Contacts of the helix formed by residues 182 - 198 (chain E) in PDB entry 6NRB
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 HIS 182 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173E LEU* 3.1 12.7 - - + +
177E VAL* 5.4 0.4 - - - +
178E VAL* 3.5 41.8 - - + +
180E SER* 3.5 11.5 + - - -
181E CYS* 1.3 84.6 - - - +
183E ARG* 1.3 53.9 + - - +
184E GLN* 3.1 18.8 - - - +
185E MET* 3.2 26.9 + - + +
186E ALA* 2.7 35.2 + - - +
218E ARG* 5.5 2.2 + - - -
219E LEU* 4.4 10.3 - - + -
220E GLU* 3.0 34.6 + - + +
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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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166E ILE* 3.2 38.5 - - - +
170E LYS* 3.5 5.7 - - - +
181E CYS* 3.5 28.9 + - - -
182E HIS* 1.3 68.2 - - - +
184E GLN* 1.3 65.9 + - - +
185E MET 3.0 1.6 - - - -
186E ALA* 2.6 28.7 + - - +
187E GLU* 2.8 66.8 + - + +
188E ILE* 4.0 1.2 + - - +
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Residues in contact with GLN 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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182E HIS* 3.1 26.1 - - - +
183E ARG* 1.3 84.6 + - - +
185E MET* 1.3 66.4 + - - +
188E ILE* 2.9 41.2 - - + +
220E GLU* 3.0 58.4 - - + +
222E THR* 3.8 10.1 + - - +
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Residues in contact with MET 185 (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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173E LEU* 3.5 29.2 - - + -
177E VAL* 5.4 1.3 - - + -
182E HIS* 3.2 34.1 - - + +
183E ARG 3.0 0.4 - - - -
184E GLN* 1.3 96.7 - - - +
186E ALA* 1.3 55.4 + - - +
188E ILE* 4.6 2.2 - - - -
189E ALA* 2.7 37.1 + - - +
219E LEU* 3.2 31.9 - - + +
222E THR* 3.5 20.2 - - + -
387E ILE* 3.7 25.4 - - + -
398E ALA* 4.3 5.4 - - + -
402E LEU* 3.9 7.2 - - + +
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Residues in contact with ALA 186 (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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169E ALA* 3.3 44.1 - - + +
170E LYS 4.2 1.1 - - - +
173E LEU* 3.5 1.5 - - - +
181E CYS* 4.6 1.3 - - - -
182E HIS 2.7 20.7 + - - +
183E ARG* 2.6 33.5 + - - +
185E MET* 1.3 74.2 - - - +
187E GLU* 1.3 62.5 + - - +
189E ALA* 3.1 14.9 + - - +
190E VAL* 3.3 4.7 + - - +
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Residues in contact with GLU 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E THR* 4.2 14.7 - - - +
165E LEU 4.0 2.3 - - - +
166E ILE* 3.0 32.0 + - + +
169E ALA* 4.5 0.2 - - - +
183E ARG* 2.8 51.3 + - + +
186E ALA* 1.3 78.9 - - - +
188E ILE* 1.3 56.2 + - + +
190E VAL* 3.0 22.4 - - + +
191E ASN* 2.5 40.9 + - + +
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Residues in contact with ILE 188 (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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183E ARG 4.0 1.2 + - - -
184E GLN* 2.9 34.1 - - + +
185E MET* 3.5 2.6 + - - +
186E ALA 3.3 0.6 - - - -
187E GLU* 1.3 74.2 - - + +
189E ALA* 1.3 60.9 + - - +
191E ASN* 4.3 5.4 - - + +
192E ALA* 2.9 28.1 + - - +
222E THR* 4.8 9.9 - - - +
223E LYS 5.3 0.4 - - - -
224E LEU* 3.4 47.6 - - + +
385E ILE* 3.4 14.5 - - + +
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Residues in contact with ALA 189 (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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169E ALA* 5.0 0.2 - - + -
185E MET 2.7 23.4 + - - +
186E ALA* 3.1 7.4 + - - +
188E ILE* 1.3 76.5 - - - +
190E VAL* 1.3 61.8 + - - +
192E ALA* 3.6 1.0 - - - +
193E VAL* 3.5 14.2 + - - +
385E ILE* 4.2 6.3 - - - -
402E LEU* 3.6 22.0 - - + -
405E ALA* 4.4 14.1 - - + -
406E LEU* 3.3 32.6 - - + +
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Residues in contact with VAL 190 (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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162E THR* 5.2 0.2 - - + -
165E LEU* 3.5 49.6 - - + +
169E ALA* 3.9 13.7 - - + -
186E ALA 3.5 10.5 - - - +
187E GLU* 3.0 43.0 + - + +
