Contacts of the helix formed by residues 218 - 233 (chain H) in PDB entry 6MZL
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 VAL 218 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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785B ARG* 4.9 21.8 - - + +
843B LEU* 4.0 16.8 - - + -
217H SER* 1.3 97.3 + - - +
219H GLU* 1.3 60.0 + - - +
220H GLN 3.1 1.8 - - - -
221H GLN* 3.0 20.2 + - + +
222H LEU* 3.0 43.8 + - + +
183K ARG* 4.6 1.8 - - - +
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Residues in contact with GLU 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839B MET* 3.3 35.6 - - - +
843B LEU* 4.2 12.2 - - + +
218H VAL* 1.3 74.3 - - + +
220H GLN* 1.3 65.4 + - - +
222H LEU* 3.6 21.2 - - + +
223H TYR* 2.9 26.7 + - - +
183K ARG* 3.3 39.6 + - - +
186K VAL* 3.9 11.0 - - + +
187K GLU* 3.7 26.7 + - - +
190K LEU* 4.8 6.6 - - + +
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Residues in contact with GLN 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217H SER* 3.0 45.7 + - - +
219H GLU* 1.3 78.2 - - - +
221H GLN* 1.3 69.5 + - + +
223H TYR* 3.4 2.4 + - - +
224H TYR* 3.0 26.1 + - - +
254H GLN* 5.3 5.9 + - - +
255H MET* 3.7 38.5 - - + +
258H ARG* 3.1 35.7 + - - +
183K ARG* 3.8 8.8 - - - +
186K VAL* 4.7 5.4 - - - +
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Residues in contact with GLN 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217H SER 4.3 13.9 + - - +
218H VAL* 3.0 21.1 + - + +
220H GLN* 1.3 82.0 - - + +
222H LEU* 1.3 61.6 + - + +
224H TYR* 3.6 14.4 - - + +
225H LYS* 2.7 47.5 + - + +
258H ARG* 5.5 4.9 - - - +
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Residues in contact with LEU 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842B LEU* 5.2 21.8 - - + +
843B LEU* 3.9 18.8 - - + -
218H VAL* 3.0 35.2 + - + +
219H GLU* 3.6 21.1 - - + +
220H GLN 3.2 0.2 - - - -
221H GLN* 1.3 75.6 - - + +
223H TYR* 1.3 66.1 + - - +
225H LYS* 3.1 16.5 + - + +
226H GLU* 3.0 26.3 + - - +
190K LEU* 4.1 17.3 - - + +
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Residues in contact with TYR 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H GLU 2.9 18.4 + - - +
220H GLN 3.7 2.9 - - - +
222H LEU* 1.3 74.5 - - - +
224H TYR* 1.3 59.7 + - - +
226H GLU* 3.5 0.9 + - - +
227H ILE* 3.0 63.0 + - + +
245H SER* 3.3 16.2 + - - -
249H ASP* 3.3 23.1 + - - -
252H LEU* 3.8 32.0 - - + +
255H MET* 4.9 8.1 - - + -
259H PHE* 5.7 1.6 - + - -
186K VAL* 4.2 13.9 - - + -
189K ALA* 3.8 24.9 - - + +
190K LEU* 3.8 39.1 - - + +
193K PHE* 5.0 4.9 - + + -
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Residues in contact with TYR 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220H GLN 3.0 17.8 + - - +
221H GLN* 3.6 15.0 - - + +
223H TYR* 1.3 79.6 - - + +
225H LYS* 1.3 57.0 + - + +
227H ILE* 3.7 5.1 - - + +
228H THR* 2.6 59.1 + - + +
255H MET* 5.2 12.1 - - + -
258H ARG* 3.4 50.3 + - + +
259H PHE* 4.3 17.7 - + - -
262H PHE* 3.6 15.6 - - + +
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Residues in contact with LYS 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221H GLN* 2.7 40.0 + - + +
222H LEU* 3.4 16.4 - - + +
224H TYR* 1.3 77.2 - - + +
226H GLU* 1.3 61.5 + - + +
228H THR* 2.7 20.2 + - - -
