Contacts of the helix formed by residues 166 - 178 (chain D) in PDB entry 2Q5E
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 LEU 166 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165D SER* 1.3 78.7 - - - +
167D ALA* 1.3 69.9 + - - +
168D LYS* 4.2 29.8 - - + +
169D TYR* 2.7 18.7 + - + +
170D ALA 2.9 9.1 + - - -
188D PHE* 4.1 2.5 - - - -
189D ARG* 3.8 38.1 - - + +
190D GLU* 3.2 28.3 - - - +
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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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195B HIS* 4.2 6.7 - - + +
166D LEU* 1.3 73.7 - - - +
168D LYS* 1.3 60.1 + - - +
171D ASP* 2.8 50.6 + - - +
188D PHE* 3.4 40.3 - - + +
190D GLU* 5.4 1.9 + - - +
133H GLY* 5.4 9.9 - - - -
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Residues in contact with LYS 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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129D ILE* 3.9 19.1 - - + +
130D GLU* 3.4 30.3 - - + +
131D ILE* 4.0 20.7 - - - +
166D LEU* 2.8 26.3 + - + +
167D ALA* 1.3 78.0 - - - +
169D TYR* 1.3 63.6 + - - +
171D ASP* 5.4 0.2 - - - -
172D PRO* 3.3 19.4 - - - +
130H GLU* 4.8 21.8 - - - +
133H GLY* 5.1 7.4 - - - +
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Residues in contact with TYR 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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108D LEU* 3.9 14.3 - - + +
109D ASP* 2.4 40.8 + - - -
113D VAL* 4.3 7.8 - - - +
115D SER* 2.4 36.5 + - - -
117D PHE* 6.2 1.3 - + - -
129D ILE* 3.5 26.5 - - + -
138D VAL* 4.0 10.3 - - + -
165D SER* 3.6 17.7 - - - -
166D LEU* 2.7 11.6 + - + +
168D LYS* 1.3 85.9 - - + +
170D ALA* 1.3 66.8 + - - +
171D ASP 3.5 0.4 - - - -
172D PRO* 3.4 12.2 - - - +
173D VAL* 3.4 25.6 - - + +
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Residues in contact with ALA 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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108D LEU* 4.0 13.2 - - + +
161D LEU* 4.5 4.7 - - + -
163D THR* 3.9 8.5 - - + -
165D SER* 3.9 14.4 - - - +
166D LEU 2.9 7.5 + - - +
169D TYR* 1.3 82.9 - - - +
171D ASP* 1.3 64.3 + - - +
173D VAL* 3.2 3.1 + - - +
174D THR* 2.9 26.3 + - - -
188D PHE* 3.4 30.5 - - + -
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Residues in contact with ASP 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B HIS* 2.4 45.5 + - - -
224B ILE* 4.4 5.5 - - + +
225B PHE* 3.2 11.9 - - + -
167D ALA* 2.8 28.1 + - - +
170D ALA* 1.3 72.2 - - - +
172D PRO* 1.3 68.5 - - + +
173D VAL 3.0 0.5 + - - -
174D THR 3.1 0.2 + - - -
175D ASP* 2.9 31.1 + - - +
186D ARG* 2.9 32.1 + - - +
188D PHE* 3.6 4.4 - - - -
133H GLY* 5.5 1.6 - - - +
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Residues in contact with PRO 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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127D VAL* 3.8 27.1 - - + -
128D PRO* 5.3 3.1 - - + +
129D ILE* 4.5 1.6 - - + -
167D ALA 3.5 0.7 - - - +
168D LYS* 3.3 28.3 - - - +
169D TYR* 3.4 11.0 - - - +
171D ASP* 1.3 95.3 - - + +
173D VAL* 1.3 59.4 + - - +
175D ASP* 3.7 11.0 - - + +
176D LEU* 3.5 25.8 + - - +
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Residues in contact with VAL 173 (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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108D LEU* 3.9 27.1 - - + -
113D VAL* 4.5 12.6 - - + -
125D PHE* 4.8 2.9 - - + -
127D VAL* 4.3 16.2 - - + -
138D VAL* 5.4 0.2 - - + -
140D VAL* 4.2 27.1 - - + -
169D TYR* 3.4 35.9 - - + +
170D ALA 3.2 6.7 + - - +
171D ASP 3.1 0.8 - - - -
172D PRO* 1.3 76.9 - - - +
174D THR* 1.3 61.9 + - - +
176D LEU* 3.3 5.5 + - - +
177D LEU* 2.9 30.3 + - + +
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Residues in contact with THR 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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108D LEU* 4.1 11.0 - - + +
161D LEU* 3.5 22.8 - - + +
170D ALA 2.9 17.4 + - - -
173D VAL* 1.3 75.5 - - - +
175D ASP* 1.3 59.9 + - - +
177D LEU* 4.2 9.4 - - + -
178D ASP* 2.8 41.6 + - + +
183D PHE* 3.7 33.9 - - + -
186D ARG* 3.7 25.4 - - - +
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Residues in contact with ASP 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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202B ASP* 5.0 2.1 - - - +
225B PHE* 3.9 37.2 - - - +
226B HIS* 6.5 0.2 - - - -
171D ASP* 2.9 23.7 + - - +
172D PRO* 3.7 10.7 - - + +
174D THR* 1.3 75.9 - - - +
176D LEU* 1.3 61.4 + - + +
178D ASP 4.0 10.0 + - - +
179D ARG* 5.4 0.5 - - - -
186D ARG* 3.0 28.0 + - - +
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Residues in contact with LEU 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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125D PHE* 3.6 55.1 - - + -
126D ILE 4.8 4.5 - - - +
127D VAL* 3.7 22.4 - - + -
172D PRO 3.5 7.6 + - - +
173D VAL 3.3 6.3 + - - +
174D THR 3.2 0.2 - - - -
175D ASP* 1.3 78.6 - - + +
177D LEU* 1.3 67.6 + - - +
178D ASP 3.5 0.2 + - - -
179D ARG* 4.3 12.0 + - - +
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D LEU* 3.7 29.8 - - + -
112D LEU* 4.2 18.2 - - + -
113D VAL* 3.9 23.8 - - + -
125D PHE* 3.8 12.6 - - + -
142D LYS* 4.3 13.5 + - + -
146D VAL* 4.2 27.4 - - + -
147D ASP* 4.9 6.4 - - - +
150D LEU* 4.3 14.7 - - + +
173D VAL* 2.9 19.3 + - + +
174D THR* 4.0 4.7 - - - +
176D LEU* 1.3 79.1 - - - +
178D ASP* 1.3 57.3 + - - +
179D ARG* 2.8 13.5 + - - +
183D PHE* 5.1 5.6 - - + -
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Residues in contact with ASP 178 (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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205B ARG* 4.8 2.6 + - - -
150D LEU* 4.5 7.2 - - - +
174D THR* 2.8 33.7 + - + +
175D ASP* 4.3 7.1 - - - +
176D LEU 3.4 0.8 - - - -
177D LEU* 1.3 72.6 - - + +
179D ARG* 1.3 61.0 + - - +
180D CYS 4.4 0.7 + - - -
181D GLY* 3.4 11.6 + - - -
182D VAL* 3.0 31.3 + - - +
183D PHE* 3.1 44.3 + - + +
186D ARG* 4.7 6.3 + - - +
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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