Contacts of the helix formed by residues 168 - 183 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D GLY 3.7 1.8 + - - -
167D THR* 1.3 79.2 + - - +
169D PRO* 1.4 73.0 - - - +
170D ALA* 3.1 21.0 + - - +
171D ALA* 3.3 26.9 + - + +
172D LEU* 3.1 17.7 + - - +
205D GLU* 5.6 2.8 - - - +
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Residues in contact with PRO 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D CYS* 5.3 0.5 - - - -
138D GLY* 3.4 29.3 - - - +
140D THR* 3.7 10.3 - - + +
167D THR 3.2 10.0 - - - +
168D ASP* 1.4 89.0 - - - +
170D ALA* 1.3 53.9 + - - +
172D LEU* 3.6 10.0 - - + +
173D ALA* 2.7 35.9 + - - +
192D THR* 6.4 0.2 - - - -
195D ARG* 5.9 2.0 - - - +
205D GLU* 3.8 32.1 - - + +
209D VAL* 4.0 16.7 - - + +
3001D 5GP 5.2 1.8 - - - +
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Residues in contact with ALA 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ASP* 3.1 17.7 + - - +
169D PRO* 1.3 76.5 - - - +
171D ALA* 1.3 59.7 + - - +
173D ALA* 3.2 1.8 + - - +
174D TYR* 2.9 26.9 + - - +
205D GLU* 5.4 0.4 - - + +
208D LYS* 3.7 31.2 - - + +
209D VAL* 3.7 14.2 - - + +
212D ALA* 3.3 19.4 - - + +
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Residues in contact with ALA 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D THR* 5.3 2.0 - - - +
168D ASP* 3.3 28.2 + - + +
170D ALA* 1.3 78.1 - - - +
172D LEU* 1.3 57.0 + - - +
174D TYR* 3.4 8.8 - - - +
175D ASP* 3.0 37.3 + - - +
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Residues in contact with LEU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D CYS* 4.0 7.6 - - - -
137D ALA 3.3 33.0 - - - +
138D GLY* 4.1 5.6 - - - -
140D THR* 3.8 19.3 - - + -
161D ILE* 3.9 16.2 - - + +
162D GLN* 3.6 29.4 - - - +
163D GLY* 3.8 12.6 - - - +
167D THR* 4.6 5.8 + - - +
168D ASP 3.1 13.9 + - - +
169D PRO 3.6 6.5 - - - +
170D ALA 3.3 0.2 - - - -
171D ALA* 1.3 73.6 - - - +
173D ALA* 1.3 59.3 + - - +
175D ASP* 3.2 10.5 + - - +
176D ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D CYS* 3.8 12.5 - - - -
169D PRO 2.7 21.3 + - - +
170D ALA* 3.5 5.6 - - - +
172D LEU* 1.3 71.2 - - - +
174D TYR* 1.3 62.5 + - - +
176D ALA* 3.1 4.4 + - - +
177D VAL* 3.0 29.3 + - - +
188D LEU* 4.8 0.2 - - - +
190D VAL* 4.3 10.7 - - + +
209D VAL* 3.8 24.9 - - + +
212D ALA* 4.8 0.2 - - + -
213D ILE* 4.1 15.3 - - + -
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Residues in contact with TYR 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D ALA 2.9 13.0 + - - +
171D ALA* 3.4 11.9 - - - +
173D ALA* 1.3 74.7 - - - +
175D ASP* 1.3 79.4 + - - +
176D ALA 3.2 0.2 + - - -
177D VAL* 3.2 4.8 + - - +
178D GLN* 3.1 52.2 + - + +
212D ALA* 3.6 28.4 - - + +
215D LYS* 4.1 24.9 - - + -
216D ALA* 3.8 26.8 - - + +
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Residues in contact with ASP 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ILE* 4.7 9.6 - - + -
171D ALA* 3.0 18.9 + - - +
172D LEU* 3.7 11.9 - - + +
174D TYR* 1.3 92.9 - - - +
176D ALA* 1.3 57.1 + - - +
178D GLN* 3.5 6.7 + - - +
179D ALA* 2.9 29.7 + - - +
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Residues in contact with ALA 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D MET* 2.7 30.1 - - - +
