Contacts of the helix formed by residues 255 - 265 (chain f) in PDB entry 5M32
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 255 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233e SER* 3.5 13.2 + - - +
236e VAL* 3.8 33.0 - - - +
269e ALA* 3.1 36.2 + - + +
270e ILE* 5.6 1.7 - - - +
281e ALA* 4.7 8.6 + - - +
282e ASP* 5.2 1.8 - - - +
284e GLU* 6.1 0.2 - - - -
285e VAL* 4.1 24.4 - - - +
212f ALA* 5.0 4.0 - - + +
251f ARG* 3.1 56.4 + - + +
252f GLU* 3.1 44.5 + - - +
253f ILE 3.0 0.8 - - - -
254f GLN* 1.3 75.9 - - - +
256f THR* 1.3 65.5 + - - +
257f LEU 3.4 0.9 - - - -
258f MET* 3.4 12.1 + - - +
259f GLU* 3.3 15.2 + - - +
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Residues in contact with THR 256 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203f ILE* 5.1 4.3 - - + -
211f SER* 3.5 42.6 - - - +
212f ALA* 4.2 9.8 + - - +
215f ILE* 4.5 5.7 - - + +
238f ILE* 4.5 20.2 - - + -
252f GLU* 2.8 21.8 + - - -
253f ILE* 2.8 15.6 + - + +
255f ARG* 1.3 77.9 - - - +
257f LEU* 1.3 59.3 + - - +
258f MET 3.1 0.2 - - - -
259f GLU* 3.1 7.6 + - - +
260f LEU* 2.9 28.2 + - + +
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Residues in contact with LEU 257 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238f ILE* 3.3 42.5 - - + +
240f GLY* 5.1 4.7 - - - +
242f ARG* 3.4 29.2 - - - +
253f ILE* 2.7 17.9 + - + +
254f GLN* 4.5 8.1 - - + -
256f THR* 1.3 73.1 - - - +
258f MET* 1.3 56.7 + - - +
260f LEU* 4.1 17.0 - - + -
261f LEU* 2.7 48.9 + - + +
286f ASP* 3.5 16.6 - - + +
289f LEU* 4.3 16.6 - - + -
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Residues in contact with MET 258 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231e VAL* 4.6 0.5 - - - +
233e SER* 3.4 18.9 + - - +
266e GLU* 2.9 40.6 - - + +
268e ASP* 3.2 30.7 - - - +
269e ALA* 3.7 15.5 - - + +
311e THR* 5.6 0.2 - - - +
312e ASN* 4.6 4.7 - - + +
242f ARG* 3.4 38.1 - - - +
254f GLN 3.3 17.5 - - - +
255f ARG* 3.4 6.4 + - - +
256f THR 3.1 0.6 - - - -
257f LEU* 1.3 78.4 - - - +
259f GLU* 1.3 57.5 + - - +
261f LEU* 3.9 4.6 - - - +
262f ASN* 2.9 31.5 + - - +
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Residues in contact with GLU 259 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231e VAL* 3.4 22.2 - - - +
233e SER* 3.3 22.7 + - - -
212f ALA* 4.1 11.4 - - + +
215f ILE* 3.8 20.4 - - + -
216f ARG* 3.1 35.3 + - - +
255f ARG 3.3 2.9 + - - +
256f THR 3.1 7.4 + - - +
258f MET* 1.3 75.7 - - - +
260f LEU* 1.3 61.0 + - - +
262f ASN* 3.4 1.2 + - - -
263f GLN* 2.5 66.5 + - - +
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Residues in contact with LEU 260 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203f ILE* 6.4 0.9 - - + -
215f ILE* 3.7 39.4 - - + +
219f PHE* 3.9 10.4 - - + -
232f MET* 3.7 23.3 - - + -
235f ILE* 4.8 1.8 - - + -
238f ILE* 3.9 18.8 - - + -
