Contacts of the helix formed by residues 163 - 177 (chain E) in PDB entry 1QO0
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 163 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158D GLN* 4.8 23.2 - - + +
157E MET* 4.0 7.9 - - - -
161E GLY 4.0 0.8 + - - -
162E TRP* 1.3 76.5 - - - +
164E GLU* 1.3 64.8 + - - +
165E ARG* 3.1 14.0 + - - +
166E GLU* 2.8 47.3 + - - +
167E ALA* 3.0 18.7 + - - +
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Residues in contact with GLU 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D GLN* 6.0 2.4 - - - +
154D VAL* 3.6 37.6 - - + +
158D GLN* 5.0 6.4 - - - +
153E LYS* 2.5 38.4 + - - +
157E MET* 3.7 22.8 - - - +
163E ASP* 1.3 75.1 - - - +
165E ARG* 1.3 75.0 + - + +
167E ALA* 3.7 2.0 - - - +
168E HIS* 2.8 33.8 + - + +
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Residues in contact with ARG 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D GLN* 5.6 6.5 - - - +
163E ASP* 3.1 13.6 + - + +
164E GLU* 1.3 86.6 - - + +
166E GLU* 1.3 57.2 + - + +
168E HIS* 3.4 5.5 + - - +
169E GLN* 2.7 61.5 + - - +
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Residues in contact with GLU 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E GLY 4.6 1.2 - - - +
162E TRP* 3.4 33.9 + - + -
163E ASP* 2.8 49.0 + - - +
165E ARG* 1.3 73.4 - - + +
167E ALA* 1.3 67.4 + - - +
169E GLN* 3.1 9.7 + - + +
170E HIS* 2.8 25.8 + - - +
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Residues in contact with ALA 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E LYS* 3.8 24.2 - - + +
156E LEU* 3.8 16.8 - - + +
157E MET* 3.7 21.8 - - + -
162E TRP* 3.9 13.2 - - + -
163E ASP 3.0 16.3 + - - +
164E GLU 3.7 4.0 - - - +
166E GLU* 1.3 78.7 - - - +
168E HIS* 1.3 62.7 + - - +
170E HIS* 3.1 2.9 + - - +
171E LEU* 3.1 19.1 + - - +
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Residues in contact with HIS 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E ILE* 5.7 3.3 - - + +
153E LYS* 4.0 21.7 - - + +
164E GLU* 2.8 26.3 + - + +
165E ARG* 3.8 6.3 - - - +
167E ALA* 1.3 74.4 - - - +
169E GLN* 1.3 71.8 + - - +
171E LEU* 3.3 4.5 + - - +
172E SER* 3.1 44.0 + - - -
182E ILE* 4.4 14.3 - - + +
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Residues in contact with GLN 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E ARG* 2.7 58.3 + - - +
166E GLU* 3.5 8.3 - - + +
168E HIS* 1.3 81.6 - - - +
170E HIS* 1.3 58.1 - - - +
172E SER* 3.9 5.9 + - - -
173E ARG* 3.0 30.7 + - - +
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Residues in contact with HIS 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E LEU* 3.9 22.7 - - + +
160E HIS* 5.9 1.9 + + - -
162E TRP* 3.6 35.3 - + + -
166E GLU 2.8 12.6 + - - +
167E ALA 3.1 7.6 + - - +
169E GLN* 1.3 71.0 - - - +
171E LEU* 1.3 58.3 + - - +
173E ARG* 3.7 4.2 - - - +
174E GLU* 2.7 57.4 + - + +
189E LEU* 5.3 5.6 - - + +
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Residues in contact with LEU 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E ILE* 4.1 22.0 - - + +
152E ALA* 4.7 2.7 - - + -
153E LYS* 3.6 40.2 - - + +
156E LEU* 3.8 10.1 - - + -
167E ALA 3.1 4.7 + - - +
168E HIS* 3.3 9.2 + - - +
170E HIS* 1.3 80.4 - - + +
172E SER* 1.3 54.0 + - - +
174E GLU* 3.3 3.0 + - + +
175E ALA* 2.6 37.8 + - - +
182E ILE* 3.9 16.0 - - + +
185E ILE* 4.1 20.2 - - + +
186E ALA* 4.2 9.2 - - + +
189E LEU* 3.7 28.9 - - + -
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Residues in contact with SER 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E HIS* 3.1 31.9 + - - -
169E GLN* 3.9 6.7 - - - -
171E LEU* 1.3 74.9 - - - +
173E ARG* 1.3 57.8 + - - +
175E ALA* 3.0 3.4 + - - +
176E MET* 2.6 41.0 + - - +
182E ILE* 3.6 20.5 - - - +
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Residues in contact with ARG 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E GLN 3.0 19.7 + - - +
170E HIS* 3.8 5.8 - - - +
172E SER* 1.3 74.2 - - - +
174E GLU* 1.3 65.0 + - - +
176E MET* 3.8 10.6 - - + +
177E LYS* 3.0 28.2 + - - +
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Residues in contact with GLU 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E HIS* 2.7 45.6 + - + +
171E LEU* 3.7 4.7 - - + +
173E ARG* 1.3 75.8 - - - +
175E ALA* 1.3 62.6 + - - +
177E LYS* 3.3 10.1 - - - +
178E ARG* 3.3 22.6 - - + +
185E ILE* 5.0 12.8 - - + -
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Residues in contact with ALA 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E LEU 2.6 22.2 + - - +
172E SER* 3.6 2.9 - - - +
174E GLU* 1.3 72.5 - - - +
176E MET* 1.3 68.4 + - - +
177E LYS 3.2 0.2 + - - -
178E ARG* 3.4 8.9 + - - +
179E ARG* 3.5 5.4 + - - -
180E GLU* 3.2 24.1 + - - +
181E PRO 3.9 0.9 - - - +
182E ILE* 3.3 38.6 - - + +
185E ILE* 4.8 7.7 - - + +
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Residues in contact with MET 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E SER* 2.6 23.3 + - - +
173E ARG* 3.8 9.0 - - + +
175E ALA* 1.3 76.0 - - - +
177E LYS* 1.3 82.4 + - + +
178E ARG 3.3 3.5 + - - -
179E ARG* 3.7 7.4 + - - -
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Residues in contact with LYS 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E ARG 3.0 12.8 + - - +
174E GLU* 3.3 11.1 - - - +
176E MET* 1.3 93.3 - - + +
178E ARG* 1.3 64.2 + - - +
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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