Contacts of the helix formed by residues 136 - 159 (chain A) in PDB entry 2OQ1
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 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG* 3.4 35.2 + - - +
135A LEU* 1.3 84.1 - - - +
137A GLY* 1.3 74.7 + - - +
139A ALA* 3.3 12.4 + - - +
140A LEU* 3.2 22.1 + - - +
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Residues in contact with GLY 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU* 1.3 83.0 + - - +
138A GLU* 1.3 64.6 + - - -
140A LEU* 3.0 12.9 + - - +
141A GLU* 3.1 21.2 + - - +
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Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU 3.6 0.2 + - - -
137A GLY* 1.3 71.6 - - - -
139A ALA* 1.3 56.4 + - - +
141A GLU* 3.3 16.3 + - - +
142A GLN* 2.8 65.1 + - + +
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 4.0 26.2 - - + +
136A GLU 3.3 12.1 + - - +
137A GLY 3.1 0.4 - - - -
138A GLU* 1.3 75.2 - - - +
140A LEU* 1.3 64.8 + - - +
142A GLN* 3.2 8.6 + - - +
143A ALA* 3.0 23.2 + - - +
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 4.1 17.5 - - + +
129A VAL* 3.6 28.5 - - + -
130A ARG* 3.8 43.5 - - + +
135A LEU* 3.9 15.6 - - + +
136A GLU* 3.2 37.9 + - - +
137A GLY 3.0 9.7 + - - +
139A ALA* 1.3 77.5 - - - +
141A GLU* 1.3 61.8 + - - +
143A ALA* 3.1 3.7 + - - +
144A ILE* 2.9 44.8 + - + +
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 2.9 41.5 + - - -
137A GLY* 3.1 22.6 + - - +
138A GLU* 3.4 24.7 - - - +
139A ALA 3.2 0.2 - - - -
140A LEU* 1.3 82.6 - - - +
142A GLN* 1.3 71.5 + - - +
144A ILE* 3.0 24.6 - - + +
145A ILE* 3.1 17.6 - - + +
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Residues in contact with GLN 142 (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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138A GLU* 2.8 57.1 + - + +
139A ALA* 3.6 9.0 - - - +
141A GLU* 1.3 79.4 - - - +
143A ALA* 1.3 64.6 + - - +
145A ILE* 3.2 10.3 + - - +
146A SER* 3.1 25.2 + - - +
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 3.8 15.3 - - + -
133A TRP* 5.4 3.1 - - + -
135A LEU* 3.6 23.6 - - + -
139A ALA 3.0 12.0 + - - +
140A LEU 3.5 7.4 - - - +
142A GLN* 1.3 75.9 - - - +
144A ILE* 1.3 53.8 + - - +
146A SER* 3.0 7.3 + - - -
147A GLN* 2.7 43.3 + - + +
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Residues in contact with ILE 144 (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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122A ASP* 5.7 2.5 - - - +
125A VAL* 4.7 7.0 - - + +
126A ARG* 3.3 46.0 - - + +
129A VAL* 3.9 30.1 - - + -
140A LEU* 2.9 30.8 + - + +
141A GLU* 3.0 33.7 - - + +
143A ALA* 1.3 72.9 - - - +
145A ILE* 1.3 67.2 + - + +
148A ALA* 2.7 38.0 + - + +
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Residues in contact with ILE 145 (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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141A GLU* 3.1 23.1 - - + +
142A GLN* 3.2 12.2 + - - +
144A ILE* 1.3 96.6 - - + +
146A SER* 1.3 66.5 + - - +
148A ALA* 4.4 3.0 - - - +
149A PRO* 3.6 14.4 - - - +
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Residues in contact with SER 146 (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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142A GLN* 3.1 15.2 + - - +
143A ALA* 3.0 9.9 + - - -
145A ILE* 1.3 82.7 - - - +
147A GLN* 1.3 65.3 + - - +
149A PRO* 4.0 7.5 - - - +
150A GLN* 2.8 22.1 + - - -
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Residues in contact with GLN 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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129A VAL* 4.2 17.0 - - + -
133A TRP* 4.1 40.0 + - + +
143A ALA* 2.7 25.3 + - + +
146A SER* 1.3 79.5 + - - +
148A ALA* 1.3 63.5 + - - +
149A PRO* 3.3 4.5 - - - -
150A GLN* 2.8 50.6 + - - +
151A VAL* 3.1 28.8 + - + +
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Residues in contact with ALA 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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125A VAL* 4.0 23.3 - - + +
144A ILE* 2.7 25.0 + - - +
145A ILE* 4.4 2.9 - - - +
147A GLN* 1.3 70.8 - - - +
149A PRO* 1.3 63.9 - - + +
151A VAL* 3.5 1.9 + - - +
152A GLU* 2.9 43.1 + - - +
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Residues in contact with PRO 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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145A ILE 3.6 14.4 - - - +
146A SER 4.0 10.3 - - - +
147A GLN 3.3 2.9 - - - +
148A ALA* 1.3 96.1 - - + +
150A GLN* 1.3 66.9 + - + +
152A GLU* 3.5 20.1 - - + +
153A LYS 5.0 0.3 + - - -
