Contacts of the helix formed by residues 214 - 228 (chain X) in PDB entry 3EXG
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 ARG 214 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120X ALA* 5.2 2.0 + - - +
148X TRP* 3.8 9.7 + - - -
172X ASN* 3.4 20.6 - - - +
174X LEU* 3.4 44.3 - - - +
175X MET* 4.0 24.5 - - + +
213X SER* 1.3 80.5 + - - +
215X PRO* 1.3 67.5 - - + +
216X VAL 2.5 14.9 + - - -
217X GLY* 3.0 14.0 + - - -
218X HIS* 3.8 35.3 + - + +
313X ILE* 4.8 19.0 - - - +
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Residues in contact with PRO 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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172X ASN* 5.3 0.2 - - - +
211X SER* 3.5 16.8 - - - +
212X HIS 3.7 6.5 - - - +
213X SER* 3.6 3.4 - - - -
214X ARG* 1.3 96.9 - - + +
216X VAL* 1.3 63.1 + - - +
217X GLY 3.2 0.2 - - - -
218X HIS* 3.0 22.6 + - + +
219X CYS* 2.9 23.2 + - - -
262X VAL* 3.8 17.0 - - + +
263X GLU 4.1 1.8 - - - -
264X GLY* 3.7 30.7 - - - +
313X ILE* 5.8 4.3 - - + -
314X PRO* 4.9 6.5 - - + -
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Residues in contact with VAL 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148X TRP* 3.6 31.0 - - + -
201X GLU* 4.2 8.1 - - + -
211X SER* 3.6 11.4 - - - -
212X HIS 3.4 26.2 - - - +
213X SER 2.9 17.8 + - - +
214X ARG 2.5 7.3 + - - -
215X PRO* 1.3 74.7 - - - +
217X GLY* 1.3 60.1 + - - +
219X CYS* 3.3 6.8 + - - +
220X LEU* 3.2 22.8 + - + +
235X VAL* 4.4 5.6 - - + +
236X ILE 5.0 0.4 - - - +
237X ASN* 3.5 35.2 - - + +
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Residues in contact with GLY 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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148X TRP* 3.3 29.8 - - - +
214X ARG 3.0 7.5 + - - -
216X VAL* 1.3 79.1 - - - +
218X HIS* 1.3 60.3 + - - +
220X LEU* 3.1 16.6 + - - +
221X GLU* 3.2 15.4 + - - +
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Residues in contact with HIS 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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214X ARG* 3.8 45.9 + - + -
215X PRO* 3.0 21.1 + - + +
217X GLY* 1.3 73.7 - - - +
219X CYS* 1.3 66.0 + - - +
221X GLU* 3.2 24.7 + - - +
222X ALA* 3.1 18.0 + - - +
313X ILE* 5.1 6.7 - - + +
314X PRO* 3.6 23.0 + - - +
315X GLN* 4.8 4.9 - - - -
316X VAL* 3.7 19.5 - - + +
319X ILE* 4.5 13.5 - - + +
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Residues in contact with CYS 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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209X VAL* 3.8 17.0 - - + -
211X SER* 3.8 16.4 - - - -
215X PRO 2.9 17.9 + - - -
216X VAL* 3.4 7.4 - - - +
217X GLY 3.2 0.2 - - - -
218X HIS* 1.3 73.3 - - - +
220X LEU* 1.3 67.1 + - - +
221X GLU 2.9 1.6 - - - -
222X ALA* 3.0 6.2 + - - +
223X ALA* 2.9 22.8 + - - +
235X VAL* 3.9 19.3 - - + +
262X VAL* 3.7 31.2 - - - -
319X ILE* 4.1 9.0 - - + -
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Residues in contact with LEU 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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148X TRP* 3.4 38.6 - - + -
201X GLU* 4.0 29.4 - - + +
202X ARG* 4.1 18.9 + - + -
216X VAL* 3.2 18.6 + - + +
217X GLY* 3.1 8.0 + - - +
219X CYS* 1.3 77.8 - - - +
221X GLU* 1.3 56.9 + - - +
223X ALA* 3.3 7.5 + - - +
224X ALA* 3.1 26.2 + - - +
235X VAL* 4.4 7.6 - - + -
