Contacts of the helix formed by residues 219 - 234 (chain E) in PDB entry 1ZMC
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 219 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217E GLY 3.6 1.8 + - - -
218E ILE* 1.3 75.7 - - - +
220E MET* 1.3 59.7 + - - +
221E GLU 3.3 15.2 + - - -
222E ILE* 3.3 18.1 + - + +
223E SER* 2.9 28.5 + - - -
370E SER* 3.8 3.6 - - - -
371E GLU* 2.8 39.6 + - - +
372E GLU* 3.3 6.8 - - - +
405E LYS* 2.9 30.6 + - - +
419E HIS* 3.7 28.9 + - + +
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Residues in contact with MET 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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211E GLY 4.6 6.1 - - - +
212E HIS* 3.5 43.7 - - + -
218E ILE 3.5 5.3 + - - +
219E ASP* 1.3 68.0 - - - +
221E GLU* 1.3 61.9 + - - +
223E SER* 3.1 3.9 + - - -
224E LYS* 2.8 50.4 + - + +
372E GLU* 3.2 38.2 + - + +
2021E SO4 3.8 20.9 - - - +
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Residues in contact with GLU 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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219E ASP* 3.3 10.1 + - - +
220E MET* 1.3 78.2 - - - +
222E ILE* 1.3 63.0 + - - +
224E LYS* 3.3 5.6 + - - +
225E ASN* 3.1 35.0 + - - +
371E GLU* 4.2 1.7 - - - +
372E GLU* 4.9 1.4 + - - -
385E LYS* 2.4 39.2 + - - +
403E MET* 3.7 22.5 - - + +
405E LYS* 2.6 33.0 + - - +
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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 ILE* 4.6 7.0 - - + -
219E ASP* 3.3 21.4 + - + +
220E MET 3.2 0.4 - - - -
221E GLU* 1.3 79.8 - - - +
223E SER* 1.3 53.7 + - - +
225E ASN* 3.3 6.2 + - - +
226E PHE* 2.8 35.8 + - + +
364E VAL* 3.8 28.5 - - + -
366E TRP* 5.7 0.9 - - + -
403E MET* 3.9 24.2 - - + +
405E LYS* 4.4 8.1 - - + -
419E HIS* 3.6 41.7 - - + +
420E ILE 5.1 0.7 - - - +
421E LEU* 3.9 24.5 - - + +
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Residues in contact with SER 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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212E HIS* 3.5 10.3 - - - +
213E VAL* 2.7 40.1 + - - +
218E ILE* 4.1 17.3 - - - -
219E ASP 2.9 17.4 + - - -
220E MET* 3.4 10.3 - - - -
222E ILE* 1.3 73.8 - - - +
224E LYS* 1.3 62.0 + - - +
226E PHE* 3.4 6.9 + - - +
227E GLN* 2.9 30.4 + - - +
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Residues in contact with LYS 224 (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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211E GLY 3.5 22.1 + - - -
212E HIS* 4.8 3.6 - - - +
220E MET* 2.8 38.3 + - + +
221E GLU* 3.6 7.2 - - - +
223E SER* 1.3 74.4 + - - +
225E ASN* 1.3 58.9 + - - +
227E GLN* 3.3 28.4 + - - +
228E ARG* 2.9 53.6 + - - +
239E LEU* 4.4 2.2 - - - +
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Residues in contact with ASN 225 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221E GLU* 3.1 20.2 + - - +
222E ILE* 3.7 1.3 - - - +
224E LYS* 1.3 76.1 - - - +
226E PHE* 1.3 58.4 + - - +
228E ARG* 3.2 31.2 - - - +
229E ILE* 3.0 34.2 + - + +
403E MET* 3.2 30.5 - - - +
421E LEU* 3.6 18.6 - - + +
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Residues in contact with PHE 226 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191E VAL* 3.8 17.3 - - + -
213E VAL* 4.0 19.5 - - + -
214E GLY* 5.5 0.9 - - - -
218E ILE* 5.2 4.0 - - + -
222E ILE* 2.8 19.1 + - + +
223E SER* 3.6 7.0 - - - +
225E ASN* 1.3 75.8 - - - +
227E GLN* 1.3 65.1 + - - +
229E ILE* 3.3 3.5 + - - -