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Residues in contact with GLN 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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146A SER 2.8 26.5 + - - +
147A GLN* 2.8 39.5 + - - +
149A PRO* 1.3 80.5 - - + +
151A VAL* 1.3 63.6 + - + +
152A GLU 3.7 0.2 + - - -
153A LYS* 5.0 3.8 + - - +
154A LEU* 5.4 1.6 + - - +
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Residues in contact with VAL 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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125A VAL* 4.1 15.5 - - + -
128A TYR* 3.9 27.1 - - + +
129A VAL* 5.2 0.9 - - + -
147A GLN* 3.6 34.8 - - + +
148A ALA* 3.7 11.4 - - - +
150A GLN* 1.3 79.9 - - + +
152A GLU* 1.3 65.9 + - - +
153A LYS 3.5 1.8 - - - -
154A LEU* 3.2 11.0 + - + +
155A ILE* 3.0 42.0 + - + +
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Residues in contact with GLU 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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45A LEU* 5.5 6.7 - - + -
65A ARG* 6.2 2.7 - - - +
121A ARG* 4.3 28.4 + - - +
125A VAL* 4.1 15.8 - - - +
148A ALA* 2.9 30.7 + - - +
149A PRO* 3.5 17.2 - - + +
150A GLN 3.3 1.2 - - - -
151A VAL* 1.3 76.6 - - - +
153A LYS* 1.3 63.3 + - - +
155A ILE* 3.3 4.8 + - - +
156A ALA* 3.0 25.0 + - + +
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Residues in contact with LYS 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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45A LEU* 4.2 22.6 - - + +
65A ARG* 6.0 2.5 - - - +
149A PRO 5.0 0.2 + - - -
150A GLN 5.0 3.7 + - - +
151A VAL 3.5 0.4 - - - -
152A GLU* 1.3 78.0 - - - +
154A LEU* 1.3 65.6 + - - +
156A ALA* 3.2 4.7 + - - -
157A THR* 2.9 53.9 + - + +
232A ASP* 4.8 13.7 + - - +
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Residues in contact with LEU 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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128A TYR* 3.8 28.3 - - + +
150A GLN 5.4 1.1 + - - +
151A VAL* 3.2 15.1 + - + +
153A LYS* 1.3 82.0 - - - +
155A ILE* 1.3 78.8 + - + +
157A THR* 3.3 13.8 + - - +
158A THR* 3.1 27.7 - - + +
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Residues in contact with ILE 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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121A ARG* 4.3 11.7 - - + +
124A MSE 3.5 45.2 - - + +
125A VAL* 4.2 21.3 - - + -
128A TYR* 4.0 17.9 - - + -
151A VAL* 3.0 40.3 + - + +
152A GLU 3.9 2.5 - - - +
154A LEU* 1.3 93.8 - - + +
156A ALA* 1.3 65.1 + - - +
158A THR* 3.4 9.6 + - + +
159A ALA* 3.1 22.3 + - - +
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Residues in contact with ALA 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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45A LEU* 3.8 30.3 - - + -
117A PHE* 3.7 6.3 - - + -
121A ARG* 3.7 25.4 - - - +
152A GLU 3.0 18.3 + - - +
153A LYS 3.7 2.9 - - - +
155A ILE* 1.3 77.9 - - - +
157A THR* 1.3 60.8 + - - +
158A THR 3.3 0.7 + - - -
159A ALA* 3.5 13.9 + - - +
160A HIS* 5.0 0.5 + - - -
233A THR* 3.4 18.5 - - + +
235A TRP* 5.0 1.2 - - - +
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Residues in contact with THR 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 LYS* 2.9 50.8 + - + +
154A LEU* 3.3 12.3 + - - +
156A ALA* 1.3 72.7 - - + +
158A THR* 1.3 57.1 + - - +
159A ALA 3.6 0.2 - - - -
160A HIS* 3.0 23.8 + - - -
223A TYR* 4.6 17.0 + - + +
232A ASP 4.3 8.5 - - - +
233A THR* 3.9 19.6 - - + +
234A LEU 5.2 1.2 + - - -
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Residues in contact with THR 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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124A MSE 6.3 0.2 - - - -
154A LEU* 3.1 31.1 + - + +
155A ILE* 3.5 11.7 - - + +
157A THR* 1.3 79.6 - - - +
159A ALA* 1.3 64.1 + - - +
160A HIS* 3.2 8.3 - - - -
161A GLU* 3.0 44.1 + - - +
162A ARG* 4.4 3.5 + - + +
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Residues in contact with ALA 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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117A PHE* 3.8 23.1 - - + -
124A MSE 3.6 30.1 - - + +
155A ILE* 3.1 16.8 + - + +
156A ALA* 3.5 12.3 + - - +
158A THR* 1.3 77.5 - - - +
160A HIS* 1.3 61.2 + - - +
162A ARG* 3.2 17.8 + - - +
163A MSE 3.7 10.6 - - - +
235A TRP* 4.2 7.0 - - + -
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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
------------------------------------------------------------
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