Contacts of the helix formed by residues 167 - 180 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ARG* 3.1 52.4 - - - +
171A GLU* 4.3 0.9 + - - -
125B GLY* 3.0 28.6 + - - +
126B GLU 2.9 14.3 + - - +
127B GLY 4.2 0.9 - - - -
128B ALA* 3.7 16.7 - - + +
165B GLY 3.4 1.0 + - - -
166B ARG* 1.3 72.3 - - - +
168B GLN* 1.3 101.3 + - - +
170B VAL* 3.3 2.3 + - - +
171B GLU* 2.6 64.6 + - - +
186B PHE* 5.7 0.2 - - + -
188B PRO* 3.8 17.3 - - + +
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Residues in contact with GLN 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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126B GLU* 4.5 4.8 - - - +
166B ARG* 3.7 28.7 + - - +
167B ARG* 1.3 123.0 + - - +
169B ALA* 1.3 61.9 + - - +
171B GLU* 3.5 6.9 + - - +
172B GLU* 3.2 31.1 + - + +
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Residues in contact with ALA 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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147B LEU* 4.2 4.7 - - + +
148B GLU* 4.6 5.2 - - + +
149B GLY 3.7 28.0 - - - +
150B VAL* 4.0 8.0 - - + +
166B ARG* 3.1 32.9 + - - +
168B GLN* 1.3 77.1 - - - +
170B VAL* 1.3 66.6 + - - +
171B GLU 3.3 0.3 + - - -
172B GLU* 3.3 14.3 + - - +
173B ALA* 3.2 21.0 + - - +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ALA* 3.5 19.7 - - + +
129B MET* 4.2 6.3 - - - +
130B ALA* 4.1 18.6 - - + +
150B VAL* 4.2 11.2 - - + +
163B ILE* 4.5 8.8 - - + +
164B SER* 3.8 6.1 - - - +
165B GLY* 3.4 29.4 - - - +
166B ARG 2.9 22.8 + - - +
167B ARG 3.7 4.0 - - - +
169B ALA* 1.3 75.0 - - - +
171B GLU* 1.3 57.4 + - - +
173B ALA* 3.3 4.5 + - - +
174B ALA* 2.9 26.0 + - - +
186B PHE* 3.7 19.1 - - + -
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Residues in contact with GLU 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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124A VAL 4.1 8.3 - - - +
125A GLY* 3.9 23.2 - - - +
126A GLU* 5.8 1.2 - - - +
167A ARG* 4.1 6.3 + - - -
167B ARG* 2.6 54.6 + - + +
168B GLN* 3.6 10.5 - - - +
170B VAL* 1.3 76.1 - - - +
172B GLU* 1.3 63.0 + - + +
174B ALA* 2.9 13.9 + - - +
175B GLU* 2.9 25.9 + - - +
186B PHE* 3.4 28.0 - - + -
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Residues in contact with GLU 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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147B LEU* 4.2 17.1 - - + +
148B GLU 5.8 0.9 + - - -
168B GLN* 3.2 19.0 - - - +
169B ALA* 3.3 12.6 + - - +
171B GLU* 1.3 77.4 - - + +
173B ALA* 1.3 62.2 + - - +
175B GLU* 3.3 18.1 + - - +
176B ARG* 3.0 33.9 + - - +
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Residues in contact with ALA 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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143B ALA 5.4 0.7 - - - -
144B LEU* 3.5 32.3 - - + -
147B LEU* 3.6 15.1 - - + +
150B VAL* 4.2 3.6 - - + -
163B ILE* 4.0 11.4 - - + -
169B ALA 3.2 6.9 + - - +
170B VAL 3.5 8.3 - - - +
171B GLU 3.1 0.4 - - - -
172B GLU* 1.3 77.2 - - - +
174B ALA* 1.3 61.1 + - - +
176B ARG* 3.2 6.5 + - - +
177B LEU* 2.8 36.0 + - + +
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Residues in contact with ALA 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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124A VAL* 4.4 9.4 - - + -
130B ALA* 5.2 2.0 - - + -
163B ILE* 4.9 1.3 - - - +
170B VAL 2.9 12.8 + - - +
171B GLU* 2.9 9.8 + - - +
173B ALA* 1.3 76.7 - - - +
175B GLU* 1.3 57.3 - - + +
177B LEU* 3.0 11.7 + - - +
178B LYS* 2.8 37.9 + - + +
184B VAL* 4.8 11.9 - - + -
186B PHE* 3.7 26.9 - - + -
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Residues in contact with GLU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PRO* 5.8 3.8 - - - +
124A VAL* 4.7 16.5 - - + +
171B GLU* 2.9 20.5 + - + +
172B GLU* 3.6 21.5 - - - +
174B ALA* 1.3 75.8 - - + +
176B ARG* 1.3 60.7 + - + +
178B LYS* 3.6 11.4 + - + +
179B GLU* 3.0 39.9 + - - +
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Residues in contact with ARG 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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142B LYS 5.1 0.6 + - - -
143B ALA* 3.0 31.2 + - + +
145B GLU 3.5 9.1 + - - -
146B GLY 5.4 2.4 + - - -
147B LEU* 2.8 41.6 - - - +
172B GLU* 3.0 23.8 + - - +
173B ALA* 3.5 7.0 - - - +
175B GLU* 1.3 74.1 - - + +
177B LEU* 1.3 61.9 + - - +
179B GLU* 3.4 14.4 - - - +
180B ARG* 3.0 34.0 + - + +
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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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132B VAL* 3.2 34.3 - - + -
135B LEU* 4.2 11.0 - - + -
140B ILE* 4.1 31.9 - - + -
143B ALA* 4.1 22.9 - - + -
144B LEU* 5.4 1.8 - - + -
163B ILE* 3.9 17.5 - - + -
173B ALA* 2.8 26.9 + - + +
174B ALA* 3.5 7.4 - - - +
176B ARG* 1.3 75.0 - - - +
178B LYS* 1.3 67.1 + - - +
180B ARG* 2.8 15.1 + - - +
182B ALA* 3.0 29.0 + - + +
184B VAL* 4.5 5.4 - - + -
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Residues in contact with LYS 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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119A GLN 6.0 0.4 + - - -
120A GLU* 6.3 1.4 - - - +
122A VAL 5.7 0.8 + - - -
123A PRO* 5.7 1.2 - - - +
124A VAL* 3.1 38.7 - - + +
174B ALA* 2.8 27.0 + - + +
175B GLU* 3.8 9.6 - - + +
177B LEU* 1.3 73.2 - - - +
179B GLU* 1.3 64.6 + - + +
181B ARG* 2.8 23.2 + - - -
182B ALA 3.5 17.9 + - - +
184B VAL* 4.6 16.4 - - + +
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Residues in contact with GLU 179 (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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175B GLU* 3.0 33.5 + - - +
176B ARG* 3.4 16.5 + - - +
178B LYS* 1.3 79.5 - - + +
180B ARG* 1.3 60.3 + - + +
181B ARG* 3.0 17.7 + - - +
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Residues in contact with ARG 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.4 24.6 - - + +
139B GLU* 2.9 62.8 + - - +
142B LYS* 3.8 14.8 - - - +
143B ALA* 3.6 32.8 - - - +
176B ARG* 3.0 21.3 + - + +
177B LEU* 2.8 11.3 + - - +
179B GLU* 1.3 77.0 - - + +
181B ARG* 1.3 68.6 + - - +
182B ALA 3.1 3.4 + - - -
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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