Contacts of the helix formed by residues 213 - 234 (chain H) in PDB entry 5MGX
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 213 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211H MET 3.8 1.6 + - - -
212H LEU* 1.3 74.9 - - - +
214H GLY* 1.3 53.6 + - - +
215H GLN* 3.6 15.4 + - + +
216H GLU* 3.0 46.4 + - + +
217H ARG* 2.8 33.7 + - - +
257H VAL* 5.6 1.3 - - - -
263H GLU* 5.3 1.6 + - - -
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Residues in contact with GLY 214 (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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212H LEU 4.1 0.2 + - - -
213H THR* 1.3 74.0 + - - +
215H GLN* 1.4 55.8 + - - +
217H ARG* 3.3 10.9 + - - +
218H VAL* 3.0 35.9 + - - +
259H MET* 4.7 9.0 - - - +
263H GLU* 3.8 31.7 + - - -
267H LEU* 4.2 6.9 - - - +
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Residues in contact with GLN 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213H THR* 3.3 12.1 - - + +
214H GLY* 1.4 75.4 - - - +
216H GLU* 1.4 56.1 + - + +
218H VAL* 3.5 9.2 + - - +
219H ALA* 3.2 26.0 + - - +
263H GLU* 3.2 31.4 + - - +
266H GLN* 4.9 7.7 + - - -
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Residues in contact with GLU 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211H MET 4.7 1.7 - - - +
212H LEU* 3.8 25.3 - - + +
213H THR* 3.0 39.0 + - + +
215H GLN* 1.4 76.5 - - + +
217H ARG* 1.3 55.0 + - - +
219H ALA* 3.4 7.3 + - - +
220H LEU* 2.9 36.0 + - - +
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Residues in contact with ARG 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H LEU* 2.8 25.9 + - - +
210H GLU 4.0 5.9 + - - -
212H LEU* 3.1 41.7 + - + +
213H THR 2.8 14.7 + - - +
214H GLY* 3.4 8.6 - - - +
216H GLU* 1.3 76.5 - - - +
218H VAL* 1.3 56.3 + - - +
220H LEU* 4.2 1.6 - - - +
221H ALA* 3.1 31.0 + - - +
250H ALA* 2.9 40.0 + - - +
251H ILE 3.6 14.1 - - - -
253H SER* 2.8 28.2 + - - +
254H SER* 4.0 17.9 - - - +
257H VAL* 4.3 4.6 - - - +
267H LEU* 3.8 24.3 - - + +
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Residues in contact with VAL 218 (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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214H GLY 3.0 18.4 + - - +
215H GLN* 3.6 12.6 - - - +
217H ARG* 1.3 75.8 - - - +
219H ALA* 1.3 57.8 + - - +
222H ASN* 3.0 50.3 + - - +
263H GLU* 5.1 2.0 - - + +
266H GLN* 3.9 39.9 - - + +
267H LEU* 3.9 21.8 - - + +
270H LEU* 3.8 12.6 - - + +
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Residues in contact with ALA 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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215H GLN 3.2 16.8 + - - +
216H GLU* 3.4 8.0 + - - +
218H VAL* 1.3 75.3 - - - +
220H LEU* 1.3 62.6 + - - +
222H ASN* 4.1 4.9 - - - +
223H ARG* 3.2 22.9 + - - +
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Residues in contact with LEU 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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146H THR* 5.4 7.2 - - - +
207H PRO* 4.6 14.6 - - + -
209H LEU* 3.7 29.4 - - + -
212H LEU* 3.9 15.0 - - + -
216H GLU 2.9 20.5 + - - +
217H ARG 4.2 2.9 - - - +
219H ALA* 1.3 70.3 - - - +
221H ALA* 1.3 65.8 + - - +
223H ARG* 3.2 13.6 + - + +
224H LYS* 3.1 25.4 + - + +
250H ALA* 4.1 13.0 - - + -
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Residues in contact with ALA 221 (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 ARG 3.1 19.4 + - - +
220H LEU* 1.3 74.7 - - - +
222H ASN* 1.3 57.1 + - - +
224H LYS 3.5 0.7 + - - -
225H ARG* 3.0 28.6 + - - +
247H ALA* 3.6 22.7 - - - +
250H ALA* 4.5 5.1 - - + +
251H ILE* 3.6 31.4 - - + -
270H LEU* 3.8 14.6 - - + -
274H CYS* 4.8 0.3 - - - -
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Residues in contact with ASN 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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218H VAL* 3.0 34.4 + - - +
219H ALA* 4.1 5.6 - - - +
221H ALA* 1.3 72.4 - - - +
223H ARG* 1.3 60.4 + - - +
225H ARG* 2.9 39.1 + - - +
226H GLU* 2.9 41.4 + - - +
270H LEU* 3.5 23.4 - - - +
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Residues in contact with ARG 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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143H LEU* 4.4 15.6 - - - +
144H VAL 3.8 22.6 + - - -
151H ASP* 5.1 7.2 + - - +
152H VAL* 4.5 9.3 - - - +
219H ALA 3.2 18.3 + - - +
220H LEU* 3.2 14.7 + - + +
222H ASN* 1.3 74.6 - - - +
224H LYS* 1.3 59.1 + - - +
226H GLU* 3.3 21.7 + - - +
227H CYS* 3.0 59.0 + - - +
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Residues in contact with LYS 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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151H ASP* 5.5 4.9 - - - +
220H LEU* 3.1 17.7 + - + +
221H ALA* 4.7 0.2 - - - -
223H ARG* 1.3 75.1 - - - +
225H ARG* 1.4 54.7 + - - +
227H CYS* 3.2 10.3 + - - +
228H GLY 2.9 29.5 + - - -
243H SER* 3.4 28.1 - - - +
246H LEU* 4.5 7.6 - - + -
