Contacts of the helix formed by residues 166 - 178 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B SER* 1.3 74.7 - - - +
167B ALA* 1.3 55.1 + - - +
168B LYS* 4.2 36.1 - - + +
169B TYR* 2.8 31.0 + - + +
170B ALA* 2.9 11.1 + - - -
188B PHE* 5.1 0.2 - - - -
189B ARG* 3.3 48.0 - - + +
190B GLU* 5.2 8.7 - - + +
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Residues in contact with ALA 167 (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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165B SER 3.9 2.0 + - - -
166B LEU* 1.3 70.9 - - - +
168B LYS* 1.3 63.6 + - - +
170B ALA 4.0 2.9 - - - +
171B ASP* 2.9 39.2 + - - +
188B PHE* 3.8 41.1 - - + +
190B GLU* 4.3 9.8 + - - +
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Residues in contact with LYS 168 (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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128B PRO 5.4 0.2 - - - +
129B ILE* 3.3 28.9 - - + +
130B GLU* 3.3 28.8 + - + +
131B ILE* 4.6 14.4 - - - +
132B GLU 5.2 1.8 - - - +
166B LEU* 3.0 31.1 + - + +
167B ALA* 1.3 78.0 - - - +
169B TYR* 1.3 61.5 + - + +
172B PRO* 3.3 19.9 - - - +
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Residues in contact with TYR 169 (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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108B LEU* 3.9 12.1 - - + -
109B ASP* 2.3 38.8 + - - -
113B VAL* 4.2 7.6 - - - +
115B SER* 2.2 41.0 + - - -
129B ILE* 4.0 20.2 - - + -
138B VAL* 4.0 13.5 - - + -
165B SER* 3.4 25.1 - - - -
166B LEU* 2.8 11.2 + - + +
168B LYS* 1.3 85.4 - - + +
170B ALA* 1.3 60.4 + - - +
171B ASP 3.5 0.4 - - - -
172B PRO* 3.6 2.5 - - - +
173B VAL* 3.0 49.6 + - + +
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 3.9 17.0 - - + -
161B LEU* 4.8 0.4 - - + -
163B THR* 4.1 4.5 - - + -
165B SER* 3.5 20.9 - - - +
166B LEU 2.9 11.4 + - - +
169B TYR* 1.3 75.3 - - - +
171B ASP* 1.3 59.3 + - - +
173B VAL* 3.8 0.2 - - - +
174B THR* 2.8 37.0 + - - +
188B PHE* 3.6 28.7 - - + -
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Residues in contact with ASP 171 (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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167B ALA* 2.9 25.8 + - - +
170B ALA* 1.3 72.0 - - - +
172B PRO* 1.3 75.6 - - + +
174B THR 3.1 1.4 + - - -
175B ASP* 2.9 27.3 + - - +
186B ARG* 2.6 36.1 + - - +
188B PHE* 3.6 21.8 - - - -
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Residues in contact with PRO 172 (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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127B VAL* 4.7 11.2 - - + -
128B PRO* 5.4 5.4 - - + +
129B ILE* 4.4 10.5 - - + -
167B ALA 3.5 2.0 - - - +
168B LYS* 3.3 27.8 - - - +
169B TYR* 3.6 5.6 - - - +
171B ASP* 1.3 93.4 - - + +
173B VAL* 1.3 61.8 + - + +
175B ASP* 3.4 12.2 + - + +
176B LEU* 3.3 27.3 + - + +
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Residues in contact with VAL 173 (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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108B LEU* 4.4 18.6 - - + -
113B VAL* 4.4 17.7 - - + -
125B PHE* 4.6 2.9 - - + -
127B VAL* 3.9 27.4 - - + -
140B VAL* 4.4 17.3 - - + -
169B TYR* 3.0 43.0 + - + +
170B ALA* 3.8 4.3 - - - +
171B ASP 3.2 0.8 - - - -
172B PRO* 1.3 76.4 - - - +
174B THR* 1.3 59.6 + - - +
176B LEU* 3.3 5.4 + - - +
177B LEU* 3.0 27.0 + - + +
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Residues in contact with THR 174 (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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108B LEU* 4.0 15.2 - - - +
161B LEU* 3.7 20.2 - - + +
170B ALA 2.8 24.6 + - - -
173B VAL* 1.3 69.1 - - - +
175B ASP* 1.3 59.2 + - - +
176B LEU 3.0 1.3 - - - -
177B LEU* 4.1 7.4 - - + +
178B ASP* 2.7 37.5 + - + +
183B PHE* 3.9 31.4 - - + -
186B ARG* 3.8 25.7 + - - +
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Residues in contact with ASP 175 (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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171B ASP* 2.9 18.8 + - - +
172B PRO* 3.4 15.6 + - + +
174B THR* 1.3 75.5 - - - +
176B LEU* 1.3 65.0 + - + +
178B ASP 4.3 9.4 + - - +
179B ARG* 4.8 2.9 + - - -
186B ARG* 2.8 28.2 + - - +
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Residues in contact with LEU 176 (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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125B PHE* 3.6 42.4 - - + -
126B ILE 4.6 4.9 - - - +
127B VAL* 3.5 32.3 - - + -
172B PRO* 3.3 10.4 + - + +
173B VAL 3.7 6.5 - - - +
174B THR 3.0 0.6 - - - -
175B ASP* 1.3 85.4 - - + +
177B LEU* 1.3 61.7 + - - +
179B ARG* 4.3 8.5 + - - +
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Residues in contact with LEU 177 (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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108B LEU* 4.1 12.6 - - + -
112B LEU* 4.0 26.0 - - + -
113B VAL* 3.8 28.5 - - + -
125B PHE* 3.8 11.4 - - + -
142B LYS* 3.5 29.8 - - + -
146B VAL* 3.7 18.2 - - + -
147B ASP* 4.1 13.3 - - - +
150B LEU* 4.6 13.2 - - + +
173B VAL* 3.0 18.1 + - + +
174B THR* 3.2 4.2 + - - +
176B LEU* 1.3 80.6 - - - +
178B ASP* 1.3 57.0 + - - +
179B ARG* 3.1 8.1 + - - +
183B PHE* 5.3 5.2 - - + -
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Residues in contact with ASP 178 (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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150B LEU* 4.7 7.0 - - - +
174B THR* 2.7 26.2 + - + +
175B ASP* 4.6 5.1 - - - +
176B LEU 3.5 0.2 - - - -
177B LEU* 1.3 71.3 - - - +
179B ARG* 1.3 63.5 + - - +
180B CYS 2.8 3.1 + - - -
181B GLY* 2.9 14.1 + - - -
182B VAL* 3.0 28.4 + - - +
183B PHE* 2.9 53.8 + - + +
186B ARG* 4.9 6.1 + - - +
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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