Contacts of the helix formed by residues 210 - 223 (chain E) in PDB entry 2NYM
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 GLY 210 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161E PHE* 3.5 20.2 + - - -
169E ARG* 4.1 2.9 - - - -
208E HIS* 2.9 20.7 + - - -
209E ASN* 1.3 72.4 - - - +
211E ILE* 1.3 62.9 + - - -
212E ALA 3.2 2.0 - - - -
213E GLU* 3.6 16.9 - - - +
214E LEU* 3.0 29.8 + - - +
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Residues in contact with ILE 211 (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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197E ILE* 4.7 0.7 - - + -
198E PHE* 3.6 27.0 - - + -
201E PHE* 3.6 31.4 - - + -
208E HIS* 3.1 54.7 - - + +
209E ASN 3.4 3.2 - - - -
210E GLY* 1.3 77.3 - - - +
212E ALA* 1.3 65.1 + - - +
214E LEU* 3.2 2.8 + - - +
215E LEU* 2.9 25.8 + - + +
253E TYR* 3.2 46.9 - - + -
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Residues in contact with ALA 212 (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 ARG* 5.7 0.7 - - - +
209E ASN 4.5 3.1 + - - +
211E ILE* 1.3 80.2 - - - +
213E GLU* 1.3 72.5 + - - +
215E LEU* 3.2 12.0 + - - +
216E GLU* 3.4 18.2 + - - +
252E VAL* 4.1 17.0 - - + +
253E TYR* 3.7 23.5 - - + +
256E GLN* 4.1 17.7 - - + +
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Residues in contact with GLU 213 (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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161E PHE* 4.2 17.3 - - + -
166E PRO* 3.7 17.3 - - - +
169E ARG* 2.7 62.9 + - + -
170E ASP* 4.4 8.5 - - - +
173E LYS* 4.1 15.4 - - + +
209E ASN 3.6 8.0 - - - +
210E GLY* 3.6 6.3 - - - +
211E ILE 3.4 0.2 - - - -
212E ALA* 1.3 86.3 - - - +
214E LEU* 1.3 63.4 + - - +
216E GLU* 3.3 26.2 + - - +
217E ILE* 3.6 9.7 + - - +
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Residues in contact with LEU 214 (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 LEU* 3.6 27.8 - - + -
161E PHE* 3.4 34.8 - - + -
176E LEU* 4.4 2.0 - - + -
194E ILE* 4.1 26.5 - - + -
197E ILE* 4.2 27.6 - - + -
198E PHE* 4.1 12.3 - - + -
208E HIS* 4.3 3.8 - - + +
210E GLY 3.0 26.8 + - - +
211E ILE* 3.8 5.6 - - - +
213E GLU* 1.3 77.9 - - - +
215E LEU* 1.3 62.1 + - - +
217E ILE* 3.1 17.9 + - + +
218E LEU* 3.1 15.6 + - - +
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Residues in contact with LEU 215 (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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198E PHE* 3.5 27.8 - - + -
211E ILE* 2.9 20.5 + - + +
212E ALA 3.2 4.7 + - - +
214E LEU* 1.3 76.4 - - - +
216E GLU* 1.3 57.4 + - - +
218E LEU* 3.4 8.6 + - + -
219E GLY* 2.9 21.3 + - - -
241E LEU* 3.8 23.1 - - + -
244E LEU* 4.4 2.9 - - + -
253E TYR* 3.8 21.8 - - + +
256E GLN* 3.8 14.4 - - + +
257E LEU* 3.4 44.6 - - + +
260E CYS* 3.4 14.1 - - - -
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Residues in contact with GLU 216 (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 LYS* 2.8 44.9 + - - +
212E ALA* 3.7 15.6 - - - +
213E GLU* 3.3 15.6 + - - +
214E LEU 3.1 1.0 - - - -
215E LEU* 1.3 76.0 - - - +
217E ILE* 1.3 58.7 + - - +
219E GLY* 2.7 24.9 + - - -
220E SER* 3.3 7.1 + - - -
256E GLN* 4.1 27.7 - - + +
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Residues in contact with ILE 217 (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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161E PHE* 3.6 23.8 - - + -