247H ALA* 3.7 19.7 - - + +
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Residues in contact with ARG 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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707D GLU* 5.7 1.2 + - - -
221H ALA 3.0 18.4 + - - +
222H ASN* 2.9 30.1 + - - +
224H LYS* 1.4 75.0 - - - +
226H GLU* 1.3 83.4 + - - +
228H GLY 3.4 0.9 + - - -
229H ASN* 2.9 61.5 + - - +
244H TYR* 3.6 11.2 - - + -
247H ALA* 4.0 2.4 - - - +
270H LEU* 4.2 10.7 - - - +
273H LYS* 4.7 17.2 - - - +
274H CYS* 4.0 24.0 - - - -
277H ASN* 4.0 20.1 - - - +
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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
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222H ASN* 2.9 29.1 + - - +
223H ARG* 3.3 22.4 + - - +
225H ARG* 1.3 94.5 + - - +
227H CYS* 1.4 63.9 + - - +
229H ASN* 3.6 8.5 + - - +
230H ALA* 3.2 22.0 + - - +
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Residues in contact with CYS 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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151H ASP* 3.3 45.9 - - - +
223H ARG* 3.0 51.6 + - - -
224H LYS* 3.2 11.4 + - - +
226H GLU* 1.4 73.4 - - - +
228H GLY* 1.3 64.9 + - - +
230H ALA* 3.0 18.5 + - - +
231H HIS* 3.2 19.7 + - - -
243H SER* 4.1 8.7 - - - +
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Residues in contact with GLY 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 LYS 2.9 10.5 + - - -
225H ARG 3.4 0.2 + - - -
227H CYS* 1.3 75.7 - - - +
229H ASN* 1.4 55.3 + - - +
231H HIS* 3.3 1.6 + - - -
232H TYR 2.9 24.3 + - - -
240H ALA* 3.4 14.5 - - - +
243H SER* 3.4 21.6 - - - -
244H TYR* 3.2 25.7 + - - -
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Residues in contact with ASN 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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707D GLU* 5.0 15.2 + - - +
225H ARG* 2.9 45.0 + - - +
226H GLU* 3.7 8.7 - - - +
227H CYS 3.2 0.2 - - - -
228H GLY* 1.4 74.4 - - - +
230H ALA* 1.4 58.1 + - - +
232H TYR* 3.2 3.4 + - - +
233H GLN* 3.0 49.6 + - - +
244H TYR* 2.7 25.3 + - - -
277H ASN* 3.1 19.2 + - - +
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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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151H ASP 6.0 0.7 - - - +
184H ARG* 4.1 11.5 - - - +
226H GLU 3.2 12.4 + - - +
227H CYS* 3.0 12.4 + - - +
229H ASN* 1.4 75.9 - - - +
231H HIS* 1.4 59.7 + - + +
233H GLN* 3.7 10.1 + - - +
234H ARG* 3.6 28.1 + - - +
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Residues in contact with HIS 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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150H CYS 2.9 22.4 + - - -
151H ASP 3.5 11.0 + - - -
152H VAL 3.2 26.0 - - - -
227H CYS 3.2 19.0 + - - -
228H GLY* 3.3 2.7 + - - +
230H ALA* 1.4 74.0 - - + +
232H TYR* 1.3 60.9 + - - +
234H ARG* 2.8 30.7 + - - +
235H ALA 3.2 4.2 + - - -
236H ASP* 2.8 47.3 + - + +
239H LEU* 3.4 30.8 - - + +
240H ALA 3.5 6.5 - - - +
243H SER* 3.3 20.1 + - - -
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Residues in contact with TYR 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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705D MET 5.1 0.3 + - - -
706D GLU* 4.3 18.3 + - + -
707D GLU* 3.6 34.7 + - + -
228H GLY 2.9 17.7 + - - +
229H ASN* 3.5 5.6 - - - +
231H HIS* 1.3 77.0 - - - +
233H GLN* 1.4 63.4 + - - +
235H ALA* 3.0 20.3 + - - +
236H ASP 4.4 0.9 - - - -
237H PHE* 3.6 33.2 - + - -
240H ALA* 3.7 5.6 - - + +
244H TYR* 3.8 12.6 - + - +
277H ASN 4.9 0.2 - - - -
280H ALA* 3.9 32.9 + - + +
281H SER* 3.5 23.3 - - - -
284H LYS* 3.5 18.4 + - - -
311H ARG* 5.0 0.2 + - - -
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Residues in contact with GLN 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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707D GLU* 3.5 27.8 + - - +
182H GLN* 4.5 6.1 - - - +
184H ARG* 6.2 0.9 - - - -
185H SER* 5.3 12.6 - - - +
229H ASN* 3.0 42.3 + - - +
230H ALA* 3.9 9.6 - - - +
231H HIS 3.4 0.2 - - - -
232H TYR* 1.4 79.1 - - - +
234H ARG* 1.4 57.2 + - - +
235H ALA* 3.3 2.1 + - - +
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Residues in contact with ARG 234 (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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152H VAL 4.2 8.6 + - - -
153H ILE* 5.1 0.6 - - - +
178H CYS 4.2 8.7 + - - -
179H TYR* 3.4 45.2 + - - +
182H GLN* 3.5 20.6 + - + +
183H GLY 2.9 25.8 - - - +
184H ARG* 3.5 29.8 - - - +
230H ALA* 3.6 19.4 + - - +
231H HIS* 2.8 46.1 + - - +
232H TYR 3.2 0.4 - - - -
233H GLN* 1.4 74.4 - - - +
235H ALA* 1.4 65.7 + - - +
236H ASP* 3.4 26.1 + - + +
239H LEU* 4.0 3.2 - - - +
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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
------------------------------------------------------------
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