Contacts of the helix formed by residues 146 - 161 (chain A) in PDB entry 1OE4
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 GLU 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLY* 3.6 21.3 - - - +
99A PRO* 3.4 12.2 - - - +
100A PHE* 2.9 39.7 + - - +
101A GLY* 3.7 26.5 - - - +
109A PHE* 6.0 1.8 - - - -
111A GLU* 3.5 15.9 - - + +
144A GLN 3.9 2.6 + - - -
145A SER* 1.3 70.4 + - - +
147A VAL* 1.3 66.1 + - - +
148A SER* 4.3 13.5 + - - +
149A GLY* 3.2 13.3 + - - +
150A ALA* 2.9 19.6 + - - +
253A PRO* 6.1 0.3 - - - +
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A SER* 3.4 12.5 + - - +
146A GLU* 1.3 73.2 - - - +
148A SER* 1.3 63.1 + - - +
150A ALA* 3.2 7.3 + - + +
151A ARG* 2.9 57.1 + - + +
253A PRO* 4.1 28.7 - - + -
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Residues in contact with SER 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PHE* 4.3 9.0 - - - -
146A GLU* 3.3 16.5 + - - +
147A VAL* 1.3 79.0 - - - +
149A GLY* 1.3 58.4 + - - +
151A ARG* 3.5 0.5 + - - +
152A PHE* 3.1 27.9 + - - +
250A HIS* 3.6 9.6 - - - -
251A PRO* 3.4 25.3 - - - +
252A SER* 3.1 32.9 + - - -
253A PRO* 4.0 4.0 - - - +
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Residues in contact with GLY 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PHE* 3.2 35.9 - - - -
111A GLU* 3.9 6.5 - - - -
146A GLU* 3.2 12.0 + - - +
148A SER* 1.3 78.0 - - - +
150A ALA* 1.3 66.8 + - - +
153A TRP* 3.0 30.8 + - - +
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLU* 3.6 22.5 - - - +
114A HIS* 3.8 19.5 - - + -
145A SER* 4.0 5.6 - - - +
146A GLU 2.9 15.8 + - - +
147A VAL* 3.2 6.5 + - - +
149A GLY* 1.3 74.9 - - - +
151A ARG* 1.3 64.5 + - + +
154A SER* 3.0 30.0 + - - -
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Residues in contact with ARG 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 2.9 35.9 + - + +
148A SER 3.7 4.7 - - - +
150A ALA* 1.3 78.5 - - + +
152A PHE* 1.3 62.6 + - - +
154A SER* 3.8 3.7 - - - -
155A LEU 3.1 18.5 + - - -
251A PRO* 2.8 39.2 + - + -
252A SER 4.1 0.4 + - - -
253A PRO* 4.1 14.9 - - - +
258A ALA* 3.4 32.9 + - - +
259A ASN* 4.5 13.5 + - - +
262A TRP* 3.4 29.4 - - + +
263A GLU* 4.7 1.4 - - - +
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Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 4.2 11.7 - + + -
109A PHE* 3.9 28.0 - + + -
148A SER 3.1 18.9 + - - +
149A GLY 3.7 3.6 - - - +
151A ARG* 1.3 78.8 - - - +
153A TRP* 1.3 100.3 + + - +
155A LEU* 3.3 7.8 + - - +
156A PHE* 3.3 51.2 - + - -
172A VAL* 4.0 27.4 - - + -
224A VAL* 4.1 27.6 - - + -
248A ILE* 5.0 2.5 - - + -
251A PRO* 4.7 2.5 - - + -
262A TRP* 4.0 16.8 - + - -
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Residues in contact with TRP 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TYR* 4.7 2.5 - - - -
107A VAL* 4.7 2.5 - - + -
108A PRO 3.1 19.9 + - - -
109A PHE* 3.1 33.2 + - + +
110A GLY* 4.5 1.7 - - - -
111A GLU 4.8 2.2 - - - -
114A HIS* 3.9 29.3 - - + -
115A VAL* 5.2 1.6 - - + -
118A TRP* 3.8 30.0 - + + -
119A LEU* 4.1 23.6 - - + +
