Contacts of the helix formed by residues 168 - 184 (chain E) 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 ASP 168 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166E GLY 3.5 2.3 + - - -
167E THR* 1.3 81.7 - - - +
169E PRO* 1.3 66.9 - - - +
170E ALA* 3.2 16.7 + - - +
171E ALA* 3.3 30.3 + - + +
172E LEU 3.0 22.2 + - - -
205E GLU* 6.0 0.5 - - - +
208E LYS* 3.6 21.2 + - - -
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Residues in contact with PRO 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E CYS* 5.5 0.2 - - - -
138E GLY* 3.7 26.4 - - - +
140E THR* 3.8 11.0 - - + +
167E THR 3.4 8.7 - - - +
168E ASP* 1.3 88.7 - - - +
170E ALA* 1.3 59.9 + - - +
172E LEU* 3.7 8.0 - - + +
173E ALA* 2.8 30.7 + - - +
192E THR* 6.5 0.9 - - + -
195E ARG* 6.0 1.8 - - - +
205E GLU* 3.8 35.0 - - + +
209E VAL* 4.1 15.6 - - + +
3001E 5GP 5.3 2.0 - - - +
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Residues in contact with ALA 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ASP* 3.2 14.2 + - - +
169E PRO* 1.3 79.1 - - + +
171E ALA* 1.3 56.7 + - - +
173E ALA* 3.1 2.5 + - - +
174E TYR* 2.9 25.1 + - - +
208E LYS* 3.8 45.1 - - + +
209E VAL* 3.9 9.5 - - + +
212E ALA* 3.1 20.6 - - + +
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Residues in contact with ALA 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E THR* 5.7 2.0 - - + -
168E ASP* 3.3 27.6 + - + +
170E ALA* 1.3 78.4 - - - +
172E LEU* 1.3 62.2 + - - +
174E TYR* 3.5 8.3 + - - +
175E ASP* 3.2 31.3 + - - +
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Residues in contact with LEU 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E CYS* 4.0 8.3 - - - -
137E ALA 3.7 26.9 - - - +
138E GLY* 4.2 4.3 - - - -
140E THR* 3.8 19.3 - - + -
161E ILE* 3.7 26.9 - - + +
162E GLN 3.7 22.0 - - - +
163E GLY* 3.9 14.1 - - - +
167E THR* 4.4 9.1 - - + +
168E ASP 3.0 16.9 + - - +
169E PRO* 3.7 5.8 - - + +
171E ALA* 1.3 73.4 - - - +
173E ALA* 1.3 65.6 - - - +
175E ASP* 3.3 12.3 + - - +
176E ALA* 3.0 22.0 + - - +
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Residues in contact with ALA 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E CYS* 4.0 11.8 - - - -
169E PRO 2.8 19.1 + - - +
170E ALA 3.5 4.5 - - - +
172E LEU* 1.3 75.8 - - - +
174E TYR* 1.3 57.4 + - - +
176E ALA* 3.2 2.3 + - - +
177E VAL* 2.9 35.4 + - - +
188E LEU* 4.8 0.2 - - - +
190E VAL* 4.3 11.2 - - + -
209E VAL* 3.7 25.1 - - + +
212E ALA* 4.7 0.2 - - + -
213E ILE* 4.1 14.8 - - + -
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Residues in contact with TYR 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E ALA 2.9 12.8 + - - +
171E ALA* 3.5 13.2 - - - +
173E ALA* 1.3 75.4 - - - +
175E ASP* 1.3 75.4 + - - +
177E VAL* 3.3 3.9 + - - +
178E GLN* 3.0 54.7 + - + +
212E ALA* 3.6 30.2 - - + +
215E LYS* 3.8 38.7 + - + -
216E ALA* 3.7 22.1 - - + +
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Residues in contact with ASP 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E ILE* 4.7 9.2 - - + -
171E ALA* 3.2 18.1 + - - +
172E LEU* 3.3 14.1 + - + +
174E TYR* 1.3 90.6 - - - +
176E ALA* 1.3 56.6 + - - +
178E GLN* 3.4 6.8 + - - +
179E ALA* 2.9 29.2 + - - +
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Residues in contact with ALA 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E MET* 2.7 27.7 - - - +
