Contacts of the helix formed by residues 146 - 163 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ALA* 4.1 6.7 - - + -
143D THR* 2.8 35.8 + - - +
145D ALA* 1.3 78.5 - - - +
147D LEU* 1.3 64.8 + - - +
148D PRO* 3.5 1.6 - - - -
149D LYS* 3.5 18.5 + - + +
150D ALA* 3.0 23.0 + - - +
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Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ARG* 3.9 36.6 - - + +
139D ALA* 4.0 22.4 - - + +
142D ALA* 3.9 13.0 - - + +
143D THR 2.9 10.0 + - - +
144D PRO* 3.3 14.3 + - + +
146D ASP* 1.3 74.0 - - - +
148D PRO* 1.3 74.4 - - + +
150D ALA* 3.0 1.9 + - - +
151D MSE 2.7 43.5 + - + +
174D ASP* 5.6 0.2 - - - +
177D GLY* 5.7 1.6 - - - +
181D ILE* 3.8 27.6 - - + -
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Residues in contact with PRO 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PRO 3.4 11.0 - - - +
145D ALA 3.9 7.6 - - - +
146D ASP 3.7 2.7 - - - -
147D LEU* 1.3 93.7 - - + +
149D LYS* 1.3 57.5 + - - +
151D MSE 3.7 1.8 - - + +
152D ALA* 2.9 31.0 + - - +
177D GLY 5.2 0.2 - - - +
180D ALA* 3.7 41.5 - - + +
181D ILE* 4.2 14.1 - - + +
184D ALA* 3.4 15.2 - - + +
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Residues in contact with LYS 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ALA 5.4 1.3 + - - +
146D ASP* 3.5 21.4 + - + +
147D LEU 3.3 0.6 - - - -
148D PRO* 1.3 79.2 - - - +
150D ALA* 1.3 64.6 + - - +
152D ALA* 3.3 5.9 + - - +
153D GLU* 3.0 55.7 + - + +
184D ALA* 4.5 2.4 - - - +
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Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ALA* 3.6 24.7 - - + -
142D ALA* 4.1 9.2 - - + -
146D ASP* 3.0 18.0 + - + +
147D LEU 3.0 4.2 + - - +
149D LYS* 1.3 76.2 - - - +
151D MSE 1.3 63.4 + - - +
153D GLU* 3.3 11.6 + - - +
154D HIS* 3.0 24.0 + - - +
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Residues in contact with MSE 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D ILE* 4.1 16.7 - - + +
135D THR 3.3 42.2 - - - +
136D ARG* 3.8 11.7 - - - +
138D ASP* 4.4 6.3 - - - -
139D ALA* 4.1 13.7 - - - -
147D LEU* 2.7 39.0 + - + +
148D PRO 3.7 3.4 - - - +
150D ALA* 1.3 72.8 - - - +
152D ALA* 1.3 57.6 + - - +
154D HIS* 3.3 6.2 + - - +
155D ALA* 2.9 29.6 + - - +
169D LEU* 3.7 26.9 - - + -
181D ILE* 3.7 24.7 - - + -
185D VAL* 4.5 3.3 - - + +
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D PRO 2.9 17.9 + - - +
149D LYS* 3.6 6.7 - - - +
151D MSE 1.3 77.6 - - - +
153D GLU* 1.3 58.9 + - + +
155D ALA* 3.4 3.4 + - - +
156D VAL* 3.0 33.1 + - - +
184D ALA* 3.9 30.5 - - + +
185D VAL* 4.0 12.8 - - - +
188D ALA* 4.3 8.8 - - + +
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Residues in contact with GLU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D LYS* 3.0 46.4 + - + +
150D ALA* 3.3 8.9 + - - +
152D ALA* 1.3 73.7 - - + +
154D HIS* 1.3 67.3 + - - +
156D VAL* 3.3 8.7 + - - +
157D ARG* 3.1 32.0 + - + +
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Residues in contact with HIS 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ASN* 5.7 1.7 + - - -
21D PHE* 4.3 23.9 - - + +
133D LEU 5.5 0.8 + - - -
134D ILE* 4.1 13.6 - - + +
138D ASP* 3.2 55.4 + - + +
150D ALA 3.0 14.7 + - - +
151D MSE 3.5 11.4 - - - +
153D GLU* 1.3 77.8 - - - +
155D ALA* 1.3 62.3 + - - +
157D ARG* 3.0 13.8 + - + +
