Contacts of the helix formed by residues 240 - 251 (chain C) in PDB entry 3MP4
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 GLN 240 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207C GLY 4.2 5.8 - - - +
209C GLY 3.1 26.2 - - - +
210C THR* 3.8 5.2 - - - +
211C PRO* 4.5 2.1 - - - +
235C HIS 4.6 1.5 + - - +
236C ASP* 4.7 0.6 - - - +
238C TYR* 2.9 30.2 + - + +
239C GLY* 1.3 82.3 - - - +
241C ALA* 1.3 58.6 + - - +
242C LEU 3.6 1.3 - - - -
243C ALA* 3.4 4.7 + - + +
244C ASN* 2.9 37.5 + - - +
242D LEU* 3.7 9.7 - - - +
280D ASP* 3.3 23.2 + - - +
283D TYR* 3.6 25.6 - - + -
284D MET* 3.1 30.4 - - - +
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Residues in contact with ALA 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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234C CYS* 3.7 19.8 - - - +
235C HIS 3.7 10.8 + - - +
236C ASP* 3.0 43.6 + - + +
239C GLY 3.5 0.2 - - - -
240C GLN* 1.3 77.0 - - - +
242C LEU* 1.3 62.0 + - - +
245C THR* 3.0 26.1 + - - -
276C LEU* 3.7 16.4 - - + -
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Residues in contact with LEU 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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236C ASP* 4.5 1.6 + - - -
239C GLY 5.3 0.8 + - - -
240C GLN 3.6 0.2 - - - -
241C ALA* 1.3 78.4 - - - +
243C ALA* 1.3 59.3 + - - +
245C THR* 3.3 4.6 + - - -
246C LEU* 2.9 28.1 + - - +
276C LEU* 3.9 20.7 - - + +
280C ASP* 4.1 7.0 - - + +
281C LEU* 3.9 26.5 - - + -
284C MET* 3.7 37.0 - - + +
239D GLY 3.4 25.8 - - - +
240D GLN* 3.4 24.0 - - - +
243D ALA* 4.3 9.6 - - + +
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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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211C PRO* 4.7 2.8 - - + +
239C GLY 5.4 0.6 + - - -
240C GLN* 3.4 7.9 + - - +
241C ALA 3.3 0.6 - - - -
242C LEU* 1.3 78.2 - - - +
244C ASN* 1.3 66.1 + - - +
246C LEU* 3.4 7.9 + - - +
247C MET* 3.2 20.4 + - - +
242D LEU* 4.3 30.2 - - + +
243D ALA* 4.6 16.7 - - - +
246D LEU* 4.3 13.4 - - + +
284D MET* 4.5 12.1 - - - -
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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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172C LEU* 4.2 4.9 - - - +
204C ASP* 4.1 6.1 - - - +
209C GLY* 2.8 29.6 + - - +
210C THR* 3.0 10.7 + - - +
211C PRO* 3.0 35.0 - - - +
214C MET* 3.5 18.0 - - + +
234C CYS* 3.7 19.6 - - - +
235C HIS 5.7 0.5 - - - +
240C GLN* 2.9 27.3 + - - +
241C ALA 3.7 0.2 - - - +
243C ALA* 1.3 73.2 - - - +
245C THR* 1.3 65.9 + - - +
247C MET* 3.3 9.3 + - - +
248C ALA 3.1 16.5 + - - -
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Residues in contact with THR 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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232C VAL* 5.2 1.7 - - + +
234C CYS* 3.7 15.7 + - - +
241C ALA 3.0 14.9 + - - -
242C LEU* 3.5 11.4 - - - -
244C ASN* 1.3 74.7 - - - +
246C LEU* 1.3 66.8 + - - +
248C ALA* 2.8 21.0 + - + +
249C LEU* 2.8 24.8 + - + +
256C VAL* 3.8 30.4 - - + +
276C LEU* 3.9 12.2 - - - +
281C LEU* 4.1 19.1 - - + -
284C MET* 4.8 1.1 - - + -
