - -
87X VAL 2.7 19.3 + - - -
89X ASP* 1.3 76.6 - - - +
91X LEU* 1.3 58.7 + - - +
121X LEU 4.6 0.3 + - - -
122X GLN* 3.8 37.6 + - - -
124X LYS* 2.7 31.5 + - - -
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Residues in contact with LEU 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87X VAL* 3.3 18.2 - - + +
88X TYR* 3.1 19.5 + - - +
89X ASP 3.7 0.3 - - - +
90X SER* 1.3 81.8 - - - +
92X ASP* 1.3 68.2 + - - +
95X ARG* 3.9 29.2 - - + +
96X ARG* 3.0 30.9 + - + +
99X ALA* 4.2 9.6 - - + -
121X LEU* 4.1 19.1 - - + +
124X LYS* 4.2 1.6 - - - +
126X TRP* 3.9 32.5 - - + -
153X PHE* 4.2 11.4 - - + -
303X MR3 4.4 7.0 - - + -
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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