Contacts of the helix formed by residues 139 - 148 (chain B) in PDB entry 1OXQ
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B LEU* 5.0 8.4 - - - +
137B GLY 3.3 6.9 + - - +
138B ASP* 1.3 71.9 - - - +
140B PRO* 1.3 71.5 - - - +
141B TRP* 3.5 15.3 + - - +
142B THR* 2.6 45.3 + - - +
143B GLU* 2.9 25.5 + - - +
162B PHE* 4.7 1.4 - - - -
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Residues in contact with PRO 140 (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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103B VAL* 3.9 13.0 - - + -
107B LEU* 3.8 22.9 - - + +
108B LEU* 3.7 37.9 - - + +
111B ALA* 3.5 21.8 - - + -
113B PHE* 3.6 5.6 - - + -
134B TRP* 3.9 13.4 - - + -
138B ASP 3.4 9.2 - - - +
139B ASP* 1.3 89.0 - - - +
141B TRP* 1.3 57.1 + - + +
143B GLU* 3.3 2.4 + - - +
144B HIS* 2.8 29.3 + - - +
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Residues in contact with TRP 141 (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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107B LEU* 5.7 2.5 - - + -
110B ALA* 3.2 25.1 + - + +
111B ALA* 3.6 28.1 - - + +
139B ASP* 3.3 13.5 + - - +
140B PRO* 1.3 78.8 - - + +
142B THR* 1.3 58.8 + - - +
144B HIS* 3.2 8.7 + - - +
145B ALA* 2.9 24.6 + - - +
153B PHE* 3.5 20.0 - + - -
154B LEU* 3.7 27.8 - - + +
157B SER* 3.3 29.6 - - - -
158B LYS* 3.5 39.5 - - + +
162B PHE* 3.6 21.0 - - + -
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Residues in contact with THR 142 (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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139B ASP* 2.6 41.8 + - - +
141B TRP* 1.3 72.7 - - - +
143B GLU* 1.3 55.3 + - + +
145B ALA 3.2 0.9 + - - -
146B LYS* 2.8 36.6 + - + +
162B PHE* 4.0 16.6 - - - -
166B VAL* 3.5 15.2 - - + +
170B HIS* 3.9 33.9 - - + +
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Residues in contact with GLU 143 (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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131B LEU* 3.8 17.3 - - + -
134B TRP* 3.7 21.5 - - + -
138B ASP* 3.9 8.4 - - + +
139B ASP 2.9 19.9 + - - +
140B PRO 3.6 6.5 - - - +
142B THR* 1.3 74.3 - - - +
144B HIS* 1.3 67.3 + - - +
146B LYS* 3.1 13.9 + - - +
147B TRP* 2.9 55.5 + - - +
71C ALA* 5.9 0.2 - - - +
72C GLY* 3.8 10.0 + - - -
73C ALA* 3.4 26.9 + - + +
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Residues in contact with HIS 144 (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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111B ALA 2.7 28.7 + - - -
113B PHE* 3.6 15.9 - + + -
124B CYS* 3.3 19.3 - - + +
140B PRO 2.8 13.2 + - - +
141B TRP* 3.3 16.7 - - - +
143B GLU* 1.3 76.9 - - - +
145B ALA* 1.3 57.1 + - - +
148B PHE* 2.8 51.2 + + + -
151B CYS* 3.5 4.1 - - + -
153B PHE* 4.5 4.7 - + - -
154B LEU* 4.0 22.7 - - + -
1002B ZN 2.1 37.3 - - - -
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Residues in contact with ALA 145 (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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141B TRP 2.9 8.1 + - - +
142B THR 3.7 0.7 - - - +
144B HIS* 1.3 73.6 - - - +
146B LYS* 1.3 62.1 + - - +
147B TRP 3.6 0.2 + - - -
149B PRO* 3.7 11.3 - - - +
154B LEU* 3.6 16.1 - - + +
162B PHE* 3.6 33.4 - - + -
163B VAL* 4.0 11.4 - - - +
166B VAL* 3.7 18.6 - - + -
167B GLN* 2.8 22.1 + - - +
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Residues in contact with LYS 146 (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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142B THR* 2.8 18.6 + - + +
143B GLU* 3.1 17.9 + - - +
145B ALA* 1.3 78.0 - - - +
147B TRP* 1.3 102.7 + - + +
149B PRO* 4.3 0.5 - - - +
166B VAL* 3.6 11.2 - - + +
167B GLN* 2.9 20.6 + - - +
170B HIS* 4.1 41.3 - - + +
171B SER* 5.5 2.0 - - - -
71C ALA* 4.7 21.4 - - - +
72C GLY 5.0 2.2 - - - +
73C ALA 4.9 2.0 + - - -
150C SER* 5.6 0.5 - - - -
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Residues in contact with TRP 147 (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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131B LEU* 3.5 20.9 - - + +
143B GLU* 2.9 50.2 + - - +
146B LYS* 1.3 112.6 - - + +
148B PHE* 1.3 82.7 + - + +
149B PRO* 3.3 9.9 - - - +
73C ALA 3.7 18.4 + - - -
74C THR* 4.6 5.8 - - + -
75C LEU* 3.5 36.6 - - + -
149C PRO* 5.3 0.5 - - - +
150C SER* 2.5 38.0 + - - -
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Residues in contact with PHE 148 (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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113B PHE* 4.5 3.4 - + - -
127B CYS* 3.8 21.3 - - + -
129B GLY* 3.3 34.1 - - - -
130B GLY 3.5 9.6 - - - -
131B LEU* 3.6 26.9 - - + -
144B HIS* 2.8 38.7 + + + +
147B TRP* 1.3 98.3 - - + +
149B PRO* 1.3 66.1 - - - +
150B SER 3.0 4.3 + - - -
151B CYS* 3.0 17.2 + - + +
154B LEU* 3.4 6.1 - - - +
75C LEU* 3.6 25.1 - - + -
150C SER* 3.8 5.8 - - - -
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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