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Residues in contact with GLU 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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217X GLY 3.2 13.3 + - - +
218X HIS* 3.3 25.3 - - - +
219X CYS 2.9 0.6 - - - -
220X LEU* 1.3 73.9 - - - +
222X ALA* 1.3 63.5 + - - +
224X ALA* 3.8 5.5 + - - +
225X VAL* 3.4 27.2 + - + +
316X VAL* 3.8 26.3 - - + +
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Residues in contact with ALA 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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218X HIS 3.1 7.0 + - - +
219X CYS 3.0 7.9 + - - +
221X GLU* 1.3 75.6 - - - +
223X ALA* 1.3 61.5 + - - +
224X ALA 3.2 0.2 - - - -
225X VAL* 3.3 5.3 + - - +
226X LEU* 2.8 42.3 + - + +
316X VAL* 3.6 19.0 - - + +
319X ILE* 4.2 22.9 - - + -
320X ILE* 4.3 14.8 - - + -
323X ILE* 5.0 1.8 - - + -
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Residues in contact with ALA 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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202X ARG* 3.4 36.0 + - - +
219X CYS 2.9 12.3 + - - +
220X LEU* 3.4 12.6 - - - +
222X ALA* 1.3 78.9 - - - +
224X ALA* 1.3 56.3 + - - +
226X LEU* 3.8 1.4 - - - +
227X SER* 3.0 30.1 + - - -
231X VAL 4.5 1.4 - - - +
233X CYS* 4.0 26.1 - - + -
235X VAL* 4.1 2.7 - - + -
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Residues in contact with ALA 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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202X ARG* 4.8 2.6 - - - +
220X LEU 3.1 15.2 + - - +
221X GLU* 4.1 7.4 - - - +
222X ALA 3.2 0.2 - - - -
223X ALA* 1.3 73.2 - - - +
225X VAL* 1.3 64.6 + - + +
226X LEU 3.1 1.6 - - - -
227X SER* 3.1 17.5 + - - -
228X LYS* 3.4 21.7 + - - +
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Residues in contact with VAL 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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221X GLU* 3.4 16.8 + - + +
222X ALA* 3.3 6.5 + - - +
224X ALA* 1.3 77.5 - - + +
226X LEU* 1.3 62.0 + - + +
227X SER 3.8 0.2 + - - -
228X LYS* 3.8 27.8 - - + +
229X GLU* 4.2 14.3 - - - +
316X VAL* 5.5 2.9 - - + -
320X ILE* 3.8 25.4 - - + -
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Residues in contact with LEU 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 ALA 2.8 22.4 + - - +
223X ALA* 3.9 4.9 - - - +
225X VAL* 1.3 77.3 - - + +
227X SER* 1.3 58.9 + - - +
228X LYS 3.1 2.7 - - - -
229X GLU* 2.9 38.1 + - - +
231X VAL* 3.2 35.5 + - + +
233X CYS* 3.8 15.7 - - - -
320X ILE* 4.3 20.0 - - + -
323X ILE* 3.6 38.6 - - + -
324X LYS* 4.4 23.3 - - + -
329X ILE* 5.2 0.4 - - + -
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Residues in contact with SER 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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202X ARG* 3.4 24.0 + - - -
223X ALA 3.0 8.0 + - - -
224X ALA* 3.1 9.7 + - - -
226X LEU* 1.3 73.7 - - - +
228X LYS* 1.3 58.8 + - - +
229X GLU 2.8 8.7 + - - -
230X GLY* 3.4 10.1 + - - +
231X VAL 3.4 8.5 - - - +
232X GLU* 3.3 25.0 - - - +
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Residues in contact with LYS 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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224X ALA* 3.4 18.0 + - - +
225X VAL* 3.8 22.2 - - + +
226X LEU 3.1 0.6 - - - -
227X SER* 1.3 78.3 - - - +
229X GLU* 1.3 63.1 + - + +
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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