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Residues in contact with LEU 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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29C LEU* 4.6 7.6 - - + -
242C LEU 2.9 13.8 + - - +
243C ALA* 3.5 11.9 - - - +
245C THR* 1.3 75.5 - - - +
247C MET* 1.3 57.4 + - - +
249C LEU* 3.2 16.5 + - + +
250C GLN* 2.9 67.8 + - + +
284C MET* 4.4 16.4 - - + +
288C LEU* 4.4 7.9 - - + -
211D PRO* 4.2 30.5 - - + -
243D ALA* 5.2 9.4 - - + +
246D LEU* 4.4 15.9 - - + -
247D MET* 5.9 3.6 - - + +
250D GLN* 4.8 2.0 - - - +
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Residues in contact with MET 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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211C PRO* 3.4 38.1 - - + +
214C MET* 4.0 11.0 - - + -
215C LYS* 4.1 22.0 - - + +
243C ALA 3.2 9.3 + - - +
244C ASN 3.4 10.1 - - - +
245C THR 3.1 0.4 - - - -
246C LEU* 1.3 77.7 - - - +
248C ALA* 1.3 65.3 + - - +
250C GLN* 3.1 35.3 + - + +
251C MET* 3.0 36.9 + - + +
246D LEU* 5.3 1.8 - - + -
250D GLN* 4.6 6.1 - - - +
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Residues in contact with ALA 248 (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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214C MET* 4.3 2.9 - - + -
218C LEU* 3.3 26.2 - - + -
232C VAL* 3.6 25.6 - - + -
244C ASN 3.1 11.9 + - - +
245C THR* 2.8 13.1 + - + +
247C MET* 1.3 76.8 - - - +
249C LEU* 1.3 62.3 + - + +
251C MET* 3.1 11.1 + - - +
252C GLY 3.1 0.5 + - - -
253C VAL* 3.0 28.6 + - + +
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Residues in contact with LEU 249 (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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28C THR 3.5 3.8 - - - +
29C LEU* 3.8 17.3 - - + -
30C PRO* 3.5 21.6 - - + +
33C VAL* 3.9 28.3 - - + -
245C THR* 2.8 26.7 + - + +
246C LEU* 3.2 14.6 + - + +
248C ALA* 1.3 75.4 - - + +
250C GLN* 1.3 64.3 + - - +
252C GLY 3.0 10.0 + - - -
253C VAL* 3.3 23.1 - - + +
254C SER* 4.9 0.7 - - - -
256C VAL* 5.6 4.5 - - + -
284C MET* 3.9 19.3 - - + -
285C LEU* 3.9 25.4 - - + -
288C LEU* 5.2 0.4 - - + -
290C ILE* 4.8 2.0 - - + -
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Residues in contact with GLN 250 (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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28C THR* 3.9 22.0 + - - +
29C LEU* 4.5 16.4 - - + -
246C LEU* 2.9 38.5 + - + +
247C MET* 3.1 30.1 + - + +
249C LEU* 1.3 77.0 - - - +
251C MET* 1.3 69.0 + - + +
252C GLY 3.5 0.2 + - - -
246D LEU* 5.3 0.2 - - - +
247D MET* 4.7 5.7 - - - +
250D GLN* 2.9 43.9 + - - -
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Residues in contact with MET 251 (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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28C THR 5.9 0.7 - - - -
215C LYS* 3.9 36.6 - - + +
218C LEU* 4.0 22.7 - - + -
219C SER* 5.7 4.3 - - - -
222C MET* 3.7 37.5 - - - +
227C LEU* 3.9 2.4 - - - +
247C MET* 3.0 32.0 + - + +
248C ALA 3.4 9.6 - - - +
249C LEU 3.0 0.4 - - - -
250C GLN* 1.3 91.4 - - + +
252C GLY* 1.3 56.3 + - - +
253C VAL* 3.7 1.1 - - + +
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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