Contacts of the helix formed by residues 216 - 228 (chain X) in PDB entry 3F6E
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 ALA 216 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211X VAL* 3.0 21.3 + - + +
214X ALA* 3.1 14.1 - - + -
215X ASN* 1.3 75.3 - - - +
217X ASN* 1.3 58.6 + - - +
218X ALA 3.3 3.1 - - - -
219X ASP* 3.1 13.0 + - + +
220X CYS* 2.9 28.4 + - - -
318X ILE* 4.2 5.6 - - + +
319X GLY* 4.2 9.4 - - - +
322X ALA* 3.7 24.9 - - + -
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Residues in contact with ASN 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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211X VAL* 3.4 16.8 - - - +
212X ASP* 2.9 30.2 + - - +
215X ASN* 3.2 9.3 - - - -
216X ALA* 1.3 75.7 + - - +
218X ALA* 1.3 57.9 + - - +
220X CYS* 3.1 4.6 + - - +
221X VAL* 2.9 31.8 + - - +
240X CYS 3.5 14.1 + - - -
241X PRO* 3.6 28.3 - - - +
242X PHE* 4.1 4.4 - - - +
243X PRO* 5.3 3.8 - - + -
391X ASN 5.1 0.4 + - - -
392X PRO* 3.5 29.9 - - + +
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Residues in contact with ALA 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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215X ASN* 4.7 4.4 + - - +
216X ALA 3.3 0.4 - - - -
217X ASN* 1.3 80.1 - - - +
219X ASP* 1.3 64.0 + - - +
221X VAL* 3.2 11.0 + - - +
222X MET* 3.0 21.7 + - - +
392X PRO* 5.6 2.6 - - + +
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Residues in contact with ASP 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 ASN 5.4 1.2 + - - +
216X ALA* 3.1 16.3 + - - +
218X ALA* 1.3 81.1 - - - +
220X CYS* 1.3 58.3 + - - +
222X MET* 3.3 6.6 + - - +
223X LEU* 2.9 24.5 + - - +
319X GLY 4.5 2.3 - - - +
322X ALA* 3.7 22.0 - - + +
323X SER* 3.4 32.6 + - - -
326X ALA* 3.2 18.1 - - + +
327X ASN* 4.6 5.5 + - - -
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Residues in contact with CYS 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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205X ILE* 5.1 3.0 - - + +
207X LEU* 3.8 37.2 - - + -
211X VAL* 3.8 23.6 - - - -
216X ALA 2.9 17.3 + - - +
217X ASN* 3.5 9.0 - - - +
219X ASP* 1.3 74.8 - - - +
221X VAL* 1.3 58.4 + - - +
223X LEU* 3.4 9.0 + - + +
224X ALA* 2.9 29.5 + - - +
231X VAL* 5.4 0.2 - - - +
242X PHE* 3.6 5.0 - - + -
273X ILE* 4.4 9.2 - - - -
322X ALA* 4.1 16.8 - - - -
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Residues in contact with VAL 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 ASN 2.9 20.0 + - - +
218X ALA* 3.5 11.9 - - - +
220X CYS* 1.3 75.8 - - - +
222X MET* 1.3 64.1 + - - +
224X ALA* 3.3 1.4 + - - +
225X GLU* 2.9 52.1 + - - +
242X PHE* 3.5 14.6 - - + -
243X PRO* 3.5 35.4 - - + -
246X HIS* 3.5 15.3 - - + +
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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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218X ALA 3.0 13.4 + - - +
219X ASP* 3.3 11.9 + - - +
221X VAL* 1.3 76.8 - - - +
223X LEU* 1.3 55.9 + - - +
225X GLU* 3.2 11.0 + - - +
226X ARG* 2.9 70.8 + - + +
326X ALA* 3.3 24.5 - - + +
327X ASN* 3.8 18.8 - - - +
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Residues in contact with LEU 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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197X LEU* 4.9 2.0 - - + -
205X ILE* 4.3 12.8 - - + -
219X ASP 2.9 19.8 + - - +
220X CYS* 3.6 9.6 - - - +
221X VAL 3.3 0.2 - - - -
222X MET* 1.3 73.3 - - - +
224X ALA* 1.3 59.3 + - - +
226X ARG* 3.4 3.1 + - - +
227X LEU* 2.9 43.1 + - + +
271X LEU* 4.0 13.2 - - + -
273X ILE* 3.7 30.1 - - + -
322X ALA* 5.3 3.4 - - - +
325X LEU* 3.9 27.6 - - + +
326X ALA* 4.0 9.8 - - + +
329X VAL* 3.8 27.8 - - + -
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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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205X ILE* 3.7 13.4 - - + +
220X CYS 2.9 15.4 + - - +
221X VAL 3.9 3.4 - - - +
223X LEU* 1.3 76.6 - - - +
225X GLU* 1.3 57.8 + - - +
227X LEU 4.5 0.2 - - - +
228X LYS* 2.8 24.3 + - - -
229X ALA 3.1 17.4 + - - +
231X VAL* 3.5 32.5 - - + -
242X PHE* 4.0 8.5 - - + -
248X CYS* 4.0 8.4 - - - -
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Residues in contact with GLU 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 VAL* 2.9 33.6 + - - +
222X MET* 3.7 9.4 - - - +
224X ALA* 1.3 74.3 - - - +
226X ARG* 1.3 63.7 + - + +
228X LYS* 2.8 34.0 + - - +
246X HIS* 2.8 37.2 + - + +
331X GLU* 4.6 1.6 - - - -
336X LEU* 4.0 17.1 - - + +
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Residues in contact with ARG 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* 2.9 55.7 + - + +
223X LEU 3.8 0.4 - - - +
225X GLU* 1.3 79.0 - - + +
227X LEU* 1.3 60.0 + - - +
228X LYS* 3.3 2.1 + - - -
326X ALA 2.8 19.0 + - - +
327X ASN* 3.4 24.0 + - - +
329X VAL* 2.6 47.8 + - + +
330X GLU 3.7 8.1 - - - +
331X GLU* 3.7 32.2 + - - +
332X SER* 2.8 28.2 + - - -
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Residues in contact with LEU 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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197X LEU* 3.9 47.1 - - + +
198X ASN* 4.7 2.9 - - - +
203X PRO* 3.9 14.5 - - + +
205X ILE* 4.3 13.9 - - + -
223X LEU* 2.9 42.8 + - + +
226X ARG* 1.3 73.5 - - - +
228X LYS* 1.3 67.3 + - - +
229X ALA* 3.3 12.7 + - + -
271X LEU* 5.1 1.3 - - + -
329X VAL* 4.1 20.9 - - + -
330X GLU 4.5 4.7 - - - +
332X SER* 4.2 3.8 - - - -
334X ARG* 2.9 29.3 + - - +
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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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203X PRO* 5.5 1.0 - - - +
224X ALA 2.8 9.5 + - - -
225X GLU 2.8 21.9 + - - +
226X ARG 3.2 6.7 + - - +
227X LEU* 1.3 81.2 - - - +
229X ALA* 1.3 58.4 + - - +
230X PRO* 4.1 2.6 - - - +
331X GLU* 2.7 37.0 + - - -
332X SER* 3.4 23.3 + - - -
334X ARG* 3.3 34.2 + - + +
335X GLN 3.7 14.1 - - - +
336X LEU* 3.7 25.4 - - + +
337X PRO* 3.5 20.6 - - - +
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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