Contacts of the helix formed by residues 243 - 251 (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 ARG 243 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212B ASN* 3.5 30.4 + - - +
213B GLU* 5.1 4.4 + - - +
214B CYS 5.4 2.0 + - - -
219B GLN* 5.6 3.6 - - - +
156M ALA 5.5 1.6 + - - -
157M VAL* 5.5 3.6 - - - +
159M TRP* 3.4 38.2 - - - -
240M GLN* 3.6 19.0 + - - +
241M CYS 3.3 8.3 + - - +
242M VAL* 1.3 73.3 + - - +
244M LEU* 1.3 61.6 + - - +
245M SER* 3.4 4.7 - - - +
246M ARG* 3.8 26.9 + - + +
247M PHE* 3.4 18.0 + - - +
252M THR 4.7 1.9 - - - +
254M SER* 3.2 19.1 + - - +
256M ILE* 4.5 16.8 - - + +
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Residues in contact with LEU 244 (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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212B ASN* 6.2 0.2 - - - -
246B PRO* 3.3 28.8 - - + +
247B ARG* 3.4 26.7 - - - +
249B SER* 3.3 33.9 - - - +
250B HIS* 3.9 24.7 - - + -
238M PHE* 3.6 27.8 - - + -
239M HIS 5.0 1.3 - - - +
240M GLN 5.6 0.4 - - - +
242M VAL* 3.2 15.5 + - + +
243M ARG* 1.3 72.7 - - - +
245M SER* 1.3 60.2 + - - +
247M PHE* 3.4 7.5 + - + +
248M GLU* 2.9 28.9 + - - +
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Residues in contact with SER 245 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ASN* 4.3 25.2 + - - +
246B PRO* 4.4 10.0 - - - +
247B ARG* 4.8 2.4 - - - +
243M ARG* 5.0 3.5 - - - +
244M LEU* 1.3 78.8 + - - +
246M ARG* 1.3 68.2 + - - +
248M GLU* 3.1 6.8 + - - +
249M ASN* 3.0 37.5 + - - -
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Residues in contact with ARG 246 (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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209M GLU* 3.1 26.3 + - - -
211M ARG* 4.4 19.0 - - - +
243M ARG* 3.8 23.9 + - + +
244M LEU 3.4 0.4 - - - -
245M SER* 1.3 87.5 + - - +
247M PHE* 1.3 61.8 + - - +
249M ASN* 4.4 9.2 - - - +
250M ASP* 3.3 26.8 + - - +
252M THR* 3.7 22.7 + - - +
254M SER* 3.5 19.7 + - - -
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Residues in contact with PHE 247 (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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249B SER* 4.0 21.3 - - - -
216M ASP* 4.5 4.3 - - - -
236M VAL* 4.4 12.6 - - + -
238M PHE* 3.5 44.9 - + + -
242M VAL* 4.8 2.0 - - + -
243M ARG 3.4 12.3 + - - +
244M LEU* 3.4 13.6 + - + +
245M SER 3.2 0.4 - - - -
246M ARG* 1.3 79.5 - - - +
248M GLU* 1.3 66.4 + - - +
251M ARG* 3.1 78.4 + - - -
252M THR 3.3 12.9 + - - +
253M ILE* 3.9 18.4 - - + -
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Residues in contact with GLU 248 (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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242B GLU 5.6 2.0 - - - +
245B THR* 4.9 5.6 - - + +
246B PRO* 3.7 33.2 - - + +
249B SER* 5.1 4.9 + - - -
283B LYS* 2.6 40.0 + - - +
244M LEU 2.9 17.3 + - - +
245M SER* 3.1 5.3 + - - +
247M PHE* 1.3 84.1 - - + +
249M ASN* 1.3 68.2 + - - +
251M ARG* 5.0 6.4 + - - +
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Residues in contact with ASN 249 (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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245M SER* 3.0 25.7 + - - +
246M ARG* 4.1 7.6 - - - +
247M PHE 3.3 0.4 - - - -
248M GLU* 1.3 81.6 - - - +
250M ASP* 1.3 71.1 + - + +
251M ARG* 3.8 1.8 - - - +
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Residues in contact with ASP 250 (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* 4.2 12.5 - - - +
222M ASN* 5.7 4.5 - - + -
246M ARG* 3.3 11.8 + - - +
249M ASN* 1.3 83.2 - - + +
251M ARG* 1.3 72.9 + - - +
252M THR* 3.1 21.1 + - - -
204N LYS* 2.6 34.2 + - - +
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Residues in contact with ARG 251 (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* 2.4 38.7 + - - +
218M VAL* 3.5 44.4 - - + +
219M LEU* 4.3 31.7 - - + +
222M ASN* 4.6 4.5 - - - +
233M LEU* 4.6 14.3 + - - +
236M VAL* 4.8 3.0 - - - +
247M PHE* 3.1 59.5 + - + -
248M GLU* 5.5 5.5 + - - +
249M ASN 5.3 0.9 - - - +
250M ASP* 1.3 80.7 - - - +
252M THR* 1.3 59.4 + - - +
253M ILE* 3.9 5.9 + - - +
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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