256f THR* 2.9 17.9 + - + +
257f LEU* 4.1 20.2 - - + +
259f GLU* 1.3 76.0 - - - +
261f LEU* 1.3 59.6 + - - +
263f GLN 3.8 0.3 - - - -
264f MET* 2.9 56.7 + - - +
277f MET* 4.3 9.6 - - + -
289f LEU* 4.7 4.0 - - + -
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Residues in contact with LEU 261 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266e GLU* 3.7 15.0 - - - +
312e ASN* 3.8 3.8 - - - +
242f ARG* 4.8 0.4 - - - +
257f LEU* 2.7 34.4 + - + +
258f MET* 3.9 6.7 - - - +
260f LEU* 1.3 79.3 - - - +
262f ASN* 1.3 56.4 + - - +
263f GLN 3.1 1.6 - - - -
264f MET* 3.5 4.3 + - - +
265f ASP* 2.9 29.8 + - - +
288f ALA* 3.6 24.0 - - + -
289f LEU* 3.7 24.9 - - + -
294f ARG* 2.9 60.0 + - + +
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Residues in contact with ASN 262 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213e THR* 6.0 1.0 - - - +
229e ARG* 5.0 9.1 + - - +
231e VAL* 3.4 30.5 - - + +
265e ASP* 3.1 40.8 + - - +
266e GLU* 3.7 12.5 + - - +
258f MET 2.9 20.1 + - - +
259f GLU* 3.5 3.7 - - - +
261f LEU* 1.3 74.4 - - - +
263f GLN* 1.3 63.9 + - - +
265f ASP* 4.2 8.4 - - - +
266f GLY* 3.5 27.2 + - - +
267f PHE* 5.0 3.5 - - - -
294f ARG* 5.3 1.6 - - - +
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Residues in contact with GLN 263 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229e ARG* 6.3 0.4 - - - +
231e VAL* 6.1 0.7 - - + -
215f ILE* 3.6 1.4 - - - +
216f ARG* 3.4 35.4 + - - +
219f PHE* 3.2 41.8 - - + +
220f ASN* 5.0 6.1 + - - +
223f ARG* 5.0 4.4 + - - +
259f GLU* 2.5 40.8 + - - +
262f ASN* 1.3 84.3 - - - +
264f MET* 1.3 61.5 + - - +
265f ASP 3.2 0.4 - - - -
266f GLY* 3.9 8.0 + - - +
270f LEU* 3.4 27.0 - - + +
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Residues in contact with MET 264 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168f LYS* 3.8 22.2 - - - +
219f PHE* 4.2 13.4 - - + -
260f LEU* 2.9 44.6 + - + +
261f LEU* 3.8 3.1 - - - +
263f GLN* 1.3 77.5 - - - +
265f ASP* 1.3 63.3 + - - +
269f THR 5.1 0.3 - - - +
270f LEU* 4.1 5.2 - - - +
275f MET* 3.7 24.2 - - + -
277f MET* 4.0 14.6 - - + -
289f LEU* 4.7 8.3 - - + -
293f GLY 5.1 2.1 - - - +
294f ARG* 2.9 59.2 - - + +
295f LEU* 4.0 14.4 - - + -
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Residues in contact with ASP 265 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213e THR* 3.7 26.1 + - - +
217e LYS* 5.7 1.2 + - - -
501e ADP 3.9 11.5 + - - +
261f LEU 2.9 17.9 + - - +
262f ASN* 4.2 8.3 - - - +
263f GLN 4.3 0.9 - - - -
264f MET* 1.3 81.2 - - - +
266f GLY* 1.3 76.0 + - - +
267f PHE* 5.2 0.2 - - - -
268f ASP* 2.8 21.7 - - - +
269f THR* 4.4 2.9 - - - -
270f LEU* 5.5 0.5 - - - +
291f ARG* 4.9 1.2 + - - -
293f GLY 6.1 0.4 - - - -
294f ARG* 3.8 33.3 + - - +
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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