Contacts of the helix formed by residues 217 - 230 (chain M) in PDB entry 6FF7
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 ASN 217 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181M GLU* 6.1 0.7 - - - -
213M ALA* 5.4 0.4 - - - -
214M GLY 5.8 0.2 - - - +
215M LYS 3.3 6.5 + - - +
216M SER* 1.3 71.2 - - - +
218M TYR* 1.3 60.4 + - - +
219M GLN* 3.7 2.4 + - + +
220M LEU* 4.3 23.6 - - + +
221M TRP* 3.4 21.1 + - - +
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Residues in contact with TYR 218 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177M PRO 5.4 3.8 - - - +
181M GLU* 4.4 26.5 - - + +
200M LEU* 5.3 4.3 - - - +
203M VAL* 4.6 20.6 - - + +
213M ALA* 5.6 3.6 - - + +
216M SER 4.0 3.4 + - - -
217M ASN* 1.3 72.3 - - - +
219M GLN* 1.3 59.8 + - - +
221M TRP* 4.2 6.3 - - - +
222M HIS* 3.6 19.2 + - - +
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Residues in contact with GLN 219 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217M ASN* 3.3 2.6 - - + +
218M TYR* 1.3 75.8 - - - +
220M LEU* 1.3 55.7 + - - +
221M TRP 3.0 1.3 - - - -
222M HIS* 2.9 9.5 + - - +
223M GLU* 2.7 34.6 + - - +
250M ARG* 5.3 16.2 - - + +
251M PHE* 6.0 4.9 - - + -
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Residues in contact with LEU 220 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217M ASN* 4.3 18.1 - - + +
219M GLN* 1.3 79.1 - - - +
221M TRP* 1.3 56.0 + - - +
223M GLU* 3.6 11.7 - - + +
224M LEU* 2.9 25.3 + - - +
251M PHE* 6.0 6.3 - - + -
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Residues in contact with TRP 221 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217M ASN 3.4 20.4 + - - +
218M TYR* 4.4 6.1 - - - +
219M GLN 3.0 0.8 - - - -
220M LEU* 1.3 76.8 - - - +
222M HIS* 1.3 61.0 + - - +
224M LEU* 3.0 10.8 + - - +
225M CYS* 2.9 24.1 + - - +
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Residues in contact with HIS 222 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200M LEU* 3.9 26.2 - - + -
218M TYR 3.6 13.9 + - - +
219M GLN* 2.9 10.0 + - - +
221M TRP* 1.3 76.8 - - - +
223M GLU* 1.3 58.1 + - - +
225M CYS* 3.1 12.0 + - - +
226M ASP* 2.9 25.1 + - - +
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Residues in contact with GLU 223 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219M GLN 2.7 16.7 + - - +
220M LEU* 3.6 14.6 - - - +
222M HIS* 1.3 71.0 - - - +
224M LEU* 1.3 58.2 + - - +
226M ASP* 3.2 11.2 + - - +
227M LEU* 2.9 23.9 + - - +
247M GLY* 4.5 23.7 - - - +
250M ARG* 5.4 6.3 - - + -
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Residues in contact with LEU 224 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220M LEU 2.9 15.1 + - - +
221M TRP* 3.0 14.8 + - - +
223M GLU* 1.3 72.1 - - - +
225M CYS* 1.3 59.8 + - - +
227M LEU* 3.1 11.9 + - + +
228M ILE* 2.9 24.3 + - - +
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Residues in contact with CYS 225 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M LYS* 5.0 16.6 - - + -
196M ALA* 6.1 2.9 - - + -
221M TRP 2.9 11.3 + - - +
222M HIS* 3.1 14.3 + - + +
224M LEU* 1.3 75.2 - - - +
226M ASP* 1.3 59.4 + - - +
228M ILE* 3.0 11.8 + - - +
229M SER* 2.9 24.1 + - - -
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Residues in contact with ASP 226 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222M HIS 2.9 13.2 + - - +
223M GLU* 3.2 13.4 + - - +
225M CYS* 1.3 76.1 - - - +
227M LEU* 1.3 57.5 - - - +
229M SER* 3.1 11.0 + - - -
230M GLN* 2.9 24.4 + - - +
243M ILE* 4.0 31.5 - - + +
247M GLY* 5.6 2.5 - - - +
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Residues in contact with LEU 227 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223M GLU 2.9 13.3 + - - +
224M LEU* 3.1 15.0 + - + +
226M ASP* 1.3 72.7 - - - +
228M ILE* 1.3 61.7 + - - +
230M GLN* 3.1 26.3 + - + +
231M ASN* 3.3 7.4 + - - +
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Residues in contact with ILE 228 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224M LEU 2.9 12.4 + - - +
225M CYS* 3.0 14.6 + - - +
227M LEU* 1.3 77.2 - - - +
229M SER* 1.3 60.0 + - - +
231M ASN* 3.3 21.6 - - - +
233M ASP* 5.4 2.9 - - - +
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Residues in contact with SER 229 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225M CYS 2.9 12.0 + - - -
226M ASP* 3.1 15.4 + - - -
228M ILE* 1.3 75.3 - - - +
230M GLN* 1.3 57.7 + - - +
231M ASN 3.1 10.1 + - - +
233M ASP* 4.7 7.9 - - - +
234M LYS* 5.0 6.4 + - - +
239M ASN 6.1 1.1 - - - -
240M VAL* 5.9 1.0 - - - -
243M ILE* 5.1 7.9 - - - -
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Residues in contact with GLN 230 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226M ASP 2.9 13.1 + - - +
227M LEU* 3.1 17.6 + - - +
229M SER* 1.3 72.1 - - - +
231M ASN* 1.3 64.6 + - - +
240M VAL* 5.3 21.2 - - + +
243M ILE* 5.3 6.7 - - + +
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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