149A GLY 3.0 17.3 + - - +
152A PHE* 1.3 93.8 - + - +
154A SER* 1.3 59.8 + - - +
156A PHE* 3.3 5.9 + - + +
157A LYS* 2.8 29.5 + - - +
166A PHE* 3.9 14.6 - + - -
167A PHE* 3.6 28.0 - + - -
172A VAL* 3.6 27.8 - - + -
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Residues in contact with SER 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A HIS* 3.7 20.2 + - - -
150A ALA 3.0 21.2 + - - -
151A ARG* 3.8 4.7 - - - -
153A TRP* 1.3 73.0 - - - +
155A LEU* 1.3 66.6 + - - +
157A LYS* 3.8 5.5 - - - +
158A SER* 3.1 28.2 + - - -
263A GLU* 4.1 7.2 + - - +
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG 3.1 13.8 + - - +
152A PHE 3.4 7.0 - - - +
154A SER* 1.3 78.5 - - - +
156A PHE* 1.3 86.8 + - + +
158A SER* 3.3 2.4 + - - -
159A LEU* 3.0 32.0 + - + +
248A ILE* 5.6 1.1 - - + -
262A TRP* 3.8 15.9 - - + -
263A GLU* 3.4 39.2 + - + +
266A VAL* 3.7 26.9 - - + -
267A ARG* 3.9 24.4 + - + +
270A LEU* 4.2 6.3 - - + -
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Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 3.5 29.4 - + - -
118A TRP* 4.0 11.4 - - + -
152A PHE* 3.3 54.2 + + - -
153A TRP* 3.3 10.0 + + + +
155A LEU* 1.3 93.2 - - + +
157A LYS* 1.3 59.3 + - - +
159A LEU* 4.3 11.0 - - + -
160A CYS* 2.8 36.5 + - - +
166A PHE* 3.3 39.9 - + + -
248A ILE* 5.5 2.0 - - + -
270A LEU* 3.9 20.6 - - + -
279A LEU* 4.0 13.0 - - + -
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Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A HIS* 4.6 7.4 - - + +
118A TRP* 3.5 49.0 - - + +
153A TRP 2.8 18.5 + - - +
154A SER* 3.8 7.0 - - - +
155A LEU 3.4 0.2 - - - -
156A PHE* 1.3 75.8 - - - +
158A SER* 1.3 57.6 + - - +
161A GLY* 2.9 29.3 + - - +
1281A GOL 3.8 32.8 - - - +
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A SER* 3.1 20.4 + - - -
155A LEU 3.6 4.5 - - - -
157A LYS* 1.3 77.5 - - - +
159A LEU* 1.3 63.0 + - - +
161A GLY* 4.4 2.1 + - - -
263A GLU* 4.2 10.8 + - - -
267A ARG* 3.8 17.8 + - - -
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 3.0 21.0 + - + +
156A PHE* 4.0 11.7 - - + +
158A SER* 1.3 78.8 - - - +
160A CYS* 1.3 63.3 + - - +
267A ARG* 3.7 32.3 - - + +
270A LEU* 4.2 11.0 - - + -
276A LEU* 3.6 35.0 - - + -
279A LEU* 3.8 22.9 - - + -
280A THR* 3.9 27.9 - - + +
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Residues in contact with CYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A TRP* 4.7 0.9 - - + -
156A PHE* 2.8 24.0 + - - +
159A LEU* 1.3 80.4 - - - +
161A GLY* 1.3 57.4 + - - +
162A GLN 3.0 12.8 + - - +
165A THR* 3.5 17.7 + - + +
166A PHE* 3.8 47.3 - - + +
279A LEU* 3.1 36.6 - - - +
280A THR* 5.4 0.4 - - - +
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Residues in contact with GLY 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A TRP* 3.0 21.5 + - - -
156A PHE 3.9 0.4 + - - -
157A LYS* 2.9 21.1 + - - +
158A SER 4.4 1.9 + - - -
159A LEU 3.7 1.2 - - - -
160A CYS* 1.3 75.1 - - - +
162A GLN* 1.3 71.7 + - - -
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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