Contacts of the helix formed by residues 216 - 224 (chain M) in PDB entry 6CM9
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 ASP 216 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214M LEU* 3.3 11.8 + - + +
215M ASN* 1.3 77.1 - - - +
217M LYS* 1.3 70.7 + - - +
218M VAL* 3.3 5.2 + - - +
219M LEU* 3.3 17.2 + - + +
220M PHE* 3.0 28.4 + - - +
231M VAL* 4.0 6.1 - - - +
233M LEU* 3.6 33.1 + - + +
247M PHE* 4.5 6.2 - - - -
251M ARG* 2.4 46.9 + - + +
253M ILE* 6.0 2.5 - - + +
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Residues in contact with LYS 217 (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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216M ASP* 1.3 80.9 + - - +
218M VAL* 1.3 59.9 + - + +
220M PHE* 3.4 1.6 + - - +
221M ASP* 2.9 54.0 + - - +
226M GLY* 6.0 0.6 + - - -
230M SER* 3.9 25.8 + - - +
231M VAL 3.1 18.5 + - - +
232M GLU* 3.6 44.4 - - + +
233M LEU 5.1 0.2 - - - +
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Residues in contact with VAL 218 (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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216M ASP* 3.3 2.3 + - - +
217M LYS* 1.3 81.2 - - + +
219M LEU* 1.3 58.2 + - - +
221M ASP* 3.8 7.5 - - + +
222M ASN* 2.9 50.5 + - - +
233M LEU 5.9 1.8 - - - +
251M ARG* 3.5 42.8 - - + +
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Residues in contact with LEU 219 (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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213M GLY* 5.6 4.7 - - - -
214M LEU 4.3 21.3 - - - +
216M ASP* 3.3 19.4 + - + +
217M LYS 3.3 0.2 - - - -
218M VAL* 1.3 79.0 - - - +
220M PHE* 1.3 63.8 + - + +
222M ASN* 3.5 5.4 + - + -
223M THR* 2.9 43.9 + - - +
225M ARG* 4.8 5.8 - - - +
250M ASP 4.2 18.4 - - - +
251M ARG* 4.3 22.9 - - + +
252M THR* 5.8 1.1 - - - +
394M TYR* 5.6 5.6 - - + +
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Residues in contact with PHE 220 (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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214M LEU 4.6 2.2 - - - -
215M ASN* 3.6 34.8 - - + -
216M ASP 3.0 15.8 + - - +
217M LYS 4.0 3.8 - - - +
219M LEU* 1.3 80.9 - - + +
221M ASP* 1.3 58.5 + - - +
223M THR* 3.9 3.4 - - - -
224M GLY 3.2 3.1 + - - -
225M ARG* 2.7 80.1 + - + +
226M GLY* 4.9 0.9 - - - +
228M SER* 4.2 12.3 - - - -
229M LYS 3.7 11.7 - - - -
230M SER* 3.6 23.8 - - - -
393M ARG* 3.7 15.7 - - - -
123N ASP* 3.3 24.7 - - - -
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Residues in contact with ASP 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 LYS* 2.9 52.6 + - - +
218M VAL* 3.8 7.8 - - + +
219M LEU 3.2 0.2 - - - -
220M PHE* 1.3 77.8 - - - +
222M ASN* 1.3 65.6 + - - +
223M THR 3.2 0.6 + - - -
224M GLY* 3.6 10.2 + - - -
226M GLY* 3.5 24.2 - - - +
202N TYR* 5.0 7.1 + - - -
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Residues in contact with ASN 222 (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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218M VAL* 2.9 41.0 + - - +
219M LEU* 4.1 7.2 - - + +
221M ASP* 1.3 76.5 - - - +
223M THR* 1.3 57.5 + - - +
250M ASP* 5.7 5.8 - - + -
251M ARG* 4.6 5.5 - - - +
202N TYR* 3.2 36.6 - - + +
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Residues in contact with THR 223 (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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219M LEU* 2.9 28.2 + - - +
220M PHE 4.2 1.3 - - - -
221M ASP 3.2 0.2 - - - -
222M ASN* 1.3 78.3 - - - +
224M GLY* 1.3 56.7 + - - +
225M ARG* 3.4 42.5 + - + +
137N LEU* 5.3 1.3 - - + +
202N TYR* 3.3 31.1 + - - +
203N PHE* 4.0 26.9 - - + -
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Residues in contact with GLY 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 PHE 3.2 4.5 + - - -
221M ASP 3.6 9.4 + - - -
223M THR* 1.3 79.2 - - - +
225M ARG* 1.3 61.6 + - - +
226M GLY 3.4 6.5 + - - -
227M LYS* 5.9 2.4 - - - -
127N TYR 4.9 4.7 - - - +
129N PRO* 5.4 7.4 - - - +
137N LEU* 3.3 19.7 - - - +
199N HIS* 6.4 0.2 - - - -
202N TYR* 4.5 10.3 - - - -
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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