Contacts of the helix formed by residues 146 - 163 (chain B) in PDB entry 2OQH
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 146 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ALA* 4.1 6.3 - - + -
143B THR* 2.7 41.6 + - - +
145B ALA* 1.3 77.1 - - - +
147B LEU* 1.3 63.6 + - - +
148B PRO* 3.4 2.9 - - - -
149B LYS* 3.4 12.8 + - + +
150B ALA* 2.9 22.6 + - + +
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Residues in contact with LEU 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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136B ARG* 3.8 46.2 - - + +
139B ALA* 3.5 33.2 - - + +
142B ALA* 3.8 14.8 - - + +
143B THR 2.7 18.7 + - - +
144B PRO* 4.0 8.5 - - + +
146B ASP* 1.3 73.0 - - - +
148B PRO* 1.3 65.5 - - + +
150B ALA* 3.1 1.0 + - - +
151B MSE 2.7 47.5 + - + +
177B GLY* 5.9 0.9 - - - +
181B ILE* 4.0 9.9 - - + -
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Residues in contact with PRO 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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144B PRO 3.5 13.9 - - - +
145B ALA 4.0 7.4 - - - +
146B ASP 3.5 3.4 - - - -
147B LEU* 1.3 94.9 - - + +
149B LYS* 1.3 56.5 + - - +
151B MSE 3.4 2.1 + - + +
152B ALA* 2.8 30.5 + - - +
177B GLY 5.1 0.2 - - - +
180B ALA* 3.5 45.8 - - + +
181B ILE* 4.0 15.5 - - + +
184B ALA* 3.4 12.7 - - + +
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Residues in contact with LYS 149 (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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145B ALA 5.3 1.7 + - - +
146B ASP* 3.4 14.2 + - + +
147B LEU 3.3 0.2 - - - -
148B PRO* 1.3 75.9 - - - +
150B ALA* 1.3 66.8 + - - +
152B ALA* 3.2 6.2 + - + +
153B GLU* 2.9 56.2 + - + +
184B ALA* 4.2 3.8 - - - +
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Residues in contact with ALA 150 (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 ALA* 3.7 22.2 - - + -
142B ALA* 3.8 12.3 - - + -
146B ASP* 2.9 18.9 + - + +
147B LEU 3.4 4.0 - - - +
149B LYS* 1.3 78.6 - - - +
151B MSE 1.3 64.1 + - - +
153B GLU* 3.2 8.6 + - - +
154B HIS* 3.0 21.8 + - - +
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Residues in contact with MSE 151 (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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134B ILE* 4.0 18.5 - - + +
135B THR 3.2 42.2 - - - +
136B ARG* 3.8 9.0 - - - +
138B ASP* 4.4 4.5 - - - -
139B ALA* 3.8 19.7 - - - -
147B LEU* 2.7 38.3 + - + +
148B PRO 3.7 3.8 - - - +
150B ALA* 1.3 73.3 - - - +
152B ALA* 1.3 57.2 - - - +
154B HIS* 3.2 7.1 + - - +
155B ALA* 2.9 27.7 + - - +
169B LEU* 3.7 26.0 - - + -
181B ILE* 3.7 23.1 - - + -
185B VAL* 4.5 3.4 - - + +
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Residues in contact with ALA 152 (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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148B PRO 2.8 18.1 + - - +
149B LYS* 3.6 6.5 - - + +
151B MSE 1.3 76.9 - - - +
153B GLU* 1.3 63.3 + - + +
155B ALA* 3.3 4.6 + - - +
156B VAL* 3.0 29.4 + - - +
184B ALA* 3.5 33.2 - - + +
185B VAL* 3.8 13.0 - - - +
188B ALA* 4.1 8.5 - - + +
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Residues in contact with GLU 153 (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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149B LYS* 2.9 54.8 + - + +
150B ALA* 3.6 7.5 + - - +
152B ALA* 1.3 77.0 - - + +
154B HIS* 1.3 64.8 + - - +
156B VAL* 3.3 8.8 + - - +
157B ARG* 3.1 29.2 + - + +
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Residues in contact with HIS 154 (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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19B ASN* 5.5 1.5 + - - -
21B PHE* 3.1 28.2 + - + -
22B THR* 5.1 1.4 - - - -
23B SER* 4.8 13.0 + - - -
133B LEU 5.2 2.2 - - - -
134B ILE* 4.0 11.1 - - + +
138B ASP* 3.3 58.2 + - + +
139B ALA* 6.1 0.2 - - + -
150B ALA 3.0 13.7 + - - +
151B MSE 3.2 11.1 + - - +
