Contacts of the helix formed by residues 177 - 189 (chain R) in PDB entry 6CNF
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 177 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176R ALA* 1.3 76.5 - - - +
178R PRO* 1.3 73.9 - - + +
179R SER* 3.0 26.5 + - - +
180R LEU* 3.4 25.8 + - - +
181R PHE* 3.1 18.7 - - - -
215R PHE* 4.6 7.6 - - + -
220R PRO* 4.8 2.5 - - - -
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Residues in contact with PRO 178 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177R ASP* 1.3 84.7 - - + +
179R SER* 1.3 58.4 + - - +
180R LEU 3.1 0.4 - - - -
181R PHE* 2.7 32.0 + - + +
182R ILE* 2.9 19.6 + - + +
206R ALA* 5.8 6.3 - - + -
215R PHE* 3.3 30.3 - - + -
220R PRO* 3.4 38.3 - - + +
221R ALA* 5.7 0.2 - - - -
223R ILE* 3.8 6.5 - - + -
224R ALA* 4.1 15.7 - - + -
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Residues in contact with SER 179 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177R ASP* 3.0 26.7 + - - +
178R PRO* 1.3 76.5 - - - +
180R LEU* 1.3 63.2 + - - +
182R ILE* 3.2 23.9 - - - +
183R GLN* 4.2 4.2 - - - +
203R VAL* 4.4 21.3 - - - +
207R GLN* 4.6 9.5 + - - +
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Residues in contact with LEU 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138R LYS* 3.5 30.1 - - + +
139R THR* 3.2 29.8 - - - +
140R HIS* 4.1 13.8 - - + +
176R ALA* 5.2 6.3 - - + -
177R ASP* 3.4 24.9 + - - +
178R PRO 3.0 0.6 + - - -
179R SER* 1.3 79.5 - - - +
181R PHE* 1.3 67.2 + - + +
183R GLN* 2.9 34.4 + - - +
184R HIS 3.9 1.2 + - - -
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Residues in contact with PHE 181 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135R ARG* 4.7 8.3 - - - -
139R THR 4.0 11.2 - - - -
140R HIS* 3.8 12.3 - - + -
141R HIS* 2.9 48.0 - - - -
142R MET* 4.4 12.6 - - + -
176R ALA* 3.8 23.3 - - + -
177R ASP 3.1 32.1 - - - -
178R PRO* 2.7 14.1 + - + +
180R LEU* 1.3 73.1 - - + +
182R ILE* 1.3 58.6 + - - +
183R GLN 3.2 0.2 - - - -
184R HIS* 3.5 4.3 + - + +
185R PHE* 2.9 56.6 + + + -
219R ARG* 5.1 15.3 - - - +
220R PRO* 5.5 2.2 - - + -
221R ALA* 6.2 1.6 - - - -
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Residues in contact with ILE 182 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178R PRO* 2.9 17.1 + - + +
179R SER* 3.2 27.6 - - - +
181R PHE* 1.3 77.0 - - - +
183R GLN* 1.3 83.0 + - + +
185R PHE* 3.2 8.7 + - - +
186R ALA* 2.4 38.7 + - + +
199R VAL* 3.5 22.2 - - + -
202R ALA* 5.9 6.5 - - + -
203R VAL* 3.9 15.5 - - + -
224R ALA* 3.7 33.9 - - + +
227R CYS* 6.3 0.9 - - + -
228R ILE* 5.2 7.8 - - + +
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Residues in contact with GLN 183 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L ARG* 4.4 25.1 - - - +
140R HIS* 5.6 5.8 - - + -
179R SER 4.2 4.0 - - - +
180R LEU* 2.9 16.6 + - - +
182R ILE* 1.3 97.6 - - + +
184R HIS* 1.3 52.1 + - - +
186R ALA* 2.7 9.4 + - - +
187R GLU* 2.7 36.2 + - - +
199R VAL* 3.4 19.9 - - - +
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Residues in contact with HIS 184 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94R LEU 5.7 2.8 + - - -
140R HIS* 3.2 55.1 + + + +
141R HIS* 5.1 9.9 + + - -
145R ASP* 5.2 9.2 - - - -
180R LEU 3.9 1.6 + - - -
181R PHE* 3.5 8.6 + - + +
183R GLN* 1.3 77.2 - - - +
185R PHE* 1.3 72.4 + + + +
187R GLU* 3.6 7.7 + - + +
188R LYS* 3.1 60.5 + - + +
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Residues in contact with PHE 185 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142R MET* 5.8 5.4 - - + -
145R ASP* 6.1 0.7 - - - -
181R PHE* 2.9 43.6 + + + +
182R ILE* 3.4 5.8 - - - +
184R HIS* 1.3 86.3 - + + +
186R ALA* 1.3 65.7 + - - +
188R LYS* 2.9 15.2 + - + +
189R LEU* 3.0 21.8 - - + +
219R ARG* 5.1 5.4 - - - -
221R ALA* 4.3 18.4 - - + -
224R ALA* 4.2 24.0 - - + -
225R GLY 5.3 0.2 - - - -
228R ILE* 4.4 13.9 - - + -
247R VAL* 3.3 46.4 - - + -
248R SER* 4.2 11.2 - - - -
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Residues in contact with ALA 186 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182R ILE 2.4 31.9 + - - +
183R GLN* 2.7 11.2 + - - +
185R PHE* 1.3 65.5 - - - +
187R GLU* 1.3 62.2 + - - +
189R LEU* 4.9 0.4 - - - -
190R ASP* 4.2 2.3 + - - +
195R LYS* 2.5 40.2 + - + +
196R ILE* 6.5 0.4 - - + -
199R VAL* 4.0 26.0 - - + -
228R ILE* 5.5 2.4 - - - +
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Residues in contact with GLU 187 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L ARG* 5.4 7.6 + - - -
183R GLN 2.7 18.4 + - - +
184R HIS* 3.8 10.1 - - + +
186R ALA* 1.3 74.9 - - - +
188R LYS* 1.3 64.8 + - + +
189R LEU 3.4 0.9 + - - -
190R ASP* 3.7 9.2 + - - -
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Residues in contact with LYS 188 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145R ASP* 5.9 0.4 + - - -
184R HIS* 3.1 47.5 + - + +
185R PHE* 2.9 10.2 + - - +
187R GLU* 1.3 80.2 - - + +
189R LEU* 1.3 59.1 + - - +
190R ASP* 3.4 1.7 + - - +
247R VAL* 3.6 23.8 - - + +
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Residues in contact with LEU 189 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185R PHE* 3.0 29.3 + - + +
186R ALA* 3.6 1.0 + - - -
187R GLU 3.4 0.8 - - - -
188R LYS* 1.3 76.3 - - - +
190R ASP* 1.3 69.5 + - - +
191R LEU* 2.9 31.0 + - + +
195R LYS* 2.9 17.7 - - - +
228R ILE* 4.6 23.3 - - + -
239R ARG* 6.4 0.2 - - + -
243R GLU* 4.0 35.6 - - + +
244R ILE* 5.3 6.3 - - + -
247R VAL* 3.6 36.3 - - + -
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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