Contacts of the helix formed by residues 164 - 180 (chain A) in PDB entry 2CNW
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 SER 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A GLY 3.5 2.9 + - - -
163A GLU* 1.3 76.3 - - - +
165A PRO* 1.3 73.5 - - - +
166A GLU* 3.3 16.0 + - - +
167A SER* 3.0 25.3 + - - -
168A ILE* 2.9 25.6 + - - +
204A ARG* 5.2 1.1 - - - -
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Residues in contact with PRO 165 (chain A).
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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163A GLU 4.4 2.0 - - - +
164A SER* 1.3 87.8 - - - +
166A GLU* 1.3 55.8 + - - +
168A ILE* 3.2 15.9 + - + +
169A ARG* 2.8 31.0 + - - +
204A ARG* 3.3 45.1 - - + +
205A LEU* 4.1 21.5 - - + +
208A VAL* 3.7 23.5 - - + +
209A LEU* 4.4 1.7 - - - +
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Residues in contact with GLU 166 (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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164A SER* 3.6 13.4 + - - +
165A PRO* 1.3 78.0 - - - +
167A SER* 1.3 57.6 + - - +
169A ARG* 3.5 24.5 + - - +
170A ARG* 3.1 26.7 + - - +
204A ARG* 2.8 36.8 + - - -
208A VAL* 3.7 22.1 - - + +
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Residues in contact with SER 167 (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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160A MET* 5.0 2.3 - - - +
163A GLU* 2.9 25.4 + - - +
164A SER* 3.0 21.6 + - - -
166A GLU* 1.3 74.7 - - - +
168A ILE* 1.3 62.7 + - - +
170A ARG* 3.3 34.6 + - - +
171A ARG* 3.1 27.0 + - - +
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Residues in contact with ILE 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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132A VAL* 4.7 5.2 - - + -
134A ALA* 5.3 5.4 - - + -
157A LEU* 5.3 2.7 - - + -
159A VAL* 3.8 44.2 - - + -
163A GLU* 3.9 14.8 - - + +
164A SER 2.9 22.3 + - - +
165A PRO* 3.5 9.4 - - + +
167A SER* 1.3 72.6 - - - +
169A ARG* 1.3 66.1 + - - +
170A ARG 3.1 0.2 + - - -
171A ARG* 3.2 3.5 + - - +
172A VAL* 3.0 38.3 + - + +
186A VAL* 6.3 0.2 - - + -
205A LEU* 4.1 20.0 - - + -
209A LEU* 4.4 18.2 - - + -
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Residues in contact with ARG 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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165A PRO 2.8 16.7 + - - +
166A GLU* 3.7 23.0 + - - +
167A SER 3.4 0.2 - - - -
168A ILE* 1.3 71.8 - - - +
170A ARG* 1.3 55.1 + - - +
172A VAL* 3.8 2.4 - - - +
173A GLU* 2.8 62.8 + - + +
207A GLU 5.4 0.2 + - - -
208A VAL* 3.1 46.7 + - + +
209A LEU* 3.4 26.8 - - + +
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Residues in contact with ARG 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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166A GLU 3.1 13.9 + - - +
167A SER* 3.3 33.5 + - - +
169A ARG* 1.3 80.8 - - - +
171A ARG* 1.3 80.1 + - - +
173A GLU* 3.8 6.3 - - - +
174A GLU* 2.9 34.2 + - + +
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Residues in contact with ARG 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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157A LEU* 3.7 31.4 - - + +
158A GLU 3.1 24.5 + - - +
159A VAL* 3.9 3.2 - - - +
160A MET* 3.5 21.6 - - - +
163A GLU* 2.8 36.0 + - - +
167A SER* 3.1 15.7 + - - +
168A ILE* 3.2 2.4 + - - +
170A ARG* 1.3 93.0 - - - +
172A VAL* 1.3 60.4 + - - +
174A GLU* 3.5 16.4 + - - +
175A LYS* 2.8 30.8 + - - +
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Residues in contact with VAL 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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100A LEU* 5.0 7.2 - - + -
130A LEU* 4.3 7.3 - - + +
132A VAL* 3.9 22.2 - - + -
157A LEU* 4.0 17.9 - - + -
168A ILE* 3.0 34.1 + - + +
169A ARG* 3.9 4.0 - - - +
171A ARG* 1.3 74.6 - - - +
173A GLU* 1.3 60.9 + - + +
175A LYS 3.3 0.4 + - - +
176A ALA* 2.9 35.2 + - - +
184A ILE* 3.6 39.5 - - + -
186A VAL* 6.1 0.2 - - + -
209A LEU* 5.5 5.6 - - + -
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Residues in contact with GLU 173 (chain A).
