Contacts of the helix formed by residues 185 - 201 (chain N) in PDB entry 5NSS
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 185 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181N GLU 2.9 18.0 + - - +
182N ARG* 3.8 2.2 - - - +
184N SER* 1.3 74.1 - - - +
186N ILE* 1.3 59.5 + - - +
187N MET 3.2 2.5 - - - -
188N LEU* 4.0 8.3 - - + +
189N MET* 2.9 33.9 + - + +
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Residues in contact with ILE 186 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182N ARG 2.7 22.3 + - - +
183N GLU* 3.8 10.3 - - - +
184N SER 3.3 1.4 - - - -
185N ASP* 1.3 78.8 - - - +
187N MET* 1.3 51.2 + - - +
189N MET* 4.7 2.5 - - - -
190N ALA* 2.7 42.0 + - + +
209N PHE* 5.4 0.2 - - - +
214N ARG* 6.2 2.9 - - + -
217N LEU* 6.2 3.8 - - + -
218N LEU* 4.9 10.5 - - + +
229N LEU* 6.2 4.3 - - + -
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Residues in contact with MET 187 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183N GLU 4.4 4.0 + - - +
184N SER 4.0 9.0 + - - +
185N ASP 3.2 0.4 - - - -
186N ILE* 1.3 77.9 - - - +
188N LEU* 1.3 58.5 + - - +
190N ALA* 4.3 0.2 - - - +
191N GLU* 2.9 31.4 + - - +
209N PHE* 4.3 23.5 - - + +
214N ARG* 6.3 2.7 - - + -
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Residues in contact with LEU 188 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184N SER 4.6 2.1 + - - +
185N ASP* 3.5 12.7 + - + +
187N MET* 1.3 77.9 - - - +
189N MET* 1.3 60.6 + - - +
191N GLU* 3.8 3.7 - - - +
192N TYR* 2.9 31.4 + - - +
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Residues in contact with MET 189 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185N ASP* 2.9 21.4 + - + +
186N ILE* 4.6 2.2 - - - +
188N LEU* 1.3 78.0 - - - +
190N ALA* 1.3 57.6 + - - +
192N TYR* 3.9 4.4 - - - +
193N PHE* 2.9 31.5 + - - +
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Residues in contact with ALA 190 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186N ILE* 2.7 25.6 + - + +
187N MET* 4.3 2.5 - - - +
189N MET* 1.3 76.2 - - - +
191N GLU* 1.3 58.2 + - - +
193N PHE* 4.2 4.1 - - - +
194N ALA* 2.9 32.1 + - - +
208N GLY 6.0 2.5 - - - +
209N PHE* 5.3 7.6 - - + -
233N VAL* 4.8 19.1 - - + +
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Residues in contact with GLU 191 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187N MET 2.9 22.4 + - - +
188N LEU* 3.8 4.9 - - - +
190N ALA* 1.3 78.8 - - - +
192N TYR* 1.3 57.9 + - - +
194N ALA* 3.8 3.3 - - - +
195N ILE* 2.9 30.1 + - - +
206N PHE* 4.8 2.1 - - - +
208N GLY* 5.5 13.2 - - - -
209N PHE* 5.5 4.2 - - + +
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Residues in contact with TYR 192 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188N LEU 2.9 17.9 + - - +
189N MET* 4.0 4.3 - - - +
191N GLU* 1.3 75.8 - - - +
193N PHE* 1.3 60.2 + - - +
195N ILE* 3.2 5.3 + - - +
196N GLN* 2.9 31.9 + - - +
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Residues in contact with PHE 193 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189N MET 2.9 20.1 + - - +
190N ALA* 4.2 4.5 - - - +
192N TYR* 1.3 76.0 - - - +
194N ALA* 1.3 57.6 + - - +
196N GLN* 4.4 3.1 - - - +
197N MET* 2.9 34.4 + - - +
230N LYS* 5.6 11.4 - - + -
234N GLU* 5.9 6.7 - - + -
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Residues in contact with ALA 194 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190N ALA 2.9 20.8 + - - +
191N GLU* 4.1 4.7 - - - +
193N PHE* 1.3 74.8 - - - +
195N ILE* 1.3 54.0 + - - +
197N MET* 4.5 2.2 - - - -
198N CYS* 2.6 40.5 + - + +
206N PHE* 3.3 12.9 - - + +
207N PRO* 5.1 2.2 - - + -
208N GLY 5.0 11.4 - - - +
233N VAL* 6.5 2.0 - - + -
234N GLU* 6.3 5.4 - - - +
237N VAL* 5.6 9.4 - - + -
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Residues in contact with ILE 195 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191N GLU 2.9 19.1 + - - +
192N TYR* 3.2 7.4 + - - +
194N ALA* 1.3 75.8 - - - +
196N GLN* 1.3 60.7 + - - +
198N CYS* 3.8 0.9 - - - +
199N ARG* 2.9 29.8 + - - +
206N PHE* 3.7 14.3 - - + +
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Residues in contact with GLN 196 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N TYR 2.9 15.2 + - - +
193N PHE* 4.4 3.4 - - - +
195N ILE* 1.3 74.8 - - - +
197N MET* 1.3 60.0 + - - +
199N ARG* 3.2 5.4 + - - +
200N GLU* 2.9 31.0 + - - +
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Residues in contact with MET 197 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193N PHE 2.9 21.8 + - - +
194N ALA* 4.5 3.1 - - - -
196N GLN* 1.3 77.1 - - - +
198N CYS* 1.3 57.2 + - - +
200N GLU* 3.4 4.9 + - - +
201N ILE* 3.0 30.5 + - - +
234N GLU* 5.4 11.2 - - + -
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Residues in contact with CYS 198 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194N ALA 2.6 24.9 + - - +
195N ILE 4.1 1.3 - - - +
197N MET* 1.3 78.4 - - - +
199N ARG* 1.3 61.1 + - - +
201N ILE* 3.5 7.2 + - - -
203N LEU* 3.2 36.6 + - + +
205N LEU* 4.1 7.4 - - - +
206N PHE* 3.8 24.0 - - + +
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Residues in contact with ARG 199 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195N ILE 2.9 20.6 + - - +
196N GLN* 3.2 6.9 + - - +
198N CYS* 1.3 77.5 - - - +
200N GLU* 1.3 59.2 + - - +
202N LYS* 3.5 12.5 + - - -
203N LEU 4.7 4.7 - - - +
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Residues in contact with GLU 200 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196N GLN 2.9 16.7 + - - +
197N MET* 3.7 5.6 - - - +
199N ARG* 1.3 72.8 - - - +
201N ILE* 1.3 57.4 + - - +
202N LYS* 3.2 6.4 + - - +
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Residues in contact with ILE 201 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197N MET 3.0 17.6 + - - +
198N CYS* 3.5 7.6 + - - +
199N ARG 3.2 0.6 - - - -
200N GLU* 1.3 76.2 - - - +
202N LYS* 1.3 63.0 + - - +
203N LEU* 3.1 12.2 + - + +
238N TYR* 6.6 0.2 - - + -
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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