Contacts of the helix formed by residues 241 - 259 (chain D) 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 SER 241 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D MET* 3.6 18.3 - - - +
239D HIS* 4.8 8.7 - - - -
240D TYR* 1.3 77.1 - - - +
242D VAL* 1.3 60.1 + - - +
243D GLN* 2.9 23.4 + - - +
244D SER* 2.7 35.5 + - - +
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Residues in contact with VAL 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D LEU* 4.7 12.1 - - + +
181D ARG* 3.9 40.6 - - + +
187D MET* 3.9 19.9 - - + +
241D SER* 1.3 81.4 + - - +
243D GLN* 1.3 75.1 + - - +
244D SER 3.1 0.4 - - - -
245D ASP* 3.0 27.1 + - + +
246D ILE* 3.2 12.4 + - + +
352D LEU* 3.8 31.0 - - + +
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Residues in contact with GLN 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D GLU* 4.6 0.4 - - - +
241D SER* 2.7 20.9 + - - +
242D VAL* 1.3 82.2 - - + +
244D SER* 1.3 60.0 + - - +
246D ILE* 3.3 20.9 + - - +
247D TRP 3.3 3.5 + - - -
346D PRO* 3.2 45.2 + - + +
349D ARG* 3.2 29.1 + - - +
350D ALA 2.6 28.8 + - - -
351D ASP* 3.4 23.1 - - - +
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Residues in contact with SER 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D MET* 4.3 7.2 - - - -
231D SER* 2.9 26.2 + - - -
233D GLU* 3.2 13.7 + - - -
234D ARG* 3.2 30.1 - - - +
240D TYR* 3.3 11.4 - - - +
241D SER 2.7 15.9 + - - +
243D GLN* 1.3 73.8 - - - +
245D ASP* 1.3 61.5 + - - -
247D TRP* 3.2 14.0 + - - +
248D SER* 3.3 15.8 + - - -
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Residues in contact with ASP 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D LEU* 3.9 23.6 - - + +
187D MET* 3.5 18.3 - - - +
188D HIS* 2.8 35.4 + - - +
189D ARG* 3.1 29.9 + - - -
190D ASP 4.0 1.4 + - - -
191D VAL* 4.0 10.3 + - + +
234D ARG* 5.3 0.3 + - - -
242D VAL* 3.0 12.9 + - + +
244D SER* 1.3 77.5 - - - +
246D ILE* 1.3 58.9 + - - +
248D SER* 3.2 7.7 + - - +
249D MET* 3.0 27.9 + - - +
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Residues in contact with ILE 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D ILE* 6.4 0.2 - - + -
177D LEU* 5.3 3.8 - - + -
242D VAL 3.2 15.8 + - - +
243D GLN* 3.3 30.7 + - - +
245D ASP* 1.3 72.2 - - - +
247D TRP* 1.3 66.2 + - - +
249D MET* 3.3 9.3 + - + +
250D GLY 3.0 19.1 + - - -
340D LYS 4.8 0.2 - - - +
341D CYS* 3.6 38.9 - - - +
349D ARG* 4.2 4.0 - - + -
350D ALA 3.6 17.5 - - - +
351D ASP 3.9 0.2 - - - -
352D LEU* 3.9 35.2 - - + +
355D LEU* 3.7 20.0 - - + -
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Residues in contact with TRP 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D TYR 3.7 11.4 + - - -
230D MET 3.5 12.3 + - - -
231D SER* 3.4 29.2 - - - -
232D PRO* 3.6 21.1 - - + -
243D GLN 3.3 2.8 + - - -
244D SER 3.2 10.6 + - - +
246D ILE* 1.3 79.9 - - - +
248D SER* 1.3 60.9 + - - +
251D LEU* 3.0 45.2 + - + +
263D ILE* 5.4 0.7 - - + -