229H GLU* 2.9 34.7 + - - +
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Residues in contact with GLU 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842B LEU* 4.7 6.2 - - - +
222H LEU 3.0 14.7 + - - +
223H TYR 4.6 1.1 - - - +
225H LYS* 1.3 80.1 - - + +
227H ILE* 1.3 58.8 + - - +
229H GLU* 3.7 15.2 - - - +
230H ALA* 2.9 30.0 + - - +
190K LEU* 4.6 6.2 - - + +
193K PHE* 3.2 28.5 - - + -
194K MET* 3.2 40.7 - - - +
197K THR* 5.6 0.5 - - - +
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Residues in contact with ILE 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223H TYR* 3.0 51.9 + - + +
224H TYR* 3.7 9.4 - - + +
226H GLU* 1.3 75.8 - - - +
228H THR* 1.3 65.9 + - + +
230H ALA* 3.6 2.5 + - - -
231H CYS* 2.9 28.1 + - + +
242H ALA* 4.2 23.0 - - + +
245H SER* 4.5 4.3 - - - +
246H ILE* 3.6 35.9 - - + -
259H PHE* 4.2 21.3 - - + -
285H MET* 6.2 1.1 - - + -
193K PHE* 5.1 10.0 - - + -
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Residues in contact with THR 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224H TYR* 2.6 54.8 + - + +
225H LYS* 2.7 15.9 + - - -
227H ILE* 1.3 79.0 - - + +
229H GLU* 1.3 59.9 + - - +
231H CYS* 3.0 8.7 + - - +
232H VAL* 2.9 32.8 + - - +
259H PHE* 5.8 1.1 - - + -
262H PHE* 4.3 30.7 - - + -
285H MET* 5.2 4.5 - - + -
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Residues in contact with GLU 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225H LYS* 2.9 41.2 + - - +
226H GLU* 3.7 15.1 - - - +
228H THR* 1.3 78.1 - - - +
230H ALA* 1.3 58.1 + - - +
232H VAL* 3.3 4.3 + - - +
233H GLY* 2.8 27.9 + - - -
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Residues in contact with ALA 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226H GLU 2.9 17.8 + - - +
227H ILE* 4.0 3.6 - - - +
229H GLU* 1.3 73.9 - - - +
231H CYS* 1.3 61.3 + - - +
233H GLY* 3.1 7.0 - - - +
235H CYS* 6.5 0.9 - - - -
238H LYS* 4.4 15.0 - - + +
239H ARG* 3.0 29.7 + - - -
242H ALA* 4.4 15.7 - - + -
193K PHE* 4.1 19.1 - - + -
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Residues in contact with CYS 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227H ILE* 2.9 19.5 + - + +
228H THR* 3.0 12.7 + - - +
230H ALA* 1.3 79.3 - - - +
232H VAL* 1.3 58.0 + - + +
239H ARG* 2.5 29.8 + - - +
243H LEU* 6.3 1.8 - - - -
262H PHE* 4.6 5.6 - - + -
278H LEU* 5.0 0.3 - - - +
281H TYR* 3.5 14.9 - - - +
282H LEU* 4.6 9.9 - - - -
285H MET* 3.5 43.1 - - + -
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Residues in contact with VAL 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228H THR* 2.9 17.5 + - - +
229H GLU* 4.0 4.3 - - - +
231H CYS* 1.3 80.6 - - - +
233H GLY* 1.3 65.8 + - - +
234H SER* 3.7 1.6 + - - -
239H ARG* 3.4 4.6 + - - -
262H PHE* 4.5 20.6 - - + -
278H LEU* 4.0 23.8 - - + +
281H TYR* 3.8 10.0 - - - -
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Residues in contact with GLY 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229H GLU 2.8 20.3 + - - -
230H ALA* 3.1 8.6 - - - +
232H VAL* 1.3 74.8 - - - +
234H SER* 1.3 55.9 + - - -
235H CYS* 3.3 13.1 + - - +
239H ARG* 2.3 27.0 + - - -
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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