153B GLU* 1.3 77.1 - - - +
155B ALA* 1.3 64.9 + - - +
157B ARG* 3.2 12.6 + - + +
158B VAL* 3.0 48.3 + - + +
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Residues in contact with ALA 155 (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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134B ILE* 4.5 17.0 - - + +
151B MSE 2.9 13.9 + - - +
152B ALA 3.4 10.5 - - - +
154B HIS* 1.3 79.5 + - - +
156B VAL* 1.3 56.7 + - - +
158B VAL* 3.2 7.1 + - - +
159B VAL* 2.9 35.0 + - - +
167B VAL* 4.9 6.3 - - + -
185B VAL* 4.0 16.4 - - + -
189B LEU* 3.7 18.8 - - + -
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Residues in contact with VAL 156 (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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152B ALA 3.0 16.2 + - - +
153B GLU* 3.6 9.6 - - - +
154B HIS 3.2 0.2 - - - -
155B ALA* 1.3 76.4 - - - +
157B ARG* 1.3 64.6 + - + +
159B VAL* 4.1 0.7 - - - +
160B GLU* 3.0 51.7 + - + +
188B ALA* 3.7 27.8 - - + +
189B LEU* 3.9 21.9 - - + +
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Residues in contact with ARG 157 (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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23B SER* 6.5 1.3 - - - -
153B GLU* 3.1 19.0 + - - +
154B HIS* 3.2 12.3 + - + +
156B VAL* 1.3 77.0 - - + +
158B VAL* 1.3 59.9 + - + +
160B GLU* 3.7 10.9 + - - +
161B GLU* 2.6 77.0 + - - +
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Residues in contact with VAL 158 (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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21B PHE* 4.1 28.3 - - + +
132B ALA* 3.6 20.0 - - + -
133B LEU 5.8 0.9 - - - +
134B ILE* 5.0 4.9 - - + -
154B HIS* 3.0 48.6 + - + +
155B ALA* 3.6 6.1 - - - +
157B ARG* 1.3 78.4 - - + +
159B VAL* 1.3 54.5 + - + +
162B GLY* 2.7 30.8 + - - -
164B PHE* 3.4 23.6 - - + -
167B VAL* 6.2 0.4 - - + -
328B TYR* 6.3 0.2 - - + -
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Residues in contact with VAL 159 (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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155B ALA 2.9 20.8 + - - +
156B VAL 4.1 2.2 - - - +
158B VAL* 1.3 77.0 - - + +
160B GLU* 1.3 60.1 + - + +
163B GLY* 2.8 28.2 + - - -
164B PHE* 3.6 28.3 - - + +
167B VAL* 3.6 29.8 - - + -
189B LEU* 4.1 25.1 - - + -
192B VAL* 4.5 9.0 - - + -
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Residues in contact with GLU 160 (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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156B VAL* 3.0 41.9 + - - +
157B ARG* 3.7 12.3 + - - +
159B VAL* 1.3 81.6 - - + +
161B GLU* 1.3 62.4 + - + +
163B GLY* 4.3 2.4 + - - -
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Residues in contact with GLU 161 (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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20B PRO 4.8 4.9 - - - +
21B PHE* 4.1 25.2 - - + -
157B ARG* 2.6 57.8 + - - +
160B GLU* 1.3 77.0 - - + +
162B GLY* 1.3 60.3 + - - +
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Residues in contact with GLY 162 (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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21B PHE* 3.8 11.3 - - - -
158B VAL 2.7 21.4 + - - -
161B GLU* 1.3 74.2 - - - +
163B GLY* 1.3 59.2 + - - +
164B PHE* 3.2 21.4 + - - -
342B ASN* 3.6 3.1 + - - -
343B GLY* 3.0 26.7 + - - -
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Residues in contact with GLY 163 (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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159B VAL* 2.8 16.1 + - - -
160B GLU 4.3 2.8 + - - -
161B GLU 3.5 2.4 + - - -
162B GLY* 1.3 77.2 - - - +
164B PHE* 1.3 65.3 + - - +
165B ASP* 3.6 10.0 + - - +
342B ASN* 3.3 34.0 + - - +
343B GLY* 3.9 2.2 - - - -
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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