317D ILE* 4.0 21.7 - - + +
322D PRO* 4.2 15.0 - - + -
323D PRO* 4.9 1.6 - - + -
341D CYS 3.5 12.3 + - - -
342D LEU* 3.1 54.4 - - + +
344D LYS* 4.2 17.5 - - + -
349D ARG* 3.4 28.0 - - - -
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Residues in contact with SER 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D ARG 6.2 0.2 - - - -
191D VAL* 3.3 29.7 + - - -
229D TYR* 2.5 27.1 + - - -
230D MET* 4.7 0.2 - - - -
231D SER 4.5 1.6 + - - -
244D SER 3.3 11.4 + - - -
245D ASP* 3.2 11.2 + - - -
246D ILE 3.2 0.4 - - - -
247D TRP* 1.3 82.7 - - - +
249D MET* 1.3 56.3 + - - +
251D LEU* 3.1 5.0 + - - +
252D SER* 2.4 38.9 + - - -
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Residues in contact with MET 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL* 6.5 0.2 - - + -
170D SER* 4.3 5.6 - - - +
173D VAL* 3.5 43.1 - - + -
174D ILE* 4.2 15.3 - - + -
177D LEU* 5.0 4.3 - - + -
191D VAL* 3.9 10.2 - - + +
196D ILE* 6.0 1.6 - - + -
245D ASP 3.0 13.6 + - - +
246D ILE* 3.6 9.0 - - + +
248D SER* 1.3 75.9 - - - +
250D GLY* 1.3 52.9 + - - +
252D SER* 3.1 6.4 + - - -
253D LEU* 2.7 52.0 + - + +
337D PHE* 3.8 22.4 - - + -
341D CYS* 3.5 31.0 - - - -
355D LEU* 4.2 10.1 - - + -
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Residues in contact with GLY 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D ILE 3.0 9.7 + - - -
247D TRP 3.7 2.5 - - - -
249D MET* 1.3 77.1 - - - +
251D LEU* 1.3 61.2 + - - +
253D LEU* 3.4 11.6 + - - +
254D VAL* 3.1 27.9 + - - +
338D VAL* 4.2 4.5 - - - +
341D CYS* 3.7 25.7 - - - +
342D LEU* 3.8 9.1 - - - +
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Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D SER 4.0 15.0 - - - +
229D TYR* 3.6 30.5 - - + -
247D TRP* 3.0 30.1 + - + +
248D SER* 3.1 7.2 + - - +
250D GLY* 1.3 77.5 - - - +
252D SER* 1.3 61.3 + - - +
254D VAL* 3.5 1.3 + - - +
255D GLU* 3.2 17.7 + - - +
261D TYR* 4.2 12.1 - - + -
262D PRO* 3.6 15.2 - - + +
263D ILE* 4.1 18.6 - - + -
317D ILE* 5.4 1.1 - - + -
323D PRO* 3.7 31.4 - - + -
342D LEU* 3.8 16.5 - - + +
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Residues in contact with SER 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D VAL* 3.9 1.0 + - - +
192D LYS* 3.6 17.5 + - - -
193D PRO* 3.4 29.1 - - - +
196D ILE* 5.2 4.0 - - - -
229D TYR* 4.0 5.3 - - - -
248D SER 2.4 29.0 + - - -
249D MET* 3.5 6.8 - - - -
251D LEU* 1.3 74.9 - - - +
253D LEU* 1.3 59.5 + - - +
255D GLU* 3.0 7.7 + - - +
256D MET* 2.9 41.1 + - - +
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Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D LEU* 4.0 32.7 - - + +
169D VAL* 5.0 3.4 - - + -
170D SER* 3.3 32.3 - - - +
249D MET* 2.7 43.1 + - + +
250D GLY* 3.6 9.6 - - - +
252D SER* 1.3 72.7 - - - +
254D VAL* 1.3 56.9 + - - +
256D MET* 3.4 12.7 + - + +
257D ALA* 2.9 30.8 + - - +
325D LEU* 5.2 0.2 - - - -
334D PHE* 4.6 7.6 - - + -
337D PHE* 3.8 23.1 - - + -
