Contacts of the helix formed by residues 92 - 100 (chain C) in PDB entry 2OX6
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 92 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C TYR 4.1 0.5 - - - +
91C PRO* 1.3 88.9 - - + +
93C GLN* 1.3 60.6 + - - +
94C ALA* 3.6 7.9 + - - +
95C ILE* 3.1 37.0 + - + +
96C TYR* 2.9 29.5 + - - +
110C THR* 3.9 6.2 - - - +
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Residues in contact with GLN 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C THR* 1.3 73.8 - - - +
94C ALA* 1.3 56.9 + - - +
96C TYR* 3.4 2.7 + - - +
97C THR* 2.9 53.3 + - + +
108C PRO 2.9 25.2 + - - -
109C LEU* 3.5 17.6 - - + +
110C THR* 2.9 37.0 + - + +
111C GLU* 4.4 1.6 - - - +
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C THR* 3.3 9.0 + - - +
93C GLN* 1.3 77.2 - - - +
95C ILE* 1.3 60.7 + - + +
97C THR* 3.1 8.1 + - - -
98C GLN* 3.0 32.7 + - - +
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Residues in contact with ILE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C TYR* 4.1 13.5 - - + -
91C PRO* 3.8 30.3 - - + -
92C THR* 3.1 24.9 + - + +
94C ALA* 1.3 75.6 - - + +
96C TYR* 1.3 67.5 + - - +
98C GLN* 3.3 8.8 + - - +
99C TYR* 3.1 45.2 + - + +
137C LEU* 4.2 9.6 - - + +
139C VAL* 4.2 20.9 - - + -
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Residues in contact with TYR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TYR* 3.7 16.5 - + + +
92C THR 2.9 18.1 + - - +
93C GLN* 3.6 9.0 - - - +
95C ILE* 1.3 77.8 - - - +
97C THR* 1.3 64.8 + - + +
100C ASN* 3.0 54.3 + - + +
103C PHE* 3.6 15.4 - + + +
104C LEU* 3.7 16.4 - - + -
107C LEU* 2.6 42.4 + - - +
108C PRO 3.9 3.4 - - - -
109C LEU 3.6 12.3 - - - -
110C THR* 3.4 33.0 - - - +
113C TYR* 3.5 34.1 - + + +
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Residues in contact with THR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C GLN* 2.9 44.9 + - + +
94C ALA* 3.1 16.5 + - - -
96C TYR* 1.3 77.7 - - + +
98C GLN* 1.3 61.7 + - - +
99C TYR 3.4 0.3 + - - -
100C ASN 3.6 5.4 + - - -
101C PRO* 3.8 14.9 - - - +
104C LEU* 4.0 33.4 - - + +
108C PRO 4.7 0.4 - - - +
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Residues in contact with GLN 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ALA* 3.0 19.9 + - - +
95C ILE* 3.5 9.3 - - - +
96C TYR 3.3 0.2 - - - -
97C THR* 1.3 79.6 + - - +
99C TYR* 1.3 89.4 + - + +
100C ASN 3.8 0.2 + - - -
101C PRO* 4.0 7.3 - - - +
139C VAL* 5.8 2.4 - - - +
143C LYS* 5.9 3.8 - - - +
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Residues in contact with TYR 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TYR* 3.8 17.9 - - + -
95C ILE* 3.1 37.7 + - + +
98C GLN* 1.3 104.1 + - + +
100C ASN* 1.3 59.9 + - - +
101C PRO* 3.4 8.1 - - - +
137C LEU* 3.7 27.6 - - + -
139C VAL* 3.6 28.6 - - + +
142C TYR* 4.1 12.1 - + - -
143C LYS* 4.6 7.4 - - - +
146C ARG* 5.9 0.9 + - - -
153C GLU* 3.8 29.8 - - + +
155C ARG* 5.9 0.5 + - - -
158C ARG* 2.9 45.0 + - - +
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Residues in contact with ASN 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C TYR* 3.5 41.3 + - - -
96C TYR* 3.0 34.2 + - + +
97C THR 4.0 3.6 - - - -
98C GLN 3.5 0.4 - - - -
99C TYR* 1.3 80.0 - - - +
101C PRO* 1.3 65.8 - - - +
102C GLU 3.1 3.1 - - - -
103C PHE* 3.0 48.1 + - + -
104C LEU* 3.5 12.4 - - - +
155C ARG* 5.0 5.0 + - - +
158C ARG* 3.5 15.9 + - - -
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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