Contacts of the helix formed by residues 168 - 183 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166F GLY 3.9 0.4 + - - -
167F THR* 1.3 72.9 + - - +
169F PRO* 1.3 74.4 - - - +
170F ALA* 3.0 22.0 + - - +
171F ALA* 3.3 29.9 + - + +
172F LEU* 3.0 23.1 + - - +
205F GLU* 5.5 2.3 - - - +
208F LYS* 3.7 21.0 + - - +
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Residues in contact with PRO 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F CYS* 5.4 0.3 - - - -
138F GLY* 3.7 26.5 - - - +
140F THR* 3.4 10.8 - - + +
167F THR 3.2 10.1 - - - +
168F ASP* 1.3 89.8 - - - +
170F ALA* 1.3 52.2 + - - +
172F LEU* 3.6 7.8 - - + +
173F ALA* 2.8 36.7 + - - +
195F ARG* 5.8 3.6 - - - +
205F GLU* 3.8 36.3 - - + +
209F VAL* 3.8 14.3 - - + +
3001F 5GP 5.1 2.9 - - - +
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Residues in contact with ALA 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F ASP* 3.0 18.4 + - - +
169F PRO* 1.3 79.2 - - - +
171F ALA* 1.3 57.1 + - - +
173F ALA* 3.2 1.4 + - - +
174F TYR* 2.9 26.2 + - - +
205F GLU* 6.5 0.7 - - + -
208F LYS* 3.6 40.6 - - + +
209F VAL* 3.6 12.0 - - + +
212F ALA* 3.2 19.1 - - + +
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Residues in contact with ALA 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F ASP* 3.2 26.2 + - + +
170F ALA* 1.3 79.0 - - - +
172F LEU* 1.3 61.0 + - - +
174F TYR* 3.7 8.1 + - - +
175F ASP* 3.1 35.0 + - - +
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Residues in contact with LEU 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F CYS* 4.1 9.4 - - - -
137F ALA 3.5 31.4 - - - +
138F GLY* 4.3 2.5 - - - -
140F THR* 3.7 18.6 - - + -
161F ILE* 4.0 18.5 - - + +
162F GLN* 3.7 26.0 - - - +
163F GLY* 3.8 11.9 - - - +
167F THR* 5.0 4.3 - - - +
168F ASP 3.0 16.7 + - - +
169F PRO* 3.6 4.9 - - + +
171F ALA* 1.3 78.6 - - - +
173F ALA* 1.3 58.0 + - - +
175F ASP* 3.2 11.7 + - + +
176F ALA* 2.9 27.0 + - - +
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Residues in contact with ALA 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F CYS* 3.8 11.8 - - - -
138F GLY* 6.5 0.2 - - - -
169F PRO 2.8 21.5 + - - +
170F ALA 3.6 3.8 - - - +
172F LEU* 1.3 74.2 - - - +
174F TYR* 1.3 55.7 + - - +
176F ALA* 3.2 3.2 + - - +
177F VAL* 3.0 35.0 + - - +
188F LEU* 4.8 0.3 - - - +
190F VAL* 4.2 15.9 - - + -
209F VAL* 3.8 24.5 - - + +
213F ILE* 4.3 12.3 - - + -
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Residues in contact with TYR 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F ALA 2.9 16.2 + - - +
171F ALA* 3.8 7.6 - - - +
173F ALA* 1.3 73.1 - - - +
175F ASP* 1.3 81.1 + - - +
177F VAL* 3.5 5.0 + - - +
178F GLN* 3.2 53.4 + - + +
212F ALA* 3.5 32.4 - - + +
215F LYS* 3.4 37.4 + - + -
216F ALA* 3.5 28.5 - - + -
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Residues in contact with ASP 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F ILE* 4.6 9.4 - - + -
171F ALA* 3.1 22.3 + - - +
172F LEU* 3.2 13.3 + - + +
174F TYR* 1.3 88.9 - - - +
176F ALA* 1.3 58.0 + - - +
178F GLN* 3.6 7.0 + - - +
179F ALA* 3.0 29.9 + - - +