158D VAL* 2.9 49.0 + - + +
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D ILE* 4.4 18.6 - - + -
151D MSE 2.9 18.2 + - - +
152D ALA 3.6 5.6 - - - +
154D HIS* 1.3 76.7 - - - +
156D VAL* 1.3 62.4 + - - +
158D VAL* 3.2 8.7 + - - +
159D VAL* 3.0 29.0 + - + +
167D VAL* 4.9 5.4 - - + -
185D VAL* 4.1 17.7 - - + -
189D LEU* 4.0 16.8 - - + -
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Residues in contact with VAL 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ALA 3.0 17.6 + - - +
153D GLU* 3.6 10.3 - - - +
154D HIS 3.2 0.2 - - - -
155D ALA* 1.3 75.2 - - - +
157D ARG* 1.3 61.8 + - + +
159D VAL* 3.4 2.6 + - - +
160D GLU* 3.0 43.1 + - - +
188D ALA* 3.5 27.8 - - + +
189D LEU* 4.2 22.4 - - + +
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Residues in contact with ARG 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D GLU* 3.1 18.5 + - - +
154D HIS* 3.0 13.3 + - - +
156D VAL* 1.3 76.4 - - + +
158D VAL* 1.3 61.2 + - + +
160D GLU* 3.3 17.8 + - - +
161D GLU* 2.9 62.7 + - - +
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Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PHE* 4.1 27.7 - - + -
132D ALA* 3.7 17.9 - - + -
133D LEU 5.6 2.0 - - - +
134D ILE* 4.7 6.5 - - + -
154D HIS* 2.9 54.2 + - + +
155D ALA* 3.7 6.5 - - - +
157D ARG* 1.3 75.7 - - + +
159D VAL* 1.3 58.6 + - + +
162D GLY* 2.9 24.4 + - - -
164D PHE* 3.4 26.9 - - + -
167D VAL* 6.2 0.4 - - + -
328D TYR* 6.1 1.1 - - + +
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Residues in contact with VAL 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ALA 3.0 16.9 + - - +
156D VAL 3.8 4.5 - - - +
158D VAL* 1.3 80.1 - - + +
160D GLU* 1.3 58.7 + - - +
163D GLY* 2.8 27.2 + - - +
164D PHE* 3.8 25.4 - - + +
167D VAL* 3.6 30.3 - - + -
189D LEU* 3.7 26.5 - - + -
192D VAL* 4.8 5.8 - - + -
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Residues in contact with GLU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LYS* 3.5 24.3 - - - +
156D VAL* 3.0 33.7 + - - +
157D ARG* 3.3 26.9 + - - +
159D VAL* 1.3 79.2 - - - +
161D GLU* 1.3 66.6 + - + +
163D GLY* 4.2 1.6 + - - -
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Residues in contact with GLU 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PHE* 4.2 3.5 - - - -
27C THR* 3.7 24.0 - - - +
28C LYS* 3.2 35.4 + - + +
20D PRO 4.5 0.9 - - - +
21D PHE* 3.5 33.0 - - + +
157D ARG* 2.9 48.9 + - - +
160D GLU* 1.3 85.9 - - + +
162D GLY* 1.3 60.1 + - - +
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Residues in contact with GLY 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PHE* 4.2 12.8 - - - -
28C LYS* 6.0 1.3 - - - -
21D PHE* 3.8 9.6 - - - -
158D VAL 2.9 16.5 + - - -
161D GLU* 1.3 79.7 - - - +
163D GLY* 1.3 58.9 + - - +
164D PHE* 3.3 18.6 - - - -
342D ASN* 3.6 3.6 - - - -
343D GLY* 2.9 25.3 + - - -
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Residues in contact with GLY 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LYS* 5.5 6.0 - - - +
159D VAL 2.8 17.1 + - - -
160D GLU 4.2 3.4 + - - -
161D GLU 3.7 1.2 - - - -
162D GLY* 1.3 78.8 - - - +
164D PHE* 1.3 65.1 + - - +
165D ASP* 3.7 9.2 + - - +
342D ASN* 3.3 25.2 - - - +
343D GLY* 3.6 3.5 - - - -
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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