Contacts of the helix formed by residues 167 - 180 (chain A) in PDB entry 2CUY
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 ARG 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A GLY 3.0 30.5 + - - +
126A GLU* 3.1 11.7 + - - +
127A GLY 4.0 7.6 - - - +
128A ALA* 3.9 19.7 - - + +
165A GLY 3.4 2.2 + - - -
166A ARG* 1.3 69.8 - - - +
168A GLN* 1.3 98.7 + - - +
170A VAL* 3.0 3.8 + - - +
171A GLU* 2.5 68.8 + - + +
167B ARG* 3.1 51.1 - - - +
171B GLU* 4.1 2.6 + - - -
188B PRO* 4.2 16.4 - - - -
189B VAL* 4.4 4.9 - - + -
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Residues in contact with GLN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLU* 4.4 6.8 - - - +
166A ARG* 4.2 6.2 - - + +
167A ARG* 1.3 119.0 + - - +
169A ALA* 1.3 62.6 + - - +
171A GLU* 3.4 6.8 + - - +
172A GLU* 3.0 25.5 + - - +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 3.6 15.6 - - + +
148A GLU 3.1 27.6 - - - +
149A GLY 3.7 17.9 - - - -
150A VAL* 3.9 6.9 - - + +
166A ARG* 2.9 16.5 + - + +
168A GLN* 1.3 78.8 - - - +
170A VAL* 1.3 57.1 + - - +
172A GLU* 3.4 5.1 + - - +
173A ALA* 3.0 23.4 + - - +
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ALA* 3.5 25.6 - - + +
129A MET* 4.8 0.2 - - - -
130A ALA* 4.0 21.1 - - + +
150A VAL* 4.2 12.1 - - + -
163A ILE* 4.1 11.7 - - + +
164A SER* 3.9 6.1 - - - -
165A GLY* 3.6 15.0 - - - +
166A ARG 2.9 20.4 + - - +
167A ARG 3.4 5.6 - - - +
169A ALA* 1.3 75.0 - - - +
171A GLU* 1.3 59.8 + - - +
173A ALA* 3.1 2.3 + - - +
174A ALA* 2.8 27.5 + - - +
186A PHE* 3.5 25.1 - - + -
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Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ARG* 2.5 60.2 + - + +
168A GLN* 3.6 7.0 - - - +
170A VAL* 1.3 76.9 - - - +
172A GLU* 1.3 62.1 + - - +
174A ALA* 3.0 5.5 + - - +
175A GLU* 3.0 29.1 + - - +
186A PHE* 3.9 22.0 - - + -
124B VAL* 4.0 7.6 - - + +
125B GLY* 3.7 31.3 - - - +
167B ARG* 4.3 0.2 + - - -
189B VAL* 4.6 2.9 - - + +
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 3.2 29.4 - - + +
168A GLN 3.0 17.5 + - - +
169A ALA* 3.7 6.8 - - - +
170A VAL 3.2 0.2 - - - -
171A GLU* 1.3 72.7 - - - +
173A ALA* 1.3 66.0 + - - +
175A GLU* 3.3 20.5 + - + +
176A ARG* 3.2 35.8 + - + +
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 3.2 34.1 - - + -
147A LEU* 3.6 9.6 - - + +
150A VAL* 4.1 2.7 - - + -
163A ILE* 3.8 13.7 - - + -
169A ALA 3.0 14.0 + - - +
170A VAL 3.1 7.8 + - - +
172A GLU* 1.3 73.4 - - - +
174A ALA* 1.3 66.1 + - - +
176A ARG* 3.0 6.8 + - - +
177A LEU* 2.8 30.1 + - + +
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ILE* 4.9 1.9 - - + +
170A VAL* 2.8 13.0 + - + +
171A GLU* 3.1 13.0 - - - +
173A ALA* 1.3 76.9 - - - +
175A GLU* 1.3 55.0 + - + +
177A LEU* 4.0 3.1 - - - +
178A LYS* 2.9 44.0 + - - +
184A VAL* 3.8 30.6 - - + +
186A PHE* 3.9 19.1 - - + -
124B VAL* 5.8 0.7 - - + -
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Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A GLU* 3.0 16.5 + - - +
172A GLU* 3.4 30.5 + - + +
173A ALA 3.1 0.4 - - - -
174A ALA* 1.3 75.9 - - + +
176A ARG* 1.3 63.5 + - + +
178A LYS* 3.4 12.2 + - + +
179A GLU* 3.1 23.0 + - - +
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Residues in contact with ARG 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LYS 5.1 1.0 + - - -
143A ALA* 3.1 39.0 + - + +
144A LEU 4.7 0.2 - - - -
145A GLU 3.3 21.4 + - - -
146A GLY* 5.2 2.0 - - - -
147A LEU* 3.3 34.6 - - - +
172A GLU* 3.2 24.0 + - + +
173A ALA 3.0 7.0 + - - +
175A GLU* 1.3 79.6 - - + +
177A LEU* 1.3 62.0 + - - +
179A GLU* 3.2 9.9 + - - +
180A ARG* 3.1 26.9 + - - +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL* 3.5 30.3 - - + -
135A LEU* 3.6 21.8 - - + -
140A ILE* 3.9 23.6 - - + +
143A ALA* 3.8 24.0 - - + -
144A LEU* 4.8 2.7 - - + -
163A ILE* 4.1 16.8 - - + -
173A ALA* 2.8 27.5 + - + +
174A ALA* 4.6 0.9 - - - +
176A ARG* 1.3 69.5 - - - +
178A LYS* 1.3 66.0 + - - +
180A ARG* 2.9 16.5 + - - +
182A ALA* 3.1 24.7 + - + +
184A VAL* 3.9 15.9 - - + -
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Residues in contact with LYS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ALA* 2.9 29.6 + - - +
175A GLU* 3.4 12.2 - - + +
177A LEU* 1.3 76.6 - - - +
179A GLU* 1.3 54.7 + - - +
181A ARG* 2.8 27.4 + - - -
182A ALA 3.7 15.2 + - - +
184A VAL* 4.0 31.2 + - + +
186A PHE* 4.8 3.0 - - - -
124B VAL* 3.8 37.6 - - - +
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A GLU 3.1 10.8 + - - +
176A ARG* 3.2 12.8 + - - +
178A LYS* 1.3 79.0 - - - +
180A ARG* 1.3 58.2 + - + +
181A ARG* 3.1 8.3 + - - +
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Residues in contact with ARG 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 3.4 27.3 - - + +
139A GLU* 3.4 36.2 + - - +
142A LYS* 3.8 35.3 - - - +
143A ALA* 3.1 36.2 - - - +
176A ARG* 3.1 14.0 + - - +
177A LEU* 2.9 14.6 + - - +
179A GLU* 1.3 78.8 - - + +
181A ARG* 1.3 72.1 + - - +
182A ALA 3.3 0.9 - - - -
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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