Contacts of the helix formed by residues 228 - 247 (chain C) in PDB entry 5MLE
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 PRO 228 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A GLN* 3.6 35.2 - - - +
208C GLU* 5.5 4.5 - - + -
224C VAL* 3.7 4.4 - - + +
225C LEU* 4.0 9.2 - - - +
226C SER 3.6 7.2 - - - +
227C ARG* 1.3 92.8 - - - +
229C GLU* 1.3 61.9 + - - +
230C GLU* 3.1 19.5 + - - +
231C VAL* 3.2 28.9 + - + +
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Residues in contact with GLU 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C ARG 3.7 1.3 + - - -
228C PRO* 1.3 71.4 - - - +
230C GLU* 1.3 72.8 + - - +
231C VAL 3.2 0.4 - - - -
232C GLU* 3.1 20.7 + - - +
233C ALA* 3.1 15.0 + - - +
257C SER* 3.5 28.2 + - - -
258C LYS* 3.9 9.2 + - - +
259C SER* 2.8 38.2 + - - +
308C SER* 3.6 22.1 + - - -
309C PRO* 5.7 0.7 - - - +
310C ASP* 5.0 6.2 - - - +
313C THR* 5.2 0.9 + - - -
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Residues in contact with GLU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A THR* 3.8 14.9 + - + +
244A ASN* 6.2 4.0 - - + -
245A GLN* 4.2 22.7 + - - +
228C PRO* 3.1 12.9 + - - +
229C GLU* 1.3 94.1 + - + +
231C VAL* 1.3 55.9 + - - +
233C ALA* 4.1 4.1 - - - +
234C GLU* 3.0 30.3 + - - +
259C SER* 5.5 3.8 - - - +
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Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A THR* 4.7 5.6 - - + -
245A GLN* 4.9 3.1 - - + -
200C GLU* 4.4 11.2 - - + +
201C ASN* 3.4 27.1 + - + +
204C ILE* 4.1 32.3 - - + -
205C ILE* 4.3 26.9 - - + -
226C SER 5.8 0.2 - - - +
227C ARG* 4.4 6.5 - - - +
228C PRO* 3.2 31.9 - - + +
229C GLU 3.2 0.8 - - - -
230C GLU* 1.3 78.4 - - + +
232C GLU* 1.3 67.5 + - - +
234C GLU* 4.1 5.6 - - - +
235C ALA* 3.3 13.0 + - - +
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Residues in contact with GLU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C ALA* 3.3 22.0 - - + +
200C GLU* 4.1 7.4 - - + +
229C GLU* 3.1 12.4 + - - +
231C VAL* 1.3 80.2 - - + +
233C ALA* 1.3 59.2 + - - +
235C ALA 3.1 3.3 + - - -
236C VAL* 2.9 34.2 + - + +
252C ILE* 5.5 2.3 - - + +
253C THR 5.2 0.9 - - - +
254C LYS 3.4 8.5 - - - +
255C VAL* 3.6 3.1 - - - -
256C MET* 3.1 22.0 + - - +
257C SER* 2.7 30.5 + - - -
260C SER* 2.8 26.6 + - - -
305C PRO* 4.1 22.0 - - + +
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Residues in contact with ALA 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ASN* 5.3 0.4 - - - -
229C GLU 3.1 6.4 + - - +
230C GLU* 4.1 4.9 - - - +
232C GLU* 1.3 77.9 - - - +
234C GLU* 1.3 65.3 + - - +
236C VAL* 3.2 3.3 + - - +
237C ASN* 3.0 24.7 + - - +
259C SER* 3.6 42.2 - - - +
260C SER* 3.9 10.7 - - - +
263C VAL* 4.3 11.2 - - + +
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Residues in contact with GLU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLU* 3.4 13.2 - - - +
237A ASN* 4.1 13.1 - - - +
238A ARG* 3.6 17.6 + - + +
241A THR* 3.3 33.7 - - + +
201C ASN* 2.8 32.8 + - + +
230C GLU 3.0 21.3 + - - +
