Contacts of the helix formed by residues 139 - 148 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107E LEU* 5.0 8.7 - - - +
137E GLY 3.2 5.8 + - - +
138E ASP* 1.3 73.5 - - - +
140E PRO* 1.3 68.0 - - - +
141E TRP* 3.6 15.0 + - - +
142E THR* 2.8 42.1 + - - +
143E GLU* 2.8 32.5 + - - +
162E PHE* 4.4 2.8 - - - -
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Residues in contact with PRO 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E VAL* 3.9 21.8 - - + -
107E LEU* 3.7 36.1 - - + +
108E LEU* 3.9 15.5 - - + +
111E ALA* 3.5 22.0 - - + -
113E PHE* 3.7 4.6 - - + -
134E TRP* 3.9 12.8 - - + -
138E ASP 3.4 10.5 - - - +
139E ASP* 1.3 88.6 - - - +
141E TRP* 1.3 50.8 - - + +
143E GLU* 3.2 1.2 + - - +
144E HIS* 2.7 36.7 + - - +
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Residues in contact with TRP 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ASP* 3.3 21.8 + - - -
107E LEU* 5.7 1.8 - - + -
110E ALA* 3.2 24.5 + - + +
111E ALA* 3.6 28.9 - - + +
139E ASP* 3.3 13.8 + - - +
140E PRO* 1.3 79.4 - - + +
142E THR* 1.3 57.9 + - - +
144E HIS* 3.3 6.6 - - - +
145E ALA* 2.9 28.4 + - - +
153E PHE* 3.5 19.3 - + - -
154E LEU* 3.6 32.2 - - + +
157E SER* 3.3 31.0 - - - -
158E LYS* 3.5 40.2 - - + -
162E PHE* 3.6 6.0 - - + -
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Residues in contact with THR 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E ASP* 2.8 36.3 + - - +
141E TRP* 1.3 74.8 - - - +
143E GLU* 1.3 53.8 + - - +
145E ALA* 3.0 4.3 + - - +
146E LYS* 2.7 58.9 + - - +
162E PHE* 3.6 19.3 - - - -
166E VAL* 3.6 17.5 - - + +
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Residues in contact with GLU 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E LEU* 4.0 8.7 - - + -
134E TRP* 3.8 29.2 - - + -
138E ASP* 4.2 11.6 - - + +
139E ASP 2.8 20.8 + - - +
140E PRO 3.6 5.8 - - - +
142E THR* 1.3 76.2 - - - +
144E HIS* 1.3 65.9 + - - +
146E LYS* 2.9 34.7 + - - -
147E TRP* 3.0 43.5 + - + +
1F ALA* 3.2 36.4 + - + +
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Residues in contact with HIS 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E ALA 2.7 29.2 + - - -
113E PHE* 3.5 17.6 - + + -
124E CYS* 3.3 16.5 - - + +
127E CYS* 3.6 0.8 - - - -
131E LEU* 4.3 2.8 - - - +
140E PRO 2.7 22.3 + - - +
141E TRP* 3.3 13.9 - - - +
143E GLU* 1.3 73.5 - - - +
145E ALA* 1.3 55.3 + - - +
148E PHE* 2.9 44.9 + + + -
151E CYS* 3.4 6.1 - - + -
153E PHE* 4.4 4.0 - + - -
154E LEU* 3.9 20.4 - - + -
1005E ZN 2.0 37.6 - - - -
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Residues in contact with ALA 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E TRP 2.9 14.2 + - - +
142E THR 3.0 7.6 + - - +
144E HIS* 1.3 74.6 - - - +
146E LYS* 1.3 61.7 + - - +
147E TRP 3.4 0.3 + - - -
149E PRO* 3.5 13.1 - - - +
154E LEU* 3.6 17.4 - - + +
162E PHE* 3.7 21.1 - - + -
163E VAL* 4.3 8.1 - - - -
166E VAL* 3.6 19.3 - - + -
167E GLN* 2.8 20.6 + - - +
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Residues in contact with LYS 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E ASP* 5.9 0.2 + - - -
142E THR* 2.7 33.3 + - - +
143E GLU* 2.9 38.3 + - - +
145E ALA* 1.3 73.3 - - - +
147E TRP* 1.3 75.3 + - + +
149E PRO* 4.2 1.0 - - - +
166E VAL* 3.5 13.7 - - + +
167E GLN* 3.0 19.7 + - - +
170E HIS 4.8 6.3 - - - +
171E SER* 3.2 36.3 - - - -
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Residues in contact with TRP 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E LEU* 3.5 28.9 - - + -
143E GLU* 3.0 38.0 + - - +
146E LYS* 1.3 95.1 - - + +
148E PHE* 1.3 81.7 + - + +
149E PRO* 3.5 8.5 - - - +
171E SER 3.8 24.0 - - - -
1F ALA 3.1 23.6 + - - -
2F VAL* 4.4 6.3 - - + -
3F PRO* 3.5 35.0 - - + -
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Residues in contact with PHE 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E PHE* 4.9 1.6 - + - -
127E CYS* 3.8 22.0 - - + -
129E GLY* 3.4 38.1 - - - -
130E GLY 3.4 18.6 - - - -
131E LEU* 3.6 31.6 - - + -
144E HIS* 2.9 30.1 + + + +
147E TRP* 1.3 97.5 - - + +
149E PRO* 1.3 64.8 - - - +
150E SER* 3.1 5.8 + - - -
151E CYS* 3.1 16.7 + - + +
154E LEU* 3.5 2.6 - - - +
3F PRO* 5.0 9.0 - - + -
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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