Contacts of the helix formed by residues 216 - 231 (chain B) in PDB entry 2Z1Z
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 THR 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B ALA 3.6 2.4 + - - -
215B ALA* 1.3 76.5 - - - +
217B ARG* 1.3 58.1 + - - +
218B GLU* 3.0 26.9 - - + +
219B GLN* 3.0 30.9 + - + +
220B LEU* 3.0 27.5 + - - +
248B ASN* 3.6 17.2 + - - +
249B PRO* 4.1 2.2 - - - -
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Residues in contact with ARG 217 (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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216B THR* 1.3 74.1 - - + +
218B GLU* 1.3 51.8 + - - +
221B THR* 2.6 39.4 + - - +
247B ASP* 4.9 13.1 + - - +
248B ASN* 4.3 3.2 - - - +
249B PRO* 3.6 31.0 - - + +
254B GLU* 3.8 40.0 + - - +
255B ILE* 3.6 10.5 - - + +
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Residues in contact with GLU 218 (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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216B THR* 3.0 11.5 - - + +
217B ARG* 1.3 77.7 - - - +
219B GLN* 1.3 60.8 + - - +
221B THR* 3.5 22.9 + - - +
222B GLN* 2.9 43.3 + - - +
225B GLU* 4.1 4.3 - - - +
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Residues in contact with GLN 219 (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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187B ASN 5.0 3.6 + - - -
188B GLY 4.7 6.5 + - - +
190B PHE* 3.2 61.3 - - + +
214B ALA 4.5 1.7 - - - +
215B ALA* 3.6 8.5 - - + -
216B THR* 3.0 39.5 + - + +
218B GLU* 1.3 74.3 - - + +
220B LEU* 1.3 59.0 + - - +
222B GLN* 3.2 14.5 + - - +
223B LEU 3.0 22.5 + - - -
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Residues in contact with LEU 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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190B PHE* 5.1 0.2 - - + -
204B PHE* 4.1 10.1 - - + -
215B ALA* 3.2 33.9 - - + +
216B THR 3.0 19.8 + - - +
217B ARG 4.0 0.2 - - - +
218B GLU 3.4 0.2 - - - -
219B GLN* 1.3 76.5 - - - +
221B THR* 1.4 56.1 + - - +
223B LEU* 3.3 11.3 + - + +
224B VAL* 3.0 34.5 + - - +
236B TYR* 3.9 34.8 - - + +
249B PRO* 4.0 26.2 - - + +
251B SER 5.0 2.0 - - - +
252B ILE* 4.1 17.3 - - + +
255B ILE* 3.5 19.5 - - + -
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Residues in contact with THR 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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217B ARG* 2.6 25.3 + - - +
218B GLU* 3.6 22.1 + - - +
220B LEU* 1.4 74.6 - - - +
222B GLN* 1.3 64.1 + - - +
224B VAL* 3.6 0.9 + - - +
225B GLU* 2.8 57.8 + - + +
255B ILE* 3.7 23.7 - - + +
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Residues in contact with GLN 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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190B PHE* 3.9 17.1 - - + -
191B PRO 5.1 0.9 - - - +
193B LEU* 3.8 18.0 + - + +
218B GLU* 2.9 34.7 + - - +
219B GLN* 3.3 18.3 - - - +
221B THR* 1.3 78.1 - - - +
223B LEU* 1.3 55.9 + - - +
225B GLU* 3.2 10.4 + - - +
226B PHE* 2.9 29.3 + - - +
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Residues in contact with LEU 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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181B MET* 5.5 0.9 - - + -
190B PHE* 4.3 6.5 - - + -
193B LEU* 3.7 26.4 - - + +
202B ILE* 4.1 22.9 - - + -
204B PHE* 3.8 45.1 - - + -
219B GLN 3.0 13.1 + - - +
220B LEU* 3.5 17.9 - - + +
221B THR 3.3 0.2 - - - -
222B GLN* 1.3 71.8 - - - +
224B VAL* 1.3 53.5 + - - +
226B PHE* 3.2 9.5 + - + +
227B ALA* 2.7 34.5 + - - +
234B ILE* 3.8 23.1 - - + -
252B ILE* 4.9 4.9 - - + -
