Contacts of the helix formed by residues 240 - 251 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 3.6 15.9 - - - +
280A ASP* 3.4 23.8 + - - +
283A TYR* 3.7 24.0 - - + -
284A MET* 3.2 28.7 - - - +
207B GLY 4.6 4.9 - - - +
209B GLY 3.3 25.1 - - - +
210B THR* 4.1 5.6 - - - +
211B PRO* 4.6 1.2 - - - +
235B HIS 4.5 1.1 + - - +
236B ASP* 4.6 1.2 - - - +
238B TYR* 2.9 31.8 + - + +
239B GLY* 1.3 79.9 - - - +
241B ALA* 1.3 54.4 + - - +
242B LEU 3.5 2.0 - - - -
243B ALA* 3.3 4.9 + - - +
244B ASN* 2.7 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B CYS* 3.5 24.0 - - - +
235B HIS 3.4 22.2 + - - +
236B ASP* 3.0 25.6 + - + +
240B GLN* 1.3 75.3 - - - +
242B LEU* 1.3 58.0 + - - +
244B ASN* 3.3 2.0 + - - +
245B THR* 2.8 34.5 + - - -
276B LEU* 3.6 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLY 3.2 27.1 - - - +
240A GLN* 3.6 29.8 - - - +
243A ALA* 4.4 9.0 - - + +
236B ASP* 4.3 2.0 + - - -
239B GLY 5.3 0.8 + - - -
240B GLN 3.5 0.6 - - - -
241B ALA* 1.3 77.6 - - - +
243B ALA* 1.3 54.1 + - - +
245B THR* 3.2 4.0 + - - -
246B LEU* 2.7 34.3 + - - +
276B LEU* 4.0 22.2 - - + +
280B ASP* 4.4 6.3 - - + +
281B LEU* 4.2 25.4 - - + -
284B MET* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 4.3 31.1 - - + +
243A ALA* 4.7 11.1 - - - +
246A LEU* 4.2 10.9 - - + +
284A MET* 4.5 12.6 - - - -
211B PRO* 4.6 8.2 - - + +
239B GLY 5.2 0.8 + - - +
240B GLN* 3.3 10.6 + - - +
241B ALA 3.3 0.4 - - - -
242B LEU* 1.3 78.7 - - - +
244B ASN* 1.3 63.8 + - - +
246B LEU* 3.2 7.5 + - - +
247B MET* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 4.7 4.5 - - + -
204B ASP* 4.0 10.4 - - - +
209B GLY* 2.7 24.1 + - - +
210B THR* 3.0 37.1 + - - +
211B PRO* 3.2 8.3 - - - +
214B MET* 3.5 19.8 - - + +
234B CYS* 3.9 16.1 - - - +
235B HIS 5.3 0.5 - - - +
240B GLN* 2.7 30.0 + - - +
241B ALA* 3.7 3.4 + - - +
243B ALA* 1.3 74.5 - - - +
245B THR* 1.3 62.6 + - - +
247B MET* 3.4 7.7 + - - +
248B ALA 3.1 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B VAL* 4.7 3.9 - - + +
234B CYS* 3.9 14.8 + - - +
241B ALA 2.8 23.0 + - - -
242B LEU* 3.2 8.5 + - - -
244B ASN* 1.3 74.7 - - - +
246B LEU* 1.3 66.6 + - - +
248B ALA* 3.0 8.2 + - - +
249B LEU* 2.9 29.8 + - + +
256B VAL* 4.2 24.6 - - + +
257B ASP 5.6 0.2 + - - -
276B LEU* 3.4 14.7 - - - +
281B LEU* 4.0 26.0 - - + -
284B MET* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A PRO* 4.2 28.0 - - + -
243A ALA* 4.0 26.5 - - + +
246A LEU* 4.6 13.5 - - + -
247A MET* 5.1 3.8 - - + +
250A GLN* 5.3 0.9 - - - +
29B LEU* 4.6 12.6 - - + -
242B LEU 2.7 17.5 + - - +
243B ALA* 3.2 10.5 + - - +
245B THR* 1.3 73.1 - - - +
247B MET* 1.3 57.8 + - - +
249B LEU* 3.1 11.5 + - + +
250B GLN* 2.9 53.8 + - + +
284B MET* 4.3 17.9 - - + +
288B LEU* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 5.3 3.1 - - + +
250A GLN* 4.4 7.9 - - - +
211B PRO* 3.5 37.2 - - + +
214B MET* 4.1 10.8 - - + -
215B LYS* 3.3 47.3 - - + +
243B ALA 3.1 10.5 + - - +
244B ASN* 3.5 11.0 - - - +
245B THR 3.2 0.2 - - - -
246B LEU* 1.3 79.1 - - - +
248B ALA* 1.3 62.8 + - - +
250B GLN* 3.1 27.2 + - + +
251B MET* 3.1 48.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B MET* 4.2 5.1 - - + +
218B LEU* 3.4 26.7 - - + -
232B VAL* 3.9 26.2 - - + -
244B ASN 3.1 12.7 + - - +
245B THR 3.0 9.2 + - - +
247B MET* 1.3 74.8 - - - +
249B LEU* 1.3 63.8 + - + +
251B MET* 2.9 13.9 + - - +
252B GLY 3.2 0.5 + - - -
253B VAL* 3.2 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR 3.6 2.6 - - - +
29B LEU* 3.8 15.7 - - + +
30B PRO* 3.4 20.6 - - + +
33B VAL* 3.8 24.2 - - + -
245B THR* 2.9 26.2 + - + +
246B LEU* 3.4 11.4 - - + +
248B ALA* 1.3 76.9 - - - +
250B GLN* 1.3 56.8 + - - +
252B GLY 2.9 15.8 + - - -
253B VAL* 3.3 21.8 - - + +
256B VAL* 4.0 17.7 - - + -
281B LEU* 5.4 0.2 - - + -
284B MET* 3.7 29.6 - - + -
285B LEU* 3.8 17.0 - - + -
288B LEU* 5.7 1.6 - - + -
290B ILE* 5.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 5.4 1.4 - - - +
247A MET* 4.5 7.8 - - - +
250A GLN* 3.0 42.1 + - - -
28B THR* 3.4 26.6 + - - +
29B LEU* 3.9 15.7 - - + -
246B LEU* 2.9 39.9 + - + +
247B MET* 3.1 30.9 + - + +
249B LEU* 1.3 75.8 - - - +
251B MET* 1.3 67.8 + - + +
252B GLY 3.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR* 4.1 4.6 + - - -
215B LYS* 3.8 38.8 - - + +
218B LEU* 3.9 23.1 - - + -
219B SER* 5.5 4.3 - - - -
222B MET* 3.6 36.4 - - - +
227B LEU* 3.8 2.1 - - - +
247B MET* 3.1 34.7 + - + +
248B ALA 2.9 11.0 + - - +
250B GLN* 1.3 86.5 - - + +
252B GLY* 1.3 59.1 + - - +
253B VAL 3.6 0.6 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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