Contacts of the helix formed by residues 242 - 259 (chain H) in PDB entry 4MNE
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 VAL 242 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177H LEU* 4.8 12.3 - - + +
181H ARG* 4.4 28.5 - - + -
187H MET* 4.2 15.9 - - + +
241H SER* 1.3 74.7 - - - +
243H GLN* 1.3 63.8 + - - +
244H SER 3.2 0.4 - - - -
245H ASP* 3.3 27.0 + - + +
246H ILE* 3.6 14.6 + - + +
352H LEU* 3.8 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 243 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233H GLU* 4.8 1.1 - - - +
241H SER* 2.8 18.3 + - - +
242H VAL* 1.3 81.0 - - - +
244H SER* 1.3 61.7 + - - +
246H ILE* 3.0 22.3 + - - +
247H TRP 3.2 9.5 + - - -
346H PRO* 3.8 21.2 + - + +
347H ALA* 6.0 0.4 - - - -
349H ARG* 3.4 39.7 + - - +
350H ALA 3.0 24.0 + - - -
351H ASP* 3.1 27.9 - - - +
352H LEU 4.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 244 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187H MET* 4.5 4.7 - - - -
231H SER* 3.0 23.6 + - - -
233H GLU* 3.0 19.2 + - - -
234H ARG* 3.5 26.6 - - - +
240H TYR* 3.7 8.0 - - - +
241H SER 2.9 14.8 + - - -
243H GLN* 1.3 77.7 - - - +
245H ASP* 1.3 60.4 + - - +
247H TRP* 3.4 5.7 - - - +
248H SER* 3.0 28.2 + - - -
349H ARG* 4.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 245 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177H LEU* 4.2 16.0 - - + +
187H MET* 3.3 20.9 - - - +
188H HIS* 3.1 26.3 + - - +
189H ARG* 3.1 31.1 + - - -
190H ASP 4.0 1.6 + - - -
191H VAL* 4.1 16.4 + - + +
234H ARG* 5.0 1.0 + - - -
242H VAL* 3.3 14.0 + - + +
243H GLN 3.2 0.6 - - - -
244H SER* 1.3 76.6 - - - +
246H ILE* 1.3 61.1 + - - +
248H SER* 3.4 8.7 + - - -
249H MET* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 246 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177H LEU* 4.9 2.9 - - + -
242H VAL* 3.7 16.4 - - + +
243H GLN* 3.0 25.4 + - - +
245H ASP* 1.3 74.9 - - - +
247H TRP* 1.3 65.3 + - - +
249H MET* 3.3 13.2 + - + +
250H GLY 3.0 18.2 + - - -
341H CYS* 3.8 27.1 - - - +
349H ARG* 4.4 2.9 - - + -
350H ALA 3.3 28.9 - - - +
351H ASP 4.0 0.9 - - - -
352H LEU* 3.9 33.4 - - + +
355H LEU* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 247 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229H TYR 3.7 6.3 - - - -
230H MET 3.0 14.7 + - - -
231H SER* 3.3 29.6 - - - -
232H PRO* 3.3 27.6 - - + -
243H GLN 3.2 3.8 + - - +
244H SER 3.4 8.3 - - - +
246H ILE* 1.3 79.2 - - - +
248H SER* 1.3 65.9 + - - +
250H GLY 3.2 1.0 + - - -
251H LEU* 3.2 42.9 + - + +
263H ILE* 5.3 1.8 - - + -
317H ILE* 4.0 24.0 - - + -
322H PRO* 4.2 16.2 - - + -
323H PRO* 5.0 3.6 - - + -
341H CYS 3.4 13.2 + - - -
342H LEU* 3.1 56.1 - - + +
344H LYS* 4.5 6.5 - - + -
349H ARG* 3.8 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 248 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H ARG 6.0 0.5 - - - -
190H ASP* 5.9 0.3 + - - -
191H VAL* 3.3 30.2 + - - +
229H TYR* 2.8 28.2 + - - -
230H MET* 4.7 0.7 - - - -
231H SER 4.6 2.3 + - - -
244H SER 3.0 15.1 + - - -
245H ASP* 3.6 11.3 + - - -
246H ILE 3.3 0.4 - - - -
247H TRP* 1.3 79.3 - - - +
249H MET* 1.3 51.5 + - - +
251H LEU* 3.6 4.4 - - - +
252H SER* 2.6 37.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 249 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H SER* 4.1 15.9 - - - +
173H VAL* 3.5 41.5 - - + -
174H ILE* 3.9 20.0 - - + -
177H LEU* 4.9 2.9 - - + -
191H VAL* 4.3 6.4 - - + +
245H ASP 2.9 14.9 + - - +
246H ILE* 3.6 17.5 - - + +
247H TRP 3.2 0.2 - - - -
248H SER* 1.3 75.0 - - - +
250H GLY* 1.3 53.6 + - - +
252H SER* 2.9 8.9 + - - -
253H LEU* 2.7 55.0 + - + +
337H PHE* 4.7 0.2 - - + -
341H CYS* 4.3 9.4 - - - -
355H LEU* 4.2 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 250 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H ILE 3.0 10.3 + - - -