136D CYS* 3.6 29.4 - - + -
161D ILE* 3.9 18.8 - - + +
172D LEU 2.9 14.1 + - - +
173D ALA 3.4 8.3 - - - +
174D TYR 3.1 0.2 - - - -
175D ASP* 1.3 74.7 - - - +
177D VAL* 1.3 61.4 + - - +
179D ALA 3.4 0.2 + - - -
180D MET* 2.9 10.9 + - - +
188D LEU* 3.8 10.3 - - + -
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Residues in contact with VAL 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D VAL* 4.2 13.9 - - + -
173D ALA 3.0 15.1 + - - +
174D TYR 3.2 1.1 + - - +
176D ALA* 1.3 75.0 - - - +
178D GLN* 1.3 58.2 + - - +
180D MET* 3.1 8.4 + - + +
181D LYS* 2.9 42.8 + - + +
188D LEU* 3.6 20.4 - - + -
190D VAL* 5.4 0.2 - - + -
213D ILE* 3.9 33.2 - - + +
216D ALA* 3.8 21.8 - - + -
217D ASP* 4.1 14.6 - - + +
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Residues in contact with GLN 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D TYR* 3.1 46.3 + - + +
175D ASP* 3.6 7.0 - - - +
177D VAL* 1.3 76.2 - - - +
179D ALA* 1.3 56.5 + - - +
181D LYS* 2.8 34.8 + - - +
182D ALA* 2.9 30.2 + - - +
216D ALA* 3.4 22.0 - - + +
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Residues in contact with ALA 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D MET* 3.8 14.6 - - + -
161D ILE* 4.4 12.6 - - + -
175D ASP 2.9 18.0 + - - +
176D ALA 3.8 3.8 - - - +
177D VAL 3.3 0.2 - - - -
178D GLN* 1.3 75.7 - - - +
180D MET* 1.3 63.2 + - - +
182D ALA* 3.4 5.9 + - - +
183D ARG* 3.1 42.4 + - - +
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Residues in contact with MET 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ARG* 3.4 59.2 + - + +
104D VAL* 4.5 4.9 - - + -
134D MET* 3.4 16.1 - - + +
176D ALA 2.9 15.7 + - - +
177D VAL* 3.4 16.4 - - + +
179D ALA* 1.3 76.4 - - - +
181D LYS* 1.3 81.1 + - + +
183D ARG* 3.4 1.6 + - - -
184D GLY 3.2 2.8 + - - -
185D TYR* 3.1 53.8 + - + +
187D LEU 4.6 2.7 - - - +
188D LEU* 3.8 27.4 - - + -
217D ASP* 5.5 1.1 - - + +
220D GLU* 6.1 0.9 - - + -
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Residues in contact with LYS 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ARG* 3.5 27.9 + - - +
177D VAL* 2.9 28.6 + - + +
178D GLN* 2.8 23.7 + - - +
180D MET* 1.3 81.6 - - + +
182D ALA* 1.3 66.9 + - - +
183D ARG 3.1 1.0 + - - -
184D GLY* 3.2 12.3 + - - -
216D ALA 2.8 28.5 + - - +
217D ASP* 4.1 13.9 - - + +
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Residues in contact with ALA 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D GLN 2.9 19.3 + - - +
179D ALA* 3.8 7.6 - - - +
181D LYS* 1.3 76.4 - - - +
183D ARG* 1.3 62.2 + - + +
184D GLY 3.7 0.2 + - - -
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Residues in contact with ARG 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LYS* 4.9 3.5 - - - +
134D MET* 4.8 8.7 - - - -
159D PRO* 4.1 24.3 - - - +
161D ILE* 4.5 17.6 - - - +
179D ALA* 3.1 28.7 + - - +
180D MET 4.1 0.7 - - - +
181D LYS 3.1 0.4 - - - -
182D ALA* 1.3 81.1 - - + +
184D GLY* 1.3 61.0 + - - +
185D TYR* 3.5 35.3 + - + -
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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