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Residues in contact with ALA 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F MET* 2.6 30.3 - - - +
136F CYS* 3.6 30.7 - - + -
161F ILE* 4.0 19.0 - - + +
172F LEU 2.9 13.8 + - - +
173F ALA 3.2 9.8 + - - +
175F ASP* 1.3 76.4 - - - +
177F VAL* 1.3 58.1 + - - +
179F ALA 3.3 0.3 + - - -
180F MET* 2.9 10.6 + - - +
188F LEU* 3.7 9.6 - - + -
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Residues in contact with VAL 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F VAL* 4.4 13.2 - - + -
173F ALA 3.0 17.3 + - - +
174F TYR 3.5 0.6 + - - +
176F ALA* 1.3 72.3 - - - +
178F GLN* 1.3 61.7 + - - +
180F MET* 3.1 6.4 + - + +
181F LYS* 2.9 43.6 + - + +
188F LEU* 3.7 19.3 - - + -
213F ILE* 4.0 36.1 - - + +
216F ALA* 3.8 21.5 - - + -
217F ASP* 4.0 14.8 - - + -
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Residues in contact with GLN 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F TYR* 3.2 45.5 + - + +
175F ASP* 3.6 9.4 - - - +
177F VAL* 1.3 76.5 - - - +
179F ALA* 1.3 58.2 + - - +
181F LYS* 2.7 37.2 + - - +
182F ALA* 2.8 31.8 + - - +
216F ALA* 3.5 12.2 - - + +
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Residues in contact with ALA 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F MET* 3.8 12.3 - - + -
161F ILE* 4.3 14.8 - - + -
175F ASP 3.0 18.8 + - - +
176F ALA 3.6 5.2 - - - +
178F GLN* 1.3 75.8 - - - +
180F MET* 1.3 63.5 + - - +
182F ALA* 3.3 5.5 + - - +
183F ARG* 3.1 35.1 + - - +
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Residues in contact with MET 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ARG* 3.5 59.5 - - + +
104F VAL* 4.5 4.9 - - + -
134F MET* 3.3 16.9 - - + +
176F ALA 2.9 14.2 + - - +
177F VAL* 3.4 16.6 - - + +
179F ALA* 1.3 77.6 - - - +
181F LYS* 1.3 73.9 + - + +
183F ARG 3.4 0.7 + - - -
184F GLY 3.1 8.0 + - - -
185F TYR* 3.0 52.8 + - + +
187F LEU 4.3 2.9 - - - +
188F LEU* 3.7 30.5 - - + -
217F ASP* 5.1 2.2 - - - +
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Residues in contact with LYS 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ARG* 3.6 27.6 + - - +
177F VAL* 2.9 28.1 + - + +
178F GLN* 2.7 26.5 + - - +
180F MET* 1.3 84.3 - - + +
182F ALA* 1.3 63.4 + - - +
184F GLY* 3.3 11.8 + - - -
216F ALA 2.6 29.7 + - - +
217F ASP* 4.2 11.7 - - + +
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Residues in contact with ALA 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F GLN 2.8 21.4 + - - +
179F ALA* 3.3 7.6 + - - +
181F LYS* 1.3 74.6 - - - +
183F ARG* 1.3 63.0 + - + +
184F GLY 3.7 0.2 + - - -
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Residues in contact with ARG 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F LYS* 4.5 5.2 - - - -
134F MET* 5.5 5.8 - - - -
159F PRO* 4.0 24.0 - - - +
161F ILE* 5.2 9.9 - - - +
179F ALA* 3.1 20.6 + - - +
180F MET 4.1 0.2 - - - +
182F ALA* 1.3 79.3 - - + +
184F GLY* 1.3 63.4 + - - +
185F TYR* 3.3 45.8 + - + -
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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