189E ALA* 1.3 76.4 - - + +
191E ASN* 1.3 55.4 + - + +
193E VAL* 3.2 9.8 + - - +
194E LEU* 2.6 45.2 + - + +
405E ALA* 4.6 7.4 - - + +
409E ILE* 3.9 3.2 - - + +
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Residues in contact with ASN 191 (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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187E GLU* 2.5 25.7 + - + +
188E ILE* 4.3 4.9 - - + -
190E VAL* 1.3 71.3 - - + +
192E ALA* 1.3 52.9 + - - +
194E LEU* 3.6 22.2 - - + +
195E THR* 2.3 55.6 + - - -
224E LEU* 5.0 11.6 - - + +
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Residues in contact with ALA 192 (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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188E ILE 2.9 21.8 + - - +
189E ALA 3.6 5.8 - - - +
190E VAL 3.3 0.2 - - - -
191E ASN* 1.3 75.6 - - - +
193E VAL* 1.3 65.2 + - - +
195E THR* 3.1 9.7 + - - -
196E VAL 3.0 14.7 + - - -
209E ILE* 3.2 25.2 - - + +
224E LEU* 4.0 9.7 - - + +
383E VAL* 4.3 8.7 - - + +
385E ILE* 3.4 23.1 - - + -
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Residues in contact with VAL 193 (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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189E ALA 3.5 9.8 + - - +
190E VAL 3.2 7.8 + - - +
192E ALA* 1.3 75.2 - - - +
194E LEU* 1.3 50.9 + - - +
196E VAL 2.6 8.3 + - - -
197E ALA* 2.2 35.4 + - + +
204E VAL* 3.5 26.9 - - + -
209E ILE* 3.3 23.1 - - + +
406E LEU* 3.9 14.4 - - - +
409E ILE* 3.4 46.7 - - + -
413E ILE* 3.8 9.2 - - + -
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Residues in contact with LEU 194 (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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158E ASP* 4.2 26.0 - - + +
161E ASP* 3.9 20.9 - - - +
162E THR* 4.4 18.4 - - + -
165E LEU* 4.8 0.4 - - + -
190E VAL* 2.6 37.1 + - + +
191E ASN* 3.4 24.0 - - + +
193E VAL* 1.3 71.7 - - - +
195E THR* 1.3 55.4 + - - +
197E ALA* 3.6 11.6 - - + +
198E ASP* 3.1 28.2 + - - +
409E ILE* 3.9 10.5 - - + -
413E ILE* 6.1 0.2 - - + -
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Residues in contact with THR 195 (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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191E ASN* 2.3 48.9 + - - -
192E ALA* 3.3 9.9 - - - -
193E VAL 2.8 0.8 + - - -
194E LEU* 1.3 71.4 - - - +
196E VAL* 1.3 55.5 + - - -
198E ASP* 2.7 18.0 - - - +
199E MET* 3.2 22.9 - - + +
224E LEU* 5.1 3.5 - - - +
226E LYS* 3.9 29.6 + - + -
383E VAL* 3.5 27.5 - - + +
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Residues in contact with VAL 196 (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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192E ALA 3.0 2.0 + - - -
193E VAL 2.6 7.1 + - - -
195E THR* 1.3 71.9 - - - +
197E ALA* 1.3 63.3 + - - +
198E ASP 3.2 1.8 - - - -
199E MET* 3.1 14.8 + - + -
200E GLU* 2.7 51.1 - - - +
204E VAL* 3.5 22.5 - - + +
208E LEU* 3.3 31.4 - - + +
209E ILE* 3.5 7.9 - - + -
380E SER 4.4 6.7 - - - +
381E ARG 5.0 0.2 - - - +
383E VAL* 3.3 31.0 - - + +
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Residues in contact with ALA 197 (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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158E ASP* 6.0 0.9 - - - +
193E VAL* 2.2 38.6 + - + +
194E LEU* 3.6 15.9 - - + +
195E THR 3.4 0.2 - - - -
196E VAL* 1.3 67.6 - - - +
198E ASP* 1.3 58.1 + - - +
200E GLU 2.9 6.8 - - - +
202E ARG* 2.9 9.7 - - - +
203E ASP 2.9 26.9 + - - -
204E VAL* 3.7 11.6 - - - +
413E ILE* 3.7 25.4 - - + -
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Residues in contact with ASP 198 (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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194E LEU 3.1 13.6 - - - +
195E THR* 2.7 29.8 - - - +
197E ALA* 1.3 73.1 - - + +
199E MET* 1.3 65.4 + - - +
200E GLU 3.4 2.0 - - - -
202E ARG* 4.4 28.8 + - - +
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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