338D VAL* 4.4 13.0 - - + -
341D CYS* 5.1 0.2 - - - -
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Residues in contact with VAL 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D GLY 3.1 17.9 + - - +
251D LEU* 3.7 6.3 - - - +
253D LEU* 1.3 72.1 - - - +
255D GLU* 1.3 65.8 + - - +
258D VAL* 3.1 35.7 + - + +
260D ARG 4.5 0.4 - - - +
262D PRO* 3.7 23.1 - - + -
323D PRO* 4.7 4.3 - - + -
324D LYS 4.0 22.0 - - - +
325D LEU* 4.1 13.6 - - + +
338D VAL* 3.5 25.1 - - + -
342D LEU* 3.8 12.8 - - + -
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Residues in contact with GLU 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ASP* 5.3 3.3 - - - +
155D LEU* 3.7 18.7 - - + +
193D PRO* 3.7 13.3 - - + +
227D ARG* 3.5 19.8 + - - -
229D TYR* 2.5 35.0 + - - -
251D LEU 3.2 6.3 + - - +
252D SER* 3.0 11.2 + - - +
254D VAL* 1.3 76.2 - - - +
256D MET* 1.3 56.1 + - - +
259D GLY* 2.6 38.9 + - - -
260D ARG* 3.5 20.4 - - - +
261D TYR* 4.0 14.2 + - - -
262D PRO* 3.9 12.0 - - + +
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Residues in contact with MET 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D LEU* 3.4 43.3 - - + -
155D LEU* 3.8 24.5 - - + +
160D ARG* 3.7 5.0 - - - -
161D ILE* 3.0 38.2 + - + +
166D LEU* 3.8 26.9 - - + -
169D VAL* 4.4 6.5 - - + -
193D PRO* 4.0 13.0 - - + -
196D ILE* 4.4 6.1 - - + -
252D SER* 2.9 35.8 + - - +
253D LEU* 4.0 12.6 - - + +
255D GLU* 1.3 77.6 - - - +
257D ALA* 1.3 59.9 + - - +
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Residues in contact with ALA 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ARG* 3.3 23.4 - - - +
161D ILE 4.2 4.3 - - - +
166D LEU* 3.5 21.3 - - + +
253D LEU 2.9 18.4 + - - +
254D VAL 4.0 0.4 - - - +
255D GLU 3.2 0.2 - - - -
256D MET* 1.3 75.5 - - - +
258D VAL* 1.3 60.7 + - - +
325D LEU* 4.0 15.7 - - + -
330D PHE* 3.5 34.8 - - + -
334D PHE* 4.0 1.6 - - + -
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Residues in contact with VAL 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ARG* 3.7 18.2 + - - +
254D VAL* 3.1 30.1 + - + +
257D ALA* 1.3 80.1 - - - +
259D GLY* 1.3 61.7 + - - +
260D ARG* 4.3 11.4 - - + +
262D PRO* 6.4 0.2 - - + -
266D PRO* 5.3 3.8 - - + -
271D LEU* 5.6 2.2 - - + -
274D MET* 3.6 42.7 - - + +
324D LYS 5.3 0.9 - - - +
325D LEU* 4.5 6.3 - - + -
326D PRO* 4.3 23.8 - - + -
330D PHE* 4.8 3.6 - - + -
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Residues in contact with GLY 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D LEU* 4.1 13.6 - - - +
159D GLY 3.3 24.5 - - - +
255D GLU 2.6 19.6 + - - -
256D MET 4.0 0.4 + - - -
257D ALA 3.5 1.6 - - - -
258D VAL* 1.3 74.0 - - - +
260D ARG* 1.3 57.5 + - - +
274D MET* 5.6 0.7 - - - -
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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
------------------------------------------------------------
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