231C VAL* 4.1 4.5 - - - +
232C GLU 3.4 0.2 - - - -
233C ALA* 1.3 75.9 - - - +
235C ALA* 1.3 58.9 + - - +
237C ASN* 3.2 4.2 + - - +
238C ARG* 2.8 48.9 + - - -
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Residues in contact with ALA 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C MET* 3.5 24.8 - - + +
199C ALA* 3.5 12.6 - - - -
200C GLU 3.5 24.0 - - - +
201C ASN 3.6 2.5 - - - +
231C VAL 3.3 16.0 + - - +
232C GLU 3.1 5.0 + - - +
234C GLU* 1.3 84.5 - - - +
236C VAL* 1.3 64.4 + - - +
238C ARG* 3.4 2.9 + - - +
239C ALA* 3.1 21.8 + - - +
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Residues in contact with VAL 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C ALA* 3.4 21.1 - - + +
232C GLU* 2.9 27.3 + - + +
233C ALA* 3.2 7.4 + - - +
235C ALA* 1.3 75.4 - - - +
237C ASN* 1.3 63.5 + - - +
239C ALA* 3.5 4.7 + - - +
240C ILE* 3.2 37.8 + - + +
252C ILE* 3.9 23.8 - - + -
260C SER* 4.0 16.6 - - - +
263C VAL* 4.2 7.6 - - + -
264C ILE* 4.0 22.4 - - + -
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Residues in contact with ASN 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ALA 5.3 0.2 - - - -
234A GLU* 3.9 26.0 - - - +
237A ASN* 3.9 23.1 - - - +
233C ALA 3.0 12.5 + - - +
234C GLU 3.2 10.7 + - - +
236C VAL* 1.3 76.7 - - - +
238C ARG* 1.3 62.8 + - - +
240C ILE* 3.2 8.8 + - - +
241C THR* 3.0 25.7 + - - -
263C VAL* 4.0 23.3 - - + +
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Residues in contact with ARG 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP* 4.2 4.2 + - - -
201A ASN* 4.7 1.3 - - - +
234A GLU* 3.4 30.5 - - + +
238A ARG* 3.6 11.0 - - - +
168C MET* 3.1 34.6 + - + +
176C LEU 6.0 0.4 + - - -
178C ASP* 3.2 38.0 + - - +
181C ILE* 5.4 0.6 - - - +
200C GLU 5.2 0.2 + - - -
201C ASN* 3.0 27.8 - - - +
234C GLU* 2.8 39.4 + - - +
235C ALA* 3.8 4.7 - - - +
236C VAL 3.4 0.2 - - - -
237C ASN* 1.3 79.6 + - - +
239C ALA* 1.3 63.4 + - - +
241C THR* 3.2 11.2 + - - -
242C ILE* 3.0 35.4 + - + +
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Residues in contact with ALA 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C MET* 4.1 17.9 - - - +
181C ILE* 6.0 3.6 - - + -
185C LEU* 4.7 2.1 - - - +
197C VAL* 4.4 19.5 - - + -
235C ALA 3.1 17.6 + - - +
236C VAL* 3.7 5.8 - - - +
237C ASN 3.3 0.2 - - - -
238C ARG* 1.3 75.8 - - - +
240C ILE* 1.3 58.3 + - - +
242C ILE* 3.3 8.6 + - - +
243C ALA* 2.7 29.8 + - - +
250C LEU* 3.6 16.8 - - + +
252C ILE* 4.9 1.3 - - + -
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Residues in contact with ILE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C VAL* 3.2 26.0 + - + +
237C ASN* 3.2 8.6 + - - +
239C ALA* 1.3 74.3 - - - +
241C THR* 1.3 68.0 + - - +
243C ALA* 3.1 1.6 + - - -
244C ASN* 2.8 32.6 + - - +
250C LEU* 3.7 19.3 - - + -
263C VAL* 3.9 26.9 - - + +
264C ILE* 5.0 1.3 - - - -
267C ALA* 4.2 20.4 - - + -
272C THR* 3.7 26.7 - - + +
274C VAL* 4.2 15.3 - - + -