230E LEU* 2.9 59.5 + - + +
358E ILE* 4.0 16.6 - - + -
360E THR* 3.2 27.8 - - - -
362E PRO* 3.5 13.7 - - + -
364E VAL* 3.5 21.5 - - + -
421E LEU* 3.5 26.9 - - + +
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Residues in contact with GLN 227 (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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212E HIS* 5.0 0.2 - - - -
213E VAL* 3.7 28.1 + - + +
223E SER 2.9 17.9 + - - +
224E LYS* 3.4 23.5 + - - +
226E PHE* 1.3 75.3 - - - +
228E ARG* 1.3 58.3 + - - +
230E LEU* 3.1 8.0 + - - +
231E GLN* 2.7 62.7 + - - +
237E PHE* 4.0 8.9 + - + +
239E LEU* 3.2 35.1 - - - +
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Residues in contact with ARG 228 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224E LYS* 2.9 38.5 + - - +
225E ASN* 3.2 37.8 - - - +
227E GLN* 1.3 76.1 - - - +
229E ILE* 1.3 64.7 + - + +
231E GLN* 3.1 17.8 + - - +
232E LYS* 3.1 46.7 + - - +
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Residues in contact with ILE 229 (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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225E ASN* 3.0 23.6 + - + +
226E PHE* 3.3 4.2 + - - +
228E ARG* 1.3 77.6 - - + +
230E LEU* 1.3 60.4 + - + +
232E LYS* 3.5 12.6 + - + +
233E GLN* 3.3 39.0 + - + +
362E PRO* 3.6 19.5 - - + -
401E ASP* 3.7 36.3 - - + +
402E GLY* 4.1 7.0 - - - +
421E LEU* 4.0 21.1 - - + -
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Residues in contact with LEU 230 (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 VAL* 3.5 31.9 - - + -
195E SER* 4.7 7.6 - - - +
213E VAL* 5.2 0.9 - - + -
226E PHE* 2.9 51.5 + - + +
227E GLN* 3.6 5.2 - - - +
229E ILE* 1.3 73.8 - - - +
231E GLN* 1.3 66.1 + - - +
233E GLN* 3.0 35.1 + - - +
235E PHE* 3.0 34.6 + - + +
237E PHE* 3.8 25.6 - - + -
360E THR* 4.9 5.6 - - - +
361E HIS 5.0 1.3 - - - +
362E PRO* 5.1 1.1 - - + -
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Residues in contact with GLN 231 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227E GLN* 2.7 48.5 + - - +
228E ARG* 3.3 18.3 - - - +
230E LEU* 1.3 78.4 - - - +
232E LYS* 1.3 58.6 + - + +
234E GLY* 3.0 19.6 + - - -
235E PHE 3.2 17.3 + - - +
236E LYS* 4.8 5.6 - - + +
237E PHE* 3.6 17.5 + - + +
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Residues in contact with LYS 232 (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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228E ARG* 3.1 41.1 + - - +
229E ILE* 3.9 12.6 - - + +
230E LEU 3.3 0.4 - - - -
231E GLN* 1.3 76.8 - - + +
233E GLN* 1.3 61.1 + - - +
234E GLY* 3.4 0.7 + - - -
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Residues in contact with GLN 233 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64E HIS* 5.4 13.4 - - + -
195E SER* 4.3 10.4 + - - -
198E GLN* 3.1 27.3 + - - +
199E ARG* 5.0 4.7 + - - +
229E ILE* 3.3 33.9 + - + +
230E LEU* 3.0 28.8 + - - +
232E LYS* 1.3 78.0 - - - +
234E GLY* 1.3 57.3 + - - +
235E PHE* 3.5 2.8 - - + +
361E HIS 3.1 27.4 + - - +
362E PRO* 3.5 4.2 - - - +
401E ASP* 4.9 1.8 + - - -
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Residues in contact with GLY 234 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198E GLN* 4.0 15.4 + - - +
204E VAL 4.1 2.9 + - - +
231E GLN 3.0 11.0 + - - -
232E LYS 3.2 1.2 - - - -
233E GLN* 1.3 81.7 - - - +
235E PHE* 1.3 63.0 + - - +
236E LYS* 3.3 22.0 + - - +
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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