Contacts of the helix formed by residues 231 - 246 (chain B) in PDB entry 4KMR
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 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B GLN* 6.4 2.7 - - + -
229B THR* 3.0 23.6 + - - +
230B TRP* 1.3 73.3 - - - +
232B ARG* 1.3 66.5 + - - +
233B SER* 3.5 14.5 + - - -
234B SER* 2.7 31.1 + - - -
235B GLY 3.0 17.7 + - - -
258B ASP* 4.0 13.2 - - + +
259B LEU* 3.5 8.4 - - - +
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Residues in contact with ARG 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ALA 3.8 7.9 + - - -
288A ASP* 3.4 44.6 + - - +
291A TYR* 4.1 23.6 - - + -
292A THR* 5.9 2.6 - - - +
81B ALA* 4.5 11.5 - - - +
231B ASP* 1.3 75.4 - - - +
233B SER* 1.3 64.0 + - - +
235B GLY 3.2 1.2 + - - -
236B ALA* 2.9 21.0 + - - +
258B ASP* 2.8 51.2 + - + +
261B LEU* 3.6 28.9 - - + +
262B GLY* 3.4 10.0 - - - +
286B VAL* 4.6 1.2 - - - +
288B ASP* 3.1 36.0 + - - +
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Residues in contact with SER 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A TYR* 3.2 39.0 - - - -
231B ASP* 3.3 16.7 + - - -
232B ARG* 1.3 78.6 - - - +
234B SER* 1.3 60.9 + - - +
236B ALA* 3.3 1.7 + - - +
237B GLU* 3.0 45.4 + - - +
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Residues in contact with SER 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B VAL* 4.3 4.0 - - - +
228B GLU* 3.3 27.8 + - - +
229B THR* 3.1 28.1 + - - -
231B ASP* 2.7 23.5 + - - -
233B SER* 1.3 75.9 + - - +
235B GLY* 1.3 59.4 + - - +
237B GLU* 4.0 8.8 + - - +
238B ALA* 2.9 31.9 + - - +
259B LEU* 4.2 1.6 - - - -
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Residues in contact with GLY 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B LEU* 4.3 7.5 - - - +
227B VAL* 5.2 0.2 - - - -
231B ASP 3.0 11.3 + - - -
232B ARG 3.2 2.9 + - - -
234B SER* 1.3 76.8 - - - +
236B ALA* 1.3 60.8 + - - +
238B ALA* 4.2 1.2 - - - +
239B MSE 3.0 28.2 + - - +
259B LEU* 3.6 31.3 - - - +
263B ALA* 3.8 8.3 + - - +
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Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A TYR* 3.9 23.3 - - + -
232B ARG 2.9 15.3 + - - +
233B SER 3.7 4.5 - - - +
235B GLY* 1.3 77.2 - - - +
237B GLU* 1.3 57.7 + - + +
240B ALA* 2.9 20.7 + - - +
262B GLY 3.3 23.6 - - - +
265B ARG* 5.3 4.5 - - + -
266B SER* 2.7 22.8 + - - +
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A TYR* 4.6 6.1 + - + +
233B SER* 3.0 35.7 + - - +
234B SER* 4.0 7.1 + - - +
235B GLY 3.3 0.2 - - - -
236B ALA* 1.3 78.0 - - + +
238B ALA* 1.3 62.5 + - - +
240B ALA* 3.4 5.6 + - - +
241B ARG* 3.1 22.9 + - - +
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B LEU* 4.0 11.4 - - + -
225B VAL* 4.1 10.3 - - + +
226B PRO 4.2 4.3 - - - +
227B VAL* 3.9 22.4 - - + -
234B SER 2.9 18.5 + - - +
237B GLU* 1.3 77.3 - - - +
239B MSE 1.3 64.7 + - - +
241B ARG* 3.3 8.1 + - - +
242B VAL* 3.1 27.8 + - - +
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Residues in contact with MSE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B MSE 3.4 31.2 - - - +
190B LEU* 3.8 27.6 - - + -
235B GLY 3.0 19.1 + - - +
238B ALA* 1.3 73.8 - - - +
240B ALA* 1.3 65.7 + - - +
242B VAL* 3.5 7.9 + - + +
243B LEU* 3.0 40.3 + - + +
249B MSE 5.3 2.7 - - - +
252B VAL* 4.0 21.5 - - + -
263B ALA* 3.8 32.5 - - - +
266B SER* 3.9 4.3 - - - -
267B LEU* 4.2 14.8 - - + -
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ALA 2.9 20.2 + - - +
237B GLU* 3.8 5.4 - - - +
238B ALA 3.3 0.2 - - - -
239B MSE 1.3 77.8 - - - +
241B ARG* 1.3 56.1 + - - +
243B LEU* 3.4 0.7 + - - +
244B ASP* 2.9 36.5 + - - +
266B SER* 3.8 8.4 - - - +
269B GLU* 5.0 1.3 - - - +
270B ARG* 3.5 30.5 - - - +
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ASP 5.6 1.4 + - - -
225B VAL* 4.5 11.7 - - - +
226B PRO* 5.9 2.2 - - - +
237B GLU 3.1 17.0 + - - +
238B ALA* 3.7 6.7 + - - +
239B MSE 3.3 0.2 - - - -
240B ALA* 1.3 75.9 - - - +
242B VAL* 1.3 91.9 + - - +
244B ASP* 3.9 3.1 - - - +
245B ALA* 3.0 37.1 + - - +
247B VAL* 5.1 4.9 - - - +
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B MSE 3.9 21.5 - - + -
222B ASP 5.1 0.9 - - - +
225B VAL* 3.9 20.4 - - + -
238B ALA 3.1 12.2 + - - +
239B MSE 3.5 24.9 - - + +
241B ARG* 1.3 111.9 - - - +
243B LEU* 1.3 65.5 + - - +
245B ALA* 3.4 4.3 + - - +
246B GLY 3.3 3.8 + - - -
247B VAL* 3.2 38.3 + - + +
249B MSE 4.2 7.2 - - + -
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B MSE 3.0 41.5 + - + +
240B ALA 3.9 0.9 - - - +
242B VAL* 1.3 80.0 - - + +
244B ASP* 1.3 63.7 + - - +
246B GLY* 3.1 14.2 + - - -
247B VAL 5.2 3.8 - - - +
249B MSE 4.1 22.9 - - + -
266B SER* 3.8 13.5 - - - +
267B LEU* 3.9 24.5 - - + -
270B ARG* 3.8 30.1 - - - -
272B VAL* 4.5 12.8 - - + -
278B VAL* 5.8 0.2 - - + -
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Residues in contact with ASP 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ALA* 2.9 18.5 + - - +
241B ARG* 4.2 2.9 - - - +
243B LEU* 1.3 77.0 - - - +
245B ALA* 1.3 60.3 + - - +
246B GLY* 3.2 0.9 + - - -
270B ARG* 2.9 41.2 + - - +
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Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B ARG* 3.0 36.6 + - - +
242B VAL* 3.7 7.0 - - - +
243B LEU 3.2 0.4 - - - -
244B ASP* 1.3 76.1 - - - +
246B GLY* 1.3 59.6 + - - +
247B VAL* 3.5 7.7 - - + +
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Residues in contact with GLY 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B LEU 3.1 15.1 + - - -
244B ASP 3.2 1.6 - - - -
245B ALA* 1.3 79.8 - - - +
247B VAL* 1.3 66.0 + - - +
248B ARG* 3.4 15.8 + - - +
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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