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Residues in contact with THR 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ILE* 4.2 16.4 - - + -
230A GLU* 3.9 34.8 + - + +
231A VAL* 4.7 4.3 - - + +
234A GLU* 3.1 28.5 - - + +
237C ASN* 3.0 19.7 + - - -
238C ARG 3.2 7.9 - - - -
240C ILE* 1.3 78.0 - - - +
242C ILE* 1.3 62.1 + - - +
244C ASN* 3.5 6.0 + - - +
245C GLN* 3.2 24.6 + - + +
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Residues in contact with ILE 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ILE* 3.8 22.4 - - + -
168C MET* 6.1 0.7 - - + -
178C ASP* 4.1 37.9 - - + +
181C ILE* 4.4 15.5 - - + -
182C TYR* 4.0 34.5 - - + +
185C LEU* 4.2 11.4 - - + -
238C ARG* 3.0 23.8 + - + +
239C ALA* 3.7 8.5 - - - +
240C ILE 3.0 0.2 - - - -
241C THR* 1.3 74.1 - - - +
243C ALA* 1.3 61.0 + - - +
245C GLN* 3.3 7.3 + - - +
246C THR* 2.6 35.5 + - - +
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Residues in contact with ALA 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C LEU* 3.9 15.6 - - + +
239C ALA 2.7 20.7 + - - +
240C ILE* 3.1 4.7 + - + +
242C ILE* 1.3 72.8 - - - +
244C ASN* 1.3 61.1 + - - +
246C THR* 3.2 2.0 + - - -
247C ASN* 2.8 24.8 + - - -
248C CYS 3.0 29.1 + - - +
250C LEU* 3.7 24.2 - - + -
272C THR* 5.9 2.0 - - + -
273C VAL 5.6 0.7 - - - +
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Residues in contact with ASN 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLU* 6.1 6.1 - - + +
240C ILE* 2.8 26.6 + - - +
241C THR* 3.9 4.8 - - - +
243C ALA* 1.3 69.8 - - - +
245C GLN* 1.3 66.0 + - - +
246C THR 3.2 1.6 - - - -
247C ASN* 3.3 6.9 + - - -
272C THR* 3.2 44.8 + - - +
273C VAL 4.6 0.7 + - - -
604C EDO 2.9 42.2 + - - +
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Residues in contact with GLN 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ILE* 4.2 18.2 - - + -
208A GLU* 3.0 34.9 - - - +
211A ARG* 5.7 1.7 + - - -
228A PRO* 3.5 32.1 - - - +
230A GLU* 4.1 22.6 + - - +
231A VAL* 4.9 1.9 - - + +
182C TYR* 4.2 14.1 + - + -
189C ARG* 5.4 0.3 + - - -
241C THR* 3.2 18.3 + - + +
242C ILE* 3.3 8.2 + - - +
244C ASN* 1.3 79.4 + - - +
246C THR* 1.3 58.9 + - - +
247C ASN* 3.5 4.9 - - - +
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Residues in contact with THR 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C TYR* 4.3 15.5 + - + +
185C LEU* 3.7 13.1 - - + +
186C SER* 3.5 44.4 - - - +
189C ARG* 2.7 33.1 + - - +
242C ILE* 2.6 27.7 + - - +
243C ALA 3.7 3.6 - - - -
244C ASN 3.2 0.2 - - - -
245C GLN* 1.3 78.3 - - - +
247C ASN* 1.3 69.2 + - - +
248C CYS* 4.1 6.7 - - + -
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Residues in contact with ASN 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C ARG* 3.5 20.5 + - - +
243C ALA 2.8 9.1 + - - -
244C ASN 3.3 7.2 + - - -
245C GLN 3.5 4.3 - - - +
246C THR* 1.3 80.2 - - - +
248C CYS* 1.3 57.4 + - - +
249C PRO* 3.8 4.7 - - - +
482C ILE* 5.5 13.0 - - + +
604C EDO 2.5 39.5 + - - -
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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