Contacts of the helix formed by residues 219 - 232 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B GLY 3.6 1.8 + - - -
218B ILE* 1.3 77.4 - - - +
220B MET* 1.3 53.4 + - - +
221B GLU 3.4 10.8 + - - -
222B ILE* 3.1 22.0 + - + +
223B SER* 2.8 31.9 + - - -
370B SER* 3.9 3.7 - - - -
371B GLU* 3.0 29.5 + - - +
372B GLU* 3.3 8.7 - - - +
405B LYS* 2.7 34.2 + - - -
407B LEU* 4.8 0.2 - - - +
419B HIS* 3.5 31.4 + - + +
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Residues in contact with MET 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B GLY 4.4 1.8 - - - +
212B HIS* 3.4 50.0 - - + -
218B ILE 3.5 5.9 + - - +
219B ASP* 1.3 67.4 - - - +
221B GLU* 1.3 67.5 + - - +
223B SER* 3.4 2.9 - - - -
224B LYS* 2.8 47.1 + - + +
372B GLU* 3.2 37.2 + - + +
2007B SO4 4.2 14.1 - - - +
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B ASP* 3.4 10.4 + - - +
220B MET* 1.3 77.9 - - - +
222B ILE* 1.3 62.4 + - - +
224B LYS* 3.5 6.5 + - - +
225B ASN* 3.0 38.8 + - - +
371B GLU* 4.2 1.7 - - - +
372B GLU* 4.9 1.8 + - - -
385B LYS* 2.5 37.7 + - - +
403B MET* 3.8 14.0 - - + +
405B LYS* 2.8 34.6 + - - +
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Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ILE* 4.4 7.9 - - + -
219B ASP* 3.1 25.7 + - + +
221B GLU* 1.3 79.9 - - - +
223B SER* 1.3 57.1 + - - +
225B ASN* 3.5 5.2 + - - +
226B PHE* 2.9 31.1 + - + +
364B VAL* 3.7 30.1 - - + -
366B TRP* 5.8 0.7 - - + -
403B MET* 4.0 24.5 - - + -
405B LYS* 4.4 3.4 - - + -
419B HIS* 3.8 38.6 - - + +
420B ILE 5.1 1.1 - - - +
421B LEU* 4.0 25.2 - - + +
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Residues in contact with SER 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B HIS* 3.3 11.5 - - - +
213B VAL* 2.7 42.5 + - - +
218B ILE* 4.0 19.1 - - - -
219B ASP 2.8 16.4 + - - -
220B MET* 3.4 12.3 - - - -
222B ILE* 1.3 74.6 - - - +
224B LYS* 1.3 57.5 + - - +
226B PHE* 3.1 4.6 + - - +
227B GLN* 2.8 30.8 + - - +
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Residues in contact with LYS 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B GLY 3.7 23.3 + - - -
212B HIS* 4.7 3.8 - - - +
220B MET* 2.8 39.6 + - + +
221B GLU* 3.7 6.5 - - - +
223B SER* 1.3 74.6 - - - +
225B ASN* 1.3 66.3 + - - +
227B GLN* 3.0 32.5 + - - +
228B ARG* 3.0 43.9 + - - +
239B LEU* 3.8 5.9 - - - +
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Residues in contact with ASN 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B GLU* 3.0 33.8 + - - +
222B ILE* 4.0 1.3 - - - +
224B LYS* 1.3 77.2 - - - +
226B PHE* 1.3 58.7 + - - +
228B ARG* 3.5 28.6 + - - +
229B ILE* 3.1 32.4 + - + +
403B MET* 4.4 19.4 - - - +
421B LEU* 3.6 20.8 - - + +
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Residues in contact with PHE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B VAL* 3.9 14.8 - - + -
213B VAL* 3.8 23.8 - - + -
214B GLY* 5.2 0.9 - - - -
218B ILE* 4.8 9.0 - - + -
222B ILE* 2.9 20.6 + - + +
223B SER* 3.3 4.0 - - - +
225B ASN* 1.3 74.1 - - - +
227B GLN* 1.3 65.5 + - - +
229B ILE* 3.3 3.7 + - - +
230B LEU* 3.0 57.4 + - + +
358B ILE* 3.8 18.6 - - + -
360B THR* 3.3 27.1 - - - -
362B PRO* 3.8 10.5 - - + -
364B VAL* 3.4 27.8 - - + -
421B LEU* 3.7 19.7 - - + +
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Residues in contact with GLN 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B VAL* 4.1 19.0 + - + +
223B SER 2.8 15.0 + - - +
224B LYS* 3.0 35.1 + - - +
226B PHE* 1.3 76.9 - - - +
228B ARG* 1.3 57.2 + - - +
230B LEU* 3.7 6.0 - - - +
231B GLN* 2.7 69.3 + - - +
237B PHE* 3.9 18.2 + - + +
239B LEU* 3.2 29.3 - - - +
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Residues in contact with ARG 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B LYS* 3.0 32.5 + - - +
225B ASN* 3.5 33.4 + - - +
227B GLN* 1.3 81.6 - - - +
229B ILE* 1.3 63.9 + - + +
231B GLN* 3.5 17.1 + - - +
232B LYS* 3.2 43.9 + - - +
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Residues in contact with ILE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ASN* 3.1 19.0 + - + +
226B PHE 3.7 4.3 - - - +
227B GLN 3.2 0.2 - - - -
228B ARG* 1.3 77.2 - - + +
230B LEU* 1.3 65.7 + - - +
232B LYS* 3.3 10.1 + - + +
233B GLN* 3.3 25.7 + - + +
362B PRO* 3.7 26.9 - - + -
401B ASP* 3.6 43.7 - - + +
402B GLY* 4.1 7.0 - - - +
421B LEU* 4.0 20.4 - - + -
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B VAL* 3.5 30.7 - - + -
195B SER* 4.5 11.9 - - - +
213B VAL* 5.4 0.7 - - + -
226B PHE* 3.0 48.8 + - + +
227B GLN* 3.8 4.0 - - - +
229B ILE* 1.3 76.2 - - - +
231B GLN* 1.3 58.9 + - - +
233B GLN* 2.8 47.2 + - - +
235B PHE* 3.1 24.5 + - + +
237B PHE* 3.9 22.7 - - + -
360B THR* 4.7 9.0 - - + -
361B HIS 5.0 2.5 - - - +
362B PRO* 5.0 2.5 - - + -
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Residues in contact with GLN 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B GLN* 2.7 55.7 + - - +
228B ARG* 3.7 18.8 - - - +
230B LEU* 1.3 73.6 - - - +
232B LYS* 1.3 58.3 + - + +
234B GLY* 3.0 19.9 + - - -
235B PHE 3.0 18.5 - - - +
236B LYS* 4.8 2.5 - - - +
237B PHE* 3.8 22.9 + - + +
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Residues in contact with LYS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B ARG* 3.2 30.8 + - - +
229B ILE* 3.8 8.3 - - + +
230B LEU 3.2 0.8 - - - -
231B GLN* 1.3 75.2 - - + +
233B GLN* 1.3 60.5 + - - +
234B GLY 3.3 0.7 - - - -
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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