Contacts of the helix formed by residues 163 - 176 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157D MET* 3.9 6.1 - - - -
161D GLY 4.3 0.4 + - - -
162D TRP* 1.3 76.1 - - - +
164D GLU* 1.3 57.8 + - - +
165D ARG* 3.1 28.1 + - - +
166D GLU* 2.7 55.7 + - - +
167D ALA* 2.9 26.5 + - - +
158E GLN* 5.2 13.0 - - - +
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Residues in contact with GLU 164 (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 LYS* 2.6 40.1 + - + +
157D MET* 3.9 21.1 - - - +
163D ASP* 1.3 72.6 - - - +
165D ARG* 1.3 76.1 + - - +
167D ALA* 3.1 3.6 + - - +
168D HIS* 2.8 35.9 + - - +
150E ASN* 5.5 2.9 - - - +
154E VAL* 3.5 41.4 - - + +
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Residues in contact with ARG 165 (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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163D ASP* 3.2 24.2 + - - +
164D GLU* 1.3 95.2 + - - +
166D GLU* 1.3 56.4 + - - +
168D HIS* 3.3 6.7 + - - +
169D GLN* 2.8 47.5 + - - +
154E VAL* 5.3 3.6 - - - +
158E GLN* 3.2 32.5 + - - +
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Residues in contact with GLU 166 (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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161D GLY 4.4 2.1 - - - +
162D TRP* 3.3 32.7 - - + +
163D ASP* 2.7 53.9 + - - +
165D ARG* 1.3 74.3 - - - +
167D ALA* 1.3 62.8 + - - +
169D GLN* 3.3 12.8 + - - +
170D HIS* 3.0 24.8 + - - +
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Residues in contact with ALA 167 (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 LYS* 3.6 34.5 - - + +
156D LEU* 4.0 13.4 - - + +
157D MET* 3.9 8.3 - - + +
162D TRP* 3.9 12.3 - - + -
163D ASP 2.9 13.3 + - - +
164D GLU 3.6 7.0 - - - +
166D GLU* 1.3 76.2 - - - +
168D HIS* 1.3 63.7 + - - +
170D HIS* 3.3 2.1 + - - +
171D LEU* 3.0 29.2 + - - +
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Residues in contact with HIS 168 (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 ILE* 5.8 3.2 - - + +
153D LYS* 3.8 24.2 + - - +
164D GLU* 2.8 23.1 + - - +
165D ARG* 3.6 7.0 - - - +
167D ALA* 1.3 73.2 - - - +
169D GLN* 1.3 70.0 + - + +
171D LEU* 3.4 7.8 + - - +
172D SER* 3.1 30.9 + - - -
182D ILE* 4.5 21.4 - - + +
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Residues in contact with GLN 169 (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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165D ARG* 2.8 39.9 + - - +
166D GLU* 3.3 12.5 + - - +
168D HIS* 1.3 78.7 - - + +
170D HIS* 1.3 57.6 + - - +
172D SER* 3.8 3.9 - - - -
173D ARG* 2.9 31.9 + - - +
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Residues in contact with HIS 170 (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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156D LEU* 3.5 37.5 - - + +
160D HIS* 5.7 2.5 - + - -
162D TRP* 3.4 34.7 - + + -
166D GLU 3.0 10.1 + - - +
167D ALA 3.7 1.6 - - - +
169D GLN* 1.3 73.0 - - - +
171D LEU* 1.3 68.8 + - + +
173D ARG* 3.3 4.8 + - - +
174D GLU* 3.0 33.8 + - + +
185D ILE* 5.9 2.5 - - + +
189D LEU* 5.4 4.6 - - + +
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Residues in contact with LEU 171 (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 ILE* 4.0 20.9 - - + +
152D ALA* 4.5 9.9 - - + -
153D LYS* 3.4 35.7 - - + +
156D LEU* 3.7 20.6 - - + -
167D ALA 3.0 17.1 + - - +
168D HIS* 3.7 7.4 - - - +
170D HIS* 1.3 78.1 - - + +
172D SER* 1.3 58.0 + - - +
174D GLU* 3.4 1.2 + - - +
175D ALA* 2.8 33.4 + - - +
182D ILE* 4.6 16.4 - - + +
185D ILE* 4.3 23.4 - - + +
186D ALA* 4.5 7.4 - - + +
189D LEU* 4.4 9.6 - - + -
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Residues in contact with SER 172 (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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168D HIS* 3.1 25.5 + - - -
169D GLN* 3.8 5.2 - - - -
171D LEU* 1.3 79.2 - - - +
173D ARG* 1.3 57.4 + - - +
175D ALA* 3.4 5.8 - - - +
176D MET* 2.8 36.1 + - - +
182D ILE* 4.1 18.0 - - - +
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Residues in contact with ARG 173 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169D GLN 2.9 19.7 + - - +
170D HIS* 3.7 5.2 - - - +
172D SER* 1.3 78.9 + - - +
174D GLU* 1.3 65.0 + - - +
176D MET* 3.3 4.0 + - - -
177D LYS* 3.2 22.1 + - - +
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Residues in contact with GLU 174 (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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170D HIS* 3.0 28.3 + - + +
171D LEU 4.1 1.6 - - - +
173D ARG* 1.3 73.6 - - - +
175D ALA* 1.3 64.8 + - - +
177D LYS* 3.0 17.4 + - - +
178D ARG* 3.0 17.5 + - - +
185D ILE* 4.4 18.6 - - + -
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Residues in contact with ALA 175 (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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171D LEU 2.8 19.8 + - - +
172D SER 3.4 4.0 - - - +
174D GLU* 1.3 78.3 - - - +
176D MET* 1.3 57.2 + - + +
177D LYS 3.1 3.1 + - - -
178D ARG 3.3 1.0 + - - -
179D ARG 3.3 17.0 + - - -
180D GLU 3.3 24.2 + - - +
182D ILE* 3.7 25.6 - - + -
185D ILE* 3.5 24.7 - - + +
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Residues in contact with MET 176 (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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172D SER* 2.8 24.8 + - - +
173D ARG* 3.4 4.7 - - - +
175D ALA* 1.3 70.8 - - + +
177D LYS* 1.3 56.9 + - - +
178D ARG 3.7 0.2 - - - -
179D ARG* 4.5 4.9 - - - +
180D GLU 5.2 0.2 - - - -
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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