136E CYS* 3.7 30.5 - - + -
161E ILE* 3.8 24.6 - - + +
172E LEU 3.0 16.8 + - - +
173E ALA* 3.6 4.9 - - - +
175E ASP* 1.3 73.5 - - - +
177E VAL* 1.3 59.6 + - - +
179E ALA* 3.4 0.6 + - - -
180E MET 3.0 9.0 + - - -
188E LEU* 3.7 10.1 - - + -
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Residues in contact with VAL 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E VAL* 4.2 11.2 - - + -
173E ALA* 2.9 21.8 + - + +
174E TYR 3.3 0.4 + - - +
176E ALA* 1.3 74.0 - - - +
178E GLN* 1.3 64.3 + - - +
180E MET* 3.2 5.8 + - + +
181E LYS* 3.0 28.5 + - + +
188E LEU* 3.7 19.5 - - + -
213E ILE* 3.9 35.4 - - + +
216E ALA* 3.6 25.6 - - + -
217E ASP* 3.7 24.0 - - + -
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Residues in contact with GLN 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E TYR* 3.0 52.2 + - + +
175E ASP* 3.5 7.2 - - - +
177E VAL* 1.3 77.1 - - - +
179E ALA* 1.3 57.1 - - - +
181E LYS* 3.1 34.0 + - - +
182E ALA* 3.0 28.9 + - - +
216E ALA* 3.6 12.9 - - + +
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Residues in contact with ALA 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E MET* 4.2 11.4 - - - -
161E ILE* 4.3 15.5 - - + -
175E ASP 2.9 17.8 + - - +
176E ALA 3.8 4.3 - - - +
178E GLN* 1.3 73.5 - - - +
180E MET* 1.3 66.1 + - - +
182E ALA* 3.4 5.0 + - - +
183E ARG* 3.0 40.0 + - - +
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Residues in contact with MET 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ARG* 3.5 54.1 - - + +
104E VAL* 4.2 10.3 - - + -
134E MET* 3.0 27.3 - - + +
176E ALA 3.0 7.1 + - - +
177E VAL* 3.2 10.5 + - + +
179E ALA* 1.3 76.9 - - - +
181E LYS* 1.3 76.7 + - + +
183E ARG 3.8 0.5 - - - -
184E GLY 3.0 8.0 + - - -
185E TYR* 2.9 54.8 + - + +
187E LEU 4.7 0.4 - - - -
188E LEU* 3.7 26.0 - - + +
217E ASP* 4.3 6.5 - - - +
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Residues in contact with LYS 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ARG* 3.6 19.1 + - - +
177E VAL* 3.0 22.2 + - + +
178E GLN* 3.1 21.7 + - - +
180E MET* 1.3 94.0 - - + +
182E ALA* 1.3 62.8 + - - +
184E GLY* 3.2 12.5 + - - -
216E ALA 2.7 29.3 + - - +
217E ASP* 4.0 16.6 - - + +
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Residues in contact with ALA 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E GLN 3.0 17.8 + - - +
179E ALA* 3.9 6.5 - - - +
181E LYS* 1.3 78.7 - - - +
183E ARG* 1.3 61.4 + - + +
184E GLY* 3.4 0.9 + - - -
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Residues in contact with ARG 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E LYS* 3.5 18.0 + - - -
134E MET* 5.0 6.2 - - - -
159E PRO* 4.2 23.0 - - - +
161E ILE* 5.2 9.7 - - - +
179E ALA* 3.0 30.6 + - - +
182E ALA* 1.3 76.9 - - + +
184E GLY* 1.3 62.8 + - - +
185E TYR* 3.4 33.8 + - + -
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Residues in contact with GLY 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ARG* 4.9 5.6 - - - -
132E LYS* 4.4 10.0 + - - +
180E MET 3.0 6.3 + - - -
181E LYS 3.2 8.7 + - - -
182E ALA 3.2 5.4 + - - -
183E ARG* 1.3 79.0 - - - +
185E TYR* 1.3 65.4 + - - +
186E ASP* 4.8 4.0 - - - +
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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