Contacts of the helix formed by residues 139 - 148 (chain C) in PDB entry 1OXN
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 ASP 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C LEU* 5.6 2.1 - - - +
137C GLY 3.5 4.9 + - - +
138C ASP* 1.3 72.9 - - - +
140C PRO* 1.3 58.4 - - - +
141C TRP* 3.0 28.8 + - - +
142C THR* 3.0 25.3 + - + +
143C GLU* 2.7 39.3 + - - +
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Residues in contact with PRO 140 (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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103C VAL* 3.9 13.7 - - + -
107C LEU* 3.7 31.2 - - + +
108C LEU* 3.8 29.4 - - + -
111C ALA* 3.6 20.9 - - + -
113C PHE* 3.4 8.0 - - + -
134C TRP* 3.8 14.6 - - + -
138C ASP 3.3 9.9 - - - +
139C ASP* 1.3 88.8 - - - +
141C TRP* 1.3 55.5 + - + +
143C GLU* 3.8 0.2 - - - +
144C HIS* 2.9 29.8 + - - +
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Residues in contact with TRP 141 (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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107C LEU* 5.1 3.6 + - + -
110C ALA* 3.0 36.8 - - + +
111C ALA* 3.5 21.9 - - + +
139C ASP* 3.0 16.0 + - - +
140C PRO* 1.3 73.7 - - + +
142C THR* 1.3 61.0 + - - +
144C HIS* 3.3 4.5 + - - +
145C ALA* 2.9 28.6 + - - +
153C PHE* 3.6 22.9 - + - -
154C LEU* 3.8 19.0 - - + +
157C SER* 3.6 21.8 - - - -
158C LYS* 3.3 47.7 - - + +
162C PHE* 3.8 16.3 - - + -
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Residues in contact with THR 142 (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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139C ASP* 3.0 29.9 + - + +
141C TRP* 1.3 73.6 - - - +
143C GLU* 1.3 68.2 + - - +
145C ALA 3.2 1.0 + - - -
146C LYS* 2.8 29.7 + - + +
162C PHE* 4.0 18.4 - - - -
166C VAL* 3.5 20.7 - - + +
170C HIS* 4.1 23.1 - - + +
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Residues in contact with GLU 143 (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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72B GLY* 4.4 7.9 + - - -
73B ALA* 3.5 26.6 + - + +
131C LEU* 4.0 6.7 - - + +
134C TRP* 3.7 31.9 - - + -
138C ASP* 4.5 6.1 - - + +
139C ASP 2.7 28.8 + - - +
140C PRO 3.8 4.0 - - - +
142C THR* 1.3 76.1 - - - +
144C HIS* 1.3 67.0 + - - +
146C LYS* 3.2 17.4 + - - +
147C TRP* 3.1 53.4 + - - +
170C HIS* 5.9 1.0 + - - -
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Residues in contact with HIS 144 (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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111C ALA 2.7 28.1 + - - -
113C PHE* 3.4 15.3 - + + -
124C CYS* 3.2 19.0 - - + +
127C CYS* 3.7 0.4 - - - -
140C PRO 2.9 18.6 + - - +
141C TRP* 3.3 9.7 - - - +
143C GLU* 1.3 77.6 - - - +
145C ALA* 1.3 57.2 + - - +
148C PHE* 2.9 45.8 + + + -
151C CYS* 3.4 4.9 - - - -
153C PHE* 4.1 7.8 - + - -
154C LEU* 3.6 22.8 - - + +
1003C ZN 2.0 37.7 - - - -
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Residues in contact with ALA 145 (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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141C TRP 2.9 16.9 + - - +
142C THR 3.6 4.3 - - - +
144C HIS* 1.3 74.5 - - - +
146C LYS* 1.3 54.9 + - - +
147C TRP 3.5 0.2 + - - -
149C PRO* 3.7 11.1 - - - +
154C LEU* 3.3 17.4 - - + +
162C PHE* 3.7 20.9 - - + -
163C VAL* 4.0 11.8 - - - +
166C VAL* 3.7 15.7 - - + -
167C GLN* 2.7 30.0 + - - +
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Residues in contact with LYS 146 (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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71B ALA* 4.0 28.7 - - - +
72B GLY 4.6 2.0 - - - +
73B ALA 5.0 1.4 + - - -
150B SER* 5.3 1.4 - - - -
142C THR* 2.8 17.6 + - + +
143C GLU* 3.2 21.8 + - - +
145C ALA* 1.3 77.2 - - - +
147C TRP* 1.3 100.5 + - + +
149C PRO* 4.3 0.3 - - - +
166C VAL* 3.5 11.0 - - + +
167C GLN* 2.7 21.4 + - - +
170C HIS* 4.0 43.0 - - + +
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Residues in contact with TRP 147 (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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73B ALA 3.9 13.6 + - - -
74B THR* 5.0 0.9 - - - -
75B LEU* 3.5 37.5 - - + -
148B PHE 6.0 0.2 - - - -
149B PRO* 5.4 0.5 - - - +
150B SER* 2.7 38.1 + - - -
131C LEU* 3.4 24.8 - - + +
143C GLU* 3.1 44.9 + - - +
146C LYS* 1.3 110.8 - - + +
148C PHE* 1.3 85.1 + - + +
149C PRO* 3.3 10.3 - - - +
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Residues in contact with PHE 148 (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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75B LEU* 3.6 26.0 - - + -
127B CYS* 6.5 1.3 - - + -
150B SER* 3.9 4.9 - - - -
113C PHE* 4.4 2.7 - + - -
127C CYS* 3.7 22.0 - - + -
129C GLY* 3.3 37.7 - - - -
130C GLY 3.4 11.9 - - - -
131C LEU* 3.7 20.4 - - + -
144C HIS* 2.9 32.5 + + + +
147C TRP* 1.3 107.3 - - + +
149C PRO* 1.3 64.0 - - - +
150C SER 3.1 2.9 - - - -
151C CYS* 3.0 18.9 + - + +
154C LEU* 3.4 6.8 - - - +
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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