173E LYS* 3.6 27.8 - - + +
176E LEU* 3.5 35.7 - - + +
177E HIS* 4.5 25.5 + - + +
180E TYR* 5.4 3.6 - - + -
190E ILE* 5.9 0.4 - - + -
194E ILE* 5.3 3.6 - - + -
213E GLU 3.9 9.0 - - - +
214E LEU* 3.1 11.0 + - + +
216E GLU* 1.3 78.4 - - - +
218E LEU* 1.3 59.3 + - + +
219E GLY 3.0 4.2 + - - -
220E SER* 3.3 6.7 + - - -
221E ILE* 3.0 41.1 + - + +
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Residues in contact with LEU 218 (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 ARG* 5.0 10.3 - - + -
194E ILE* 3.9 21.5 - - + -
195E ASN* 5.8 0.2 - - - +
198E PHE* 3.6 31.0 - - + -
214E LEU 3.1 13.9 + - - +
215E LEU* 3.5 14.6 - - + +
217E ILE* 1.3 72.4 - - - +
219E GLY* 1.3 67.8 + - - +
221E ILE* 3.4 28.3 - - + -
222E ILE* 2.9 29.2 + - + +
225E PHE* 6.2 0.9 - - + -
236E PHE* 3.6 34.3 - - + -
260E CYS* 3.9 8.7 - - - -
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Residues in contact with GLY 219 (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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215E LEU 2.9 9.5 + - - -
216E GLU* 2.7 14.3 + - - -
218E LEU* 1.3 82.6 - - - +
220E SER* 1.3 63.4 + - - +
221E ILE 3.1 0.2 + - - -
222E ILE* 3.2 9.9 + - - +
223E ASN* 3.3 11.7 + - - +
259E TYR* 4.1 26.4 - - - -
260E CYS* 4.0 9.9 - - - -
263E GLN* 6.0 0.2 - - - -
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Residues in contact with SER 220 (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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177E HIS* 3.5 36.2 - - - -
216E GLU 3.3 6.9 + - - -
217E ILE 3.3 4.7 + - - -
219E GLY* 1.3 73.7 - - - +
221E ILE* 1.3 65.8 + - - +
223E ASN* 3.4 21.7 + - - +
224E GLY* 4.7 0.5 - - - -
259E TYR* 5.0 0.8 - - - -
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Residues in contact with ILE 221 (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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177E HIS* 6.0 2.0 - - + -
180E TYR* 3.5 51.4 - - + +
190E ILE* 5.3 1.1 - - + -
191E ARG* 4.9 7.0 - - + -
194E ILE* 5.2 5.4 - - + -
217E ILE* 3.0 30.0 + - + +
218E LEU* 3.4 34.1 - - + +
219E GLY 3.1 0.2 + - - -
220E SER* 1.3 79.7 - - - +
222E ILE* 1.3 68.9 + - - +
223E ASN 3.6 0.2 - - - -
224E GLY* 3.2 15.1 + - - -
225E PHE* 3.5 22.6 - - + -
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Residues in contact with ILE 222 (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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218E LEU* 2.9 24.9 - - + +
219E GLY* 3.2 3.7 + - - +
221E ILE* 1.3 74.6 - - + +
223E ASN* 1.3 53.8 + - - +
224E GLY 2.3 17.8 + - - -
225E PHE* 3.0 36.6 + - + +
236E PHE* 4.4 7.9 - - + -
241E LEU* 4.3 5.2 - - + -
260E CYS* 3.7 31.9 - - + +
263E GLN* 4.2 9.6 - - + +
264E PHE* 3.2 58.8 - - + +
267E LYS* 5.0 8.0 - - + +
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Residues in contact with ASN 223 (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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219E GLY 3.3 6.6 + - - +
220E SER* 3.4 18.5 - - - +
221E ILE 3.2 1.0 + - - -
222E ILE* 1.3 74.9 - - - +
224E GLY* 1.3 56.0 + - - +
259E TYR* 4.1 7.5 + - - +
263E GLN* 2.6 46.9 - - + +
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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