Contacts of the helix formed by residues 152 - 167 (chain A) in PDB entry 2OPL
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 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A LEU* 1.3 76.2 - - - +
153A ASP* 1.3 66.2 + - - +
154A GLY* 3.4 5.4 + - - -
155A GLN* 2.9 50.0 + - - +
156A LYS* 2.9 22.3 + - - +
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Residues in contact with ASP 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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151A LEU 5.2 0.2 - - - +
152A THR* 1.3 74.9 - - - +
154A GLY* 1.3 57.0 + - - +
156A LYS* 3.1 16.8 + - - +
157A GLU* 2.8 40.0 + - - +
183B LEU* 3.9 24.7 - - + +
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Residues in contact with GLY 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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152A THR* 3.2 6.6 + - - -
153A ASP* 1.3 77.7 - - - +
155A GLN* 1.3 56.1 + - - +
157A GLU* 3.2 18.0 + - - +
158A GLU* 3.0 26.5 + - - +
161A ARG* 4.8 2.8 + - - -
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Residues in contact with GLN 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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107A ARG* 5.6 1.7 + - - +
151A LEU* 3.6 25.5 - - + +
152A THR* 2.9 45.7 + - - +
154A GLY* 1.3 73.4 - - - +
156A LYS* 1.3 64.8 + - - +
158A GLU* 3.3 8.6 + - - +
159A LEU* 3.1 26.8 + - - +
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Residues in contact with LYS 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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147A ILE* 2.8 47.7 + - + +
148A ASP* 4.9 0.4 - - - +
149A ALA 4.2 13.0 + - - +
151A LEU* 3.7 31.3 + - + -
152A THR 2.9 15.1 + - - +
153A ASP* 3.4 22.3 + - - +
155A GLN* 1.3 73.9 - - - +
157A GLU* 1.3 65.0 + - - +
159A LEU* 3.2 8.6 + - - +
160A ILE* 3.1 28.0 + - - +
183B LEU* 4.0 26.7 - - + +
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Residues in contact with GLU 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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153A ASP* 2.8 21.4 + - - +
154A GLY* 3.5 19.7 + - - +
156A LYS* 1.3 76.0 - - - +
158A GLU* 1.3 57.1 + - - +
160A ILE* 3.2 10.9 + - - +
161A ARG* 2.9 46.7 + - - +
183B LEU* 4.1 28.5 - - + +
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Residues in contact with GLU 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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107A ARG* 4.6 16.2 - - - +
154A GLY 3.0 12.2 + - - +
155A GLN* 3.5 12.1 - - - +
156A LYS 3.2 0.4 - - - -
157A GLU* 1.3 73.7 - - - +
159A LEU* 1.3 65.5 + - - +
161A ARG* 3.2 29.1 + - + +
162A MSE 2.9 41.7 + - + +
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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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100A LEU* 4.0 22.8 - - + +
103A HIS* 5.4 1.9 - - + +
104A ALA* 4.1 27.4 - - + +
107A ARG* 4.1 24.5 - - - +
109A ILE* 4.1 9.9 - - + -
111A LEU* 3.8 18.4 - - + -
147A ILE* 4.6 8.7 - - + -
151A LEU* 3.6 31.0 - - + -
155A GLN 3.1 14.3 + - - +
156A LYS* 3.2 7.4 + - - +
158A GLU* 1.3 75.6 - - - +
160A ILE* 1.3 57.7 + - - +
162A MSE 3.4 8.4 + - + +
163A ALA* 2.9 28.4 + - - +
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Residues in contact with ILE 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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100A LEU* 4.1 9.6 - - + -
145A PHE* 3.8 18.8 - - + -
147A ILE* 4.0 12.8 - - + -
156A LYS 3.1 14.8 + - - +
