Contacts of the helix formed by residues 214 - 229 (chain X) in PDB entry 5A31
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 214 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213X SER* 1.3 90.0 - - - +
215X LYS* 1.3 67.0 + - - +
216X GLY 3.3 1.8 - - - +
217X ALA* 3.3 26.4 - - + +
218X GLU* 3.2 20.4 + - - +
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Residues in contact with LYS 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210X LEU* 3.7 24.0 - - + +
213X SER* 3.3 2.4 - - - -
214X VAL* 1.3 75.5 - - - +
216X GLY* 1.3 53.9 + - - +
218X GLU* 3.0 4.2 + - - +
219X VAL* 2.8 38.9 + - + +
244X ALA* 3.3 37.9 - - + +
248X THR* 6.1 1.8 - - + -
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Residues in contact with GLY 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214X VAL* 3.3 1.0 - - - +
215X LYS* 1.3 79.0 - - - +
217X ALA* 1.3 55.6 + - - +
219X VAL* 3.3 11.5 + - - +
220X ALA* 3.0 28.1 + - - +
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Residues in contact with ALA 217 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214X VAL* 3.2 31.5 + - + +
216X GLY* 1.3 74.2 - - - +
218X GLU* 1.3 61.2 + - - +
220X ALA* 3.4 9.2 + - - +
221X SER* 3.3 20.3 + - - -
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Residues in contact with GLU 218 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193X LYS* 6.0 0.2 - - - +
196X LEU* 5.4 0.4 - - + -
206X ILE* 5.1 6.3 - - + -
209X LEU* 4.3 29.4 - - + -
210X LEU* 4.1 17.7 - - + -
214X VAL 3.2 11.1 + - - +
215X LYS 3.0 8.4 + - - +
217X ALA* 1.3 71.7 - - - +
219X VAL* 1.3 65.8 + - - +
221X SER* 2.9 22.6 + - - -
222X MET* 3.0 17.7 + - + +
240X ILE* 5.2 0.7 - - - -
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Residues in contact with VAL 219 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215X LYS* 2.8 39.0 + - + +
216X GLY* 3.3 10.3 + - - +
218X GLU* 1.3 73.3 - - - +
220X ALA* 1.3 51.6 + - - +
222X MET* 3.3 3.5 + - - +
223X THR* 2.8 54.5 + - + +
237X SER* 5.2 4.0 - - - +
240X ILE* 3.3 36.1 - - + +
241X LYS* 5.1 15.0 - - + +
244X ALA* 5.1 4.7 - - + -
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Residues in contact with ALA 220 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216X GLY 3.0 13.6 + - - +
217X ALA* 3.5 12.3 - - - +
218X GLU 3.3 0.4 - - - -
219X VAL* 1.3 75.9 - - - +
221X SER* 1.3 61.2 + - - +
223X THR* 2.7 22.7 + - - -
224X MET* 3.4 9.2 + - - +
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Residues in contact with SER 221 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193X LYS* 3.2 32.3 + - - -
196X LEU* 4.6 4.5 - - - +
217X ALA 3.3 8.1 + - - -
218X GLU* 2.9 23.2 + - - -
220X ALA* 1.3 78.1 - - - +
222X MET* 1.3 66.2 + - - +
224X MET* 3.3 9.2 + - - +
225X ASN* 3.2 20.1 + - - +
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Residues in contact with MET 222 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196X LEU* 4.1 16.6 - - + -
200X PRO* 3.1 31.6 - - + +
206X ILE* 3.5 39.3 - - + -
218X GLU 3.0 17.4 + - - +
219X VAL 3.6 1.8 - - - +
221X SER* 1.3 85.0 + - - +
223X THR* 1.3 56.0 + - - +
225X ASN* 3.2 12.1 - - + +
226X VAL* 2.8 32.2 + - - +
236X LEU* 4.3 19.1 - - + -
240X ILE* 3.4 27.1 - - + -
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Residues in contact with THR 223 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219X VAL* 2.8 38.2 + - + +
220X ALA* 2.7 25.6 + - - -
222X MET* 1.3 69.5 - - + +
224X MET* 1.3 66.4 + - - +
226X VAL* 3.2 17.8 + - + +
227X ILE* 3.2 22.2 + - - +
237X SER* 5.0 15.0 - - - -
240X ILE* 5.8 0.9 - - + -
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Residues in contact with MET 224 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220X ALA 3.4 6.3 + - - +
221X SER* 3.3 11.8 + - - +
222X MET 3.3 0.4 - - - -
223X THR* 1.3 82.2 + - - +
225X ASN* 1.3 62.9 + - - +
227X ILE* 3.5 6.8 + - - +
228X GLN* 3.3 20.1 + - - +
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Residues in contact with ASN 225 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200X PRO* 3.3 32.8 - - + +
221X SER 3.2 9.6 + - - +
222X MET* 3.2 19.5 - - + +
224X MET* 1.3 79.1 - - - +
226X VAL* 1.3 50.1 + - - +
228X GLN* 3.1 10.8 - - - +
229X THR* 2.4 39.2 + - - +
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Residues in contact with VAL 226 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222X MET* 2.8 26.7 + - + +
223X THR* 3.2 11.6 + - + +
225X ASN* 1.3 70.2 - - - +
227X ILE* 1.3 71.6 + - + +
229X THR* 3.0 28.6 + - - +
230X VAL 4.6 1.4 - - - +
233X LEU 3.8 20.4 - - - +
234X ASP* 5.5 3.6 - - - +
236X LEU* 3.5 35.7 - - + -
237X SER* 4.9 11.9 - - - +
240X ILE* 5.4 1.6 - - + -
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Residues in contact with ILE 227 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223X THR* 3.2 16.2 + - - +
224X MET* 3.5 7.6 + - - +
226X VAL* 1.3 78.4 - - + +
228X GLN* 1.3 61.8 + - - +
229X THR 3.2 8.0 - - - +
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Residues in contact with GLN 228 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200X PRO* 6.2 1.3 - - + -
224X MET 3.3 11.5 + - - +
225X ASN* 3.1 16.1 + - - +
227X ILE* 1.3 79.5 - - - +
229X THR* 1.3 58.4 + - - +
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Residues in contact with THR 229 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200X PRO* 4.4 8.0 - - - +
201X LEU* 3.7 18.9 - - + +
225X ASN* 2.4 34.2 + - - +
226X VAL* 3.0 25.0 + - - +
227X ILE 3.2 7.1 - - - +
228X GLN* 1.3 77.9 - - - +
230X VAL* 1.3 84.7 + - + +
231X PRO* 3.9 2.4 - - - +
233X LEU* 3.4 36.1 - - + -
236X LEU* 5.3 2.1 - - + +
37Y VAL* 5.3 0.7 - - + -
40Y HIS* 6.3 4.5 - - + +
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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