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Residues in contact with VAL 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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220B LEU 3.0 21.6 + - - +
221B THR 4.0 1.8 - - - +
223B LEU* 1.3 69.5 - - - +
225B GLU* 1.3 61.0 + - + +
227B ALA* 3.7 1.4 - - - +
228B LYS* 2.7 38.8 + - - +
234B ILE* 4.1 13.5 - - + -
252B ILE* 4.1 12.8 - - + -
255B ILE* 3.8 19.7 - - + -
256B PRO 4.1 10.5 - - - +
257B GLY* 3.9 9.6 - - - +
258B ALA* 3.8 37.7 - - + +
261B VAL* 4.1 6.0 - - + +
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Residues in contact with GLU 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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218B GLU* 4.1 5.9 - - - +
221B THR* 2.8 53.0 + - + +
222B GLN* 3.6 8.3 + - - +
224B VAL* 1.3 78.9 - - + +
226B PHE* 1.3 58.0 + - - +
228B LYS* 3.2 8.3 + - - +
229B LYS* 3.0 30.2 + - - +
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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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181B MET* 5.3 1.1 - - - -
193B LEU* 3.5 53.4 - - + -
196B VAL* 3.6 37.0 - - + -
197B GLY 4.3 3.4 - - - -
198B ARG* 5.2 0.4 - - - -
199B THR 6.0 0.7 - - - -
202B ILE* 3.8 25.8 - - + -
222B GLN 2.9 15.7 + - - +
223B LEU* 3.2 7.6 + - + +
225B GLU* 1.3 72.7 - - - +
227B ALA* 1.3 68.2 + - - +
228B LYS 3.1 0.3 + - - -
229B LYS* 3.1 13.4 + - + +
230B ASN* 2.8 56.3 + - - +
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Residues in contact with ALA 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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20A TYR* 3.8 1.2 + - - -
202B ILE* 4.3 4.0 - - + -
223B LEU 2.7 12.7 + - - +
224B VAL 3.9 1.3 - - - +
226B PHE* 1.3 73.5 - - - +
228B LYS* 1.3 56.9 + - - +
231B GLY* 2.9 26.3 + - - -
232B SER* 3.0 36.8 + - - +
234B ILE* 3.5 38.4 - - + -
261B VAL* 3.9 10.1 - - + -
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Residues in contact with LYS 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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20A TYR* 2.9 49.1 + - + -
224B VAL* 2.7 26.4 + - - +
225B GLU* 3.6 8.3 - - - +
226B PHE 3.1 0.2 - - - -
227B ALA* 1.3 73.5 - - - +
229B LYS* 1.3 62.4 + - - +
231B GLY* 3.4 2.4 + - - -
257B GLY* 3.1 36.3 + - - -
260B GLU* 2.2 37.3 + - - +
261B VAL* 3.9 12.5 - - - +
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Residues in contact with LYS 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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23A LYS* 4.6 9.2 + - - +
225B GLU 3.0 18.5 + - - +
226B PHE* 3.5 18.8 - - + +
228B LYS* 1.3 74.5 - - - +
230B ASN* 1.3 79.9 + - - +
231B GLY 3.3 1.0 + - - -
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Residues in contact with ASN 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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23A LYS* 3.6 13.5 + - - +
196B VAL 4.8 0.4 + - - -
197B GLY 4.7 0.2 - - - -
198B ARG* 2.8 61.6 + - + +
199B THR 5.1 0.2 - - - +
226B PHE* 2.8 61.0 + - + +
227B ALA 4.3 0.2 - - - +
229B LYS* 1.3 85.9 - - - +
231B GLY* 1.3 57.6 + - - +
232B SER* 3.6 10.7 + - - +
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Residues in contact with GLY 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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20A TYR* 3.6 15.3 - - - -
21A LYS 5.4 0.2 - - - -
22A THR* 3.4 7.8 - - - -
23A LYS* 2.7 40.0 + - - -
24A VAL* 3.6 2.6 - - - +
198B ARG* 3.4 11.7 + - - -
227B ALA 2.9 8.6 + - - -
228B LYS 3.4 1.4 + - - -
229B LYS 3.2 5.5 + - - -
230B ASN* 1.3 76.0 - - - +
232B SER* 1.4 58.1 + - - +
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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