157A GLU* 3.5 9.4 - - - +
158A GLU 3.2 0.2 - - - -
159A LEU* 1.3 74.3 - - - +
161A ARG* 1.3 65.0 + - + +
163A ALA* 3.2 9.1 + - + +
164A GLN* 3.1 29.5 + - - +
181B VAL* 3.7 36.8 - - + +
182B LEU* 4.9 0.7 - - - -
183B LEU* 3.8 43.5 - - + +
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Residues in contact with ARG 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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154A GLY 4.8 2.6 + - - -
157A GLU* 2.9 36.1 + - + +
158A GLU* 3.2 37.8 + - - +
160A ILE* 1.3 75.2 - - + +
162A MSE 1.3 72.6 + - + +
164A GLN* 3.3 17.5 + - - +
165A LYS* 2.9 28.4 + - - +
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Residues in contact with MSE 162 (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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99A SER* 3.9 0.6 + - - -
103A HIS* 4.9 13.7 - - + -
107A ARG* 6.1 4.7 - - - +
158A GLU* 2.9 32.7 + - + +
159A LEU* 3.8 8.7 - - + +
161A ARG* 1.3 89.6 - - + +
163A ALA* 1.3 64.6 + - - +
165A LYS* 3.2 27.8 + - + +
166A TYR* 3.1 55.7 + - + +
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Residues in contact with ALA 163 (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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96A LEU* 3.7 16.2 - - + +
99A SER* 2.9 24.1 + - - -
100A LEU* 3.6 34.3 - - + +
103A HIS* 5.6 0.2 - - - +
145A PHE* 6.0 1.6 - - + -
159A LEU 2.9 15.9 + - - +
160A ILE* 3.2 11.9 + - + +
162A MSE 1.3 76.2 - - - +
164A GLN* 1.3 61.6 + - - +
167A SER* 3.1 17.0 + - - -
181B VAL* 6.5 0.4 - - + -
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Residues in contact with GLN 164 (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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96A LEU* 3.9 12.1 - - + +
160A ILE* 3.1 29.6 + - - +
161A ARG* 3.5 20.0 - - - +
163A ALA* 1.3 73.3 - - - +
165A LYS* 1.3 68.0 + - - +
166A TYR 3.2 0.7 + - - -
167A SER 3.4 3.5 + - - -
170A TYR* 3.4 40.5 + - + -
171A ASN* 3.1 17.8 + - - -
179B VAL 4.3 0.9 - - - +
181B VAL* 3.6 42.8 + - + +
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Residues in contact with LYS 165 (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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161A ARG 2.9 17.9 + - - +
162A MSE 3.2 30.2 + - + +
164A GLN* 1.3 78.1 - - - +
166A TYR* 1.3 89.2 + - + +
171A ASN* 3.2 17.3 + - - +
132B GLU* 3.6 31.6 + - - -
136B VAL* 3.7 13.7 - - + +
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Residues in contact with TYR 166 (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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99A SER* 3.6 7.4 - - - +
103A HIS* 3.2 47.6 - + + -
162A MSE 3.1 44.2 + - + -
165A LYS* 1.3 111.5 + - + +
167A SER* 1.3 58.4 + - - +
168A PRO* 3.2 5.4 - - - +
126B GLY 3.4 17.3 - - - -
127B PHE* 3.1 26.3 - - - +
129B GLY* 3.6 26.3 + - - -
132B GLU* 5.7 2.4 - - - -
136B VAL* 3.3 13.3 - - + +
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Residues in contact with SER 167 (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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95A CYS* 3.0 25.3 - - - +
96A LEU* 3.9 9.8 + - - +
99A SER* 4.1 9.2 - - - -
163A ALA 3.1 18.3 + - - -
164A GLN 3.4 3.2 + - - -
165A LYS 3.5 0.4 - - - -
166A TYR* 1.3 75.8 - - - +
168A PRO* 1.3 66.4 - - - +
170A TYR* 3.0 27.7 + - - +
171A ASN* 2.9 26.3 + - - -
136B VAL* 3.8 1.6 - - - -
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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