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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169A ARG* 2.8 47.0 + - + +
170A ARG* 3.8 6.3 - - - +
172A VAL* 1.3 72.8 - - + +
174A GLU* 1.3 63.3 + - - +
176A ALA* 4.1 3.8 - - - +
177A ARG* 3.1 26.9 + - - +
184A ILE* 5.8 0.9 - - - -
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Residues in contact with GLU 174 (chain A).
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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170A ARG* 2.9 23.7 + - + +
171A ARG* 3.5 18.2 - - - +
173A GLU* 1.3 76.4 - - - +
175A LYS* 1.3 58.3 + - - +
177A ARG* 3.7 3.1 - - - +
178A LEU* 2.9 55.6 + - + +
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Residues in contact with LYS 175 (chain A).
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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130A LEU* 3.6 34.1 - - + -
155A PRO* 3.9 13.1 - - - +
156A VAL 5.1 3.4 - - - -
157A LEU* 4.4 20.9 - - + +
171A ARG 2.8 19.5 + - - +
172A VAL 4.1 1.8 - - - +
174A GLU* 1.3 71.4 - - - +
176A ALA* 1.3 65.0 + - - +
178A LEU* 3.5 5.8 + - - -
179A GLU* 2.6 75.0 + - + +
181A ARG* 5.6 0.4 - - - -
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Residues in contact with ALA 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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130A LEU* 4.3 5.3 - - + +
172A VAL 2.9 22.2 + - - +
173A GLU* 4.1 4.0 - - - +
175A LYS* 1.3 72.6 - - - +
177A ARG* 1.3 54.0 + - - +
180A ALA* 2.8 14.6 + - - -
181A ARG* 2.8 54.6 + - + +
184A ILE* 3.8 23.1 - - + -
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Residues in contact with ARG 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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173A GLU 3.1 19.7 + - - +
174A GLU* 3.7 3.1 - - - +
176A ALA* 1.3 72.9 - - - +
178A LEU* 1.3 97.2 + - - +
179A GLU 3.1 5.6 + - - -
180A ALA* 3.2 12.4 + - - +
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Residues in contact with LEU 178 (chain A).
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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174A GLU* 2.9 43.2 + - + +
175A LYS* 4.2 4.9 - - - +
177A ARG* 1.3 114.7 - - - +
179A GLU* 1.3 64.5 + - + +
180A ALA* 5.5 0.2 - - - -
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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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128A ARG* 2.9 31.3 + - - +
155A PRO* 3.9 5.9 - - - +
175A LYS* 2.6 62.9 + - - +
178A LEU* 1.3 83.0 - - + +
180A ALA* 1.3 67.2 - - - +
181A ARG* 3.4 29.3 + - - +
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Residues in contact with ALA 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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128A ARG* 2.8 30.2 + - - +
176A ALA 2.8 9.8 + - - -
177A ARG* 3.2 9.1 + - - +
178A LEU 3.6 0.4 - - - -
179A GLU* 1.3 79.7 - - - +
181A ARG* 1.3 58.0 + - - +
182A ASP* 4.1 2.4 + - - +
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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