247H TRP 3.2 1.8 + - - -
249H MET* 1.3 74.5 - - - +
251H LEU* 1.3 51.7 + - - +
253H LEU* 2.8 33.2 + - - +
254H VAL* 2.9 19.1 + - - +
338H VAL* 4.9 4.1 - - - +
341H CYS* 3.7 26.0 - - - +
342H LEU* 4.1 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228H SER 4.3 4.9 - - - +
229H TYR* 3.8 42.4 - - + +
247H TRP* 3.2 36.1 + - + +
248H SER 3.6 2.5 - - - +
250H GLY* 1.3 74.2 - - - +
252H SER* 1.3 60.7 + - - +
254H VAL* 3.6 4.7 + - + +
255H GLU* 3.1 21.7 + - - +
261H TYR* 5.3 1.3 - - + -
262H PRO* 3.5 29.9 - - + +
263H ILE* 4.1 23.1 - - + -
317H ILE* 5.1 2.0 - - + -
323H PRO* 4.2 13.5 - - + -
342H LEU* 3.4 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 252 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191H VAL* 4.0 0.5 + - - +
192H LYS* 3.4 24.0 + - - -
193H PRO* 3.5 22.5 - - - +
196H ILE* 5.2 5.4 - - - -
229H TYR* 4.1 5.1 - - - -
248H SER 2.6 21.5 + - - -
249H MET* 2.9 12.9 + - - -
251H LEU* 1.3 75.4 - - - +
253H LEU* 1.3 58.7 + - - +
255H GLU* 3.0 8.5 + - - +
256H MET* 2.9 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H LEU* 3.7 32.5 - - + +
169H VAL* 4.6 7.0 - - + -
170H SER* 3.3 29.8 - - - +
249H MET* 2.7 41.9 + - + +
250H GLY* 2.8 11.1 + - - +
252H SER* 1.3 69.8 - - - +
254H VAL* 1.3 55.1 + - - +
256H MET* 3.2 10.8 + - + +
257H ALA* 2.6 40.2 + - - +
325H LEU* 5.6 0.2 - - - -
334H PHE* 4.9 8.1 - - + -
337H PHE* 3.9 22.2 - - + -
338H VAL* 4.8 9.2 - - + -
341H CYS* 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H GLY 2.9 21.2 + - - +
251H LEU* 3.7 7.2 - - - +
253H LEU* 1.3 71.8 - - - +
255H GLU* 1.3 57.6 - - - +
257H ALA* 4.2 5.2 - - - -
258H VAL* 2.8 45.6 + - + +
262H PRO* 3.5 24.9 - - + -
323H PRO* 5.0 3.6 - - + +
324H LYS 4.3 18.6 - - - +
325H LEU* 4.5 8.3 - - + -
338H VAL* 4.4 16.8 - - + +
342H LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 255 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H LEU* 3.7 17.3 - - + +
193H PRO* 4.2 10.4 - - + +
227H ARG* 3.9 16.8 + - - -
229H TYR* 2.5 41.8 + - - -
251H LEU 3.1 9.4 + - - +
252H SER 3.0 10.6 + - - +
254H VAL* 1.3 80.4 - - - +
256H MET* 1.3 57.7 + - - +
259H GLY* 2.9 25.3 + - - -
260H ARG 3.3 22.3 + - - +
261H TYR* 3.6 17.7 + - - -
262H PRO* 3.7 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 256 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H LEU* 3.8 35.9 - - + -
155H LEU* 3.7 30.4 - - + +
160H ARG* 3.8 1.7 - - - -
161H ILE* 3.1 35.5 + - + -
166H LEU* 3.5 31.2 - - + -
169H VAL* 4.5 9.0 - - + -
193H PRO* 4.3 13.9 - - + -
196H ILE* 4.8 4.7 - - + -
252H SER* 2.9 39.1 + - - +
253H LEU* 3.8 10.8 - - + +
255H GLU* 1.3 74.2 - - - +
257H ALA* 1.3 66.6 + - - +
258H VAL 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160H ARG* 3.4 15.8 - - - +
161H ILE 4.1 4.9 - - - +
166H LEU* 3.5 21.0 - - + +
253H LEU 2.6 23.0 + - - +
254H VAL 3.7 0.9 - - - +
256H MET* 1.3 76.4 - - - +
258H VAL* 1.3 60.1 + - - +
325H LEU* 3.6 28.7 - - + -
330H PHE* 3.9 20.1 - - + -
334H PHE* 4.2 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160H ARG* 3.5 20.3 - - - +
254H VAL* 2.8 38.9 + - + +
257H ALA* 1.3 74.5 - - - +
259H GLY* 1.3 57.8 + - - +
260H ARG* 4.1 24.2 - - + +
262H PRO* 5.8 0.9 - - + -
266H PRO* 5.7 7.6 - - + -
324H LYS 5.4 0.9 - - - +
325H LEU* 4.7 4.9 - - + -
326H PRO* 4.4 25.1 - - + -
330H PHE* 5.1 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 259 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H LEU* 4.4 8.7 - - - +
159H GLY 3.8 23.1 - - - +
160H ARG* 4.2 4.9 - - - -
255H GLU* 2.9 15.8 + - - -
257H ALA 3.6 1.2 - - - -
258H VAL* 1.3 74.0 - - - +
260H ARG* 1.3 62.4 + - - +
----------------------------------------------------------
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