Contacts of the helix formed by residues 164 - 179 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C GLY 3.5 2.6 + - - -
163C GLU* 1.3 76.8 - - - +
165C PRO* 1.4 69.3 - - - +
166C GLU* 3.0 22.9 + - - +
167C SER* 3.2 14.7 + - - -
168C ILE* 2.9 31.5 + - - +
170C ARG* 5.4 0.3 + - - -
204C ARG* 4.9 2.5 - - - -
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Residues in contact with PRO 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C GLU 4.7 1.3 - - - +
164C SER* 1.4 87.8 - - - +
166C GLU* 1.3 54.7 + - - +
168C ILE* 3.5 13.4 + - + +
169C ARG* 2.8 28.1 + - - +
201C GLU* 5.6 4.3 - - + +
204C ARG* 3.6 41.3 - - + +
205C LEU* 3.8 24.5 - - + +
208C VAL* 3.4 29.4 - - + +
209C LEU* 4.2 2.4 - - - +
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Residues in contact with GLU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C SER* 3.0 15.5 + - - +
165C PRO* 1.3 76.8 - - - +
167C SER* 1.3 60.2 + - - +
169C ARG* 3.4 28.3 + - - +
170C ARG* 2.9 43.9 + - - +
204C ARG* 2.8 35.0 + - - -
208C VAL* 4.0 19.0 - - + +
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Residues in contact with SER 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C GLU* 2.8 38.5 + - - +
164C SER* 3.2 12.1 + - - -
166C GLU* 1.3 76.3 - - - +
168C ILE* 1.3 64.6 + - - +
170C ARG* 3.4 28.0 + - - +
171C ARG* 3.1 26.7 + - - +
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Residues in contact with ILE 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C VAL* 5.0 5.6 - - + -
134C ALA* 5.3 5.8 - - + -
157C LEU* 5.7 2.2 - - + -
159C VAL* 3.8 37.7 - - + -
163C GLU* 3.9 23.3 - - + +
164C SER 2.9 27.0 + - - +
165C PRO* 3.6 9.6 - - + +
167C SER* 1.3 76.5 - - - +
169C ARG* 1.3 63.6 + - - +
171C ARG* 3.3 4.6 + - - +
172C VAL* 3.0 41.4 + - + +
186C VAL* 6.1 0.9 - - + -
205C LEU* 4.4 12.1 - - + -
209C LEU* 4.2 21.1 - - + -
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Residues in contact with ARG 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C PRO 2.8 18.2 + - - +
166C GLU* 3.6 31.1 + - - +
167C SER 3.3 0.2 - - - -
168C ILE* 1.3 76.5 - - - +
170C ARG* 1.3 62.7 + - - +
172C VAL* 4.7 1.6 - - - -
173C GLU* 3.1 50.4 + - + +
208C VAL* 3.2 41.0 + - + +
209C LEU* 3.6 22.9 - - + +
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Residues in contact with ARG 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C SER* 5.4 0.6 + - - -
166C GLU* 2.9 34.7 + - - +
167C SER* 3.4 37.1 + - - +
169C ARG* 1.3 76.7 - - - +
171C ARG* 1.3 61.2 + - + +
173C GLU* 4.0 2.1 - - - +
174C GLU* 3.1 35.9 + - - +
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Residues in contact with ARG 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C LEU* 3.5 30.3 - - + +
158C GLU 3.0 27.1 + - - +
159C VAL* 3.8 3.2 - - - +
160C MET* 3.6 32.5 - - - +
163C GLU* 2.7 37.6 + - - -
167C SER* 3.1 17.9 + - - +
168C ILE* 4.1 2.9 - - - +
170C ARG* 1.3 77.0 - - + +
172C VAL* 1.3 60.4 + - - +
174C GLU* 3.6 17.9 - - - +
175C LYS* 3.0 30.8 + - - +
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Residues in contact with VAL 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C LEU* 4.7 6.7 - - + -
130C LEU* 4.3 6.6 - - + +
132C VAL* 4.3 11.9 - - + -
157C LEU* 4.2 22.0 - - + -
168C ILE* 3.0 36.4 + - + +
169C ARG* 4.0 4.7 - - - +
171C ARG* 1.3 73.2 - - - +
173C GLU* 1.3 63.6 + - + +
175C LYS* 3.4 1.0 + - - +
176C ALA* 2.8 34.0 + - - +
184C ILE* 3.7 42.4 - - + -
186C VAL* 6.0 0.9 - - + -
209C LEU* 5.2 5.6 - - + -
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Residues in contact with GLU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ARG* 6.0 6.3 - - - +
100C LEU* 6.2 2.7 - - + -
169C ARG* 3.1 42.5 + - + +
170C ARG* 4.2 2.0 - - - +
172C VAL* 1.3 80.2 - - + +
174C GLU* 1.3 60.6 - - - +
176C ALA* 4.3 4.7 - - - +
177C ARG* 3.1 27.0 + - - +
184C ILE* 5.9 3.8 - - + -
209C LEU 5.5 2.3 - - - +
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C ARG* 3.1 25.6 + - - +
171C ARG* 3.6 17.1 - - - +
173C GLU* 1.3 74.8 - - - +
175C LYS* 1.3 53.5 + - - +
177C ARG* 3.2 6.7 + - - +
178C LEU* 2.7 60.1 + - + +
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Residues in contact with LYS 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C LEU* 3.7 29.8 - - + -
155C PRO* 4.2 14.6 - - - +
156C VAL 4.9 3.6 - - - +
157C LEU* 3.8 29.6 - - + +
171C ARG 3.0 17.3 + - - +
172C VAL 4.0 2.0 - - - +
174C GLU* 1.3 77.8 - - - +
176C ALA* 1.3 56.3 + - - +
178C LEU* 4.5 7.2 - - - -
179C GLU* 2.6 62.9 + - - +
181C ARG* 4.4 1.0 - - + +
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Residues in contact with ALA 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ARG* 4.1 16.1 + - - +
130C LEU* 4.5 4.0 - - + +
172C VAL 2.8 22.8 + - - +
173C GLU* 4.3 4.7 - - - +
175C LYS* 1.3 70.0 - - - +
177C ARG* 1.3 61.1 + - - +
180C ALA* 3.0 9.4 + - - -
181C ARG* 2.9 53.5 + - + +
184C ILE* 4.1 16.6 - - + -
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Residues in contact with ARG 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ARG* 5.1 6.7 - - - +
173C GLU 3.1 20.9 + - - +
174C GLU* 3.6 3.7 + - - +
176C ALA* 1.3 73.2 - - - +
178C LEU* 1.3 106.5 + - - +
179C GLU 2.9 3.4 + - - -
180C ALA* 3.3 11.0 + - - +
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Residues in contact with LEU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C GLU* 2.7 47.4 + - + +
175C LYS* 4.1 6.7 - - - +
177C ARG* 1.3 110.4 - - - +
179C GLU* 1.3 63.1 + - + +
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Residues in contact with GLU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ARG* 2.7 33.1 + - - +
155C PRO* 4.0 11.4 - - - +
175C LYS* 2.6 56.9 + - - +
177C ARG 3.0 0.6 - - - -
178C LEU* 1.3 85.1 - - + +
180C ALA* 1.3 64.0 + - - +
181C ARG* 3.3 27.1 + - + +
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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