Contacts of the helix formed by residues 228 - 247 (chain D) in PDB entry 2VM8
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B GLN* 3.4 32.5 - - - +
204D ILE* 6.1 0.4 - - + -
208D GLU* 6.0 1.6 - - + -
224D VAL* 3.7 8.5 - - + +
225D LEU* 3.8 10.5 - - - +
226D SER 3.5 8.1 - - - +
227D ARG* 1.3 94.9 - - - +
229D GLU* 1.3 68.5 + - - +
230D GLU* 2.8 17.7 + - - +
231D VAL* 3.0 28.6 + - + +
232D GLU* 3.8 0.5 + - - +
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Residues in contact with GLU 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D ARG 3.7 1.3 + - - -
228D PRO* 1.3 72.6 - - - +
230D GLU* 1.3 71.1 + - - +
232D GLU* 3.1 12.4 + - - +
233D ALA* 3.0 28.2 + - - +
257D SER* 3.3 24.6 + - - -
258D LYS* 4.0 7.2 + - - +
259D SER* 3.1 36.4 + - - -
308D SER* 3.2 27.0 + - - +
309D PRO* 6.4 1.7 - - + +
310D ASP* 4.6 8.7 - - - +
313D THR* 4.9 0.5 + - - -
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B THR* 3.6 17.0 + - + +
244B ASN* 5.8 7.4 - - + +
245B GLN* 4.3 16.8 + - - +
270B LYS* 4.9 16.6 + - + +
228D PRO* 2.8 22.8 + - + +
229D GLU* 1.3 93.2 + - - +
231D VAL* 1.3 57.0 + - + +
232D GLU 3.4 0.2 - - - -
233D ALA* 4.0 7.8 - - + +
234D GLU* 3.2 27.4 + - - +
259D SER* 5.1 3.2 + - - +
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Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B THR* 4.7 2.0 - - + -
245B GLN* 4.7 5.8 - - + -
200D GLU* 3.3 8.3 - - + +
201D ASN* 3.0 35.5 + - + +
204D ILE* 3.9 32.5 - - + -
205D ILE* 3.7 29.8 - - + -
227D ARG* 4.0 10.3 - - - +
228D PRO* 3.0 30.6 + - + +
230D GLU* 1.3 74.9 - - - +
232D GLU* 1.3 71.8 + - + +
234D GLU* 4.1 5.4 - - - -
235D ALA* 3.4 8.5 + - - +
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Residues in contact with GLU 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ALA 3.5 22.4 - - - +
200D GLU* 4.2 8.3 - - + +
227D ARG 5.9 0.9 - - - +
228D PRO 3.8 1.1 + - - +
229D GLU* 3.1 11.5 + - - +
231D VAL* 1.3 80.5 - - + +
233D ALA* 1.3 67.4 + - - +
235D ALA 3.1 3.3 + - - -
236D VAL* 3.0 22.8 + - + +
252D ILE* 5.7 1.3 - - + +
254D LYS 3.8 3.6 - - - +
255D VAL* 3.8 5.9 - - - -
256D MET* 3.0 33.9 + - - +
257D SER* 2.9 24.8 + - - -
260D SER* 3.1 21.0 + - - -
305D PRO* 4.4 15.4 - - + +
306D PRO* 5.9 1.2 - - + +
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Residues in contact with ALA 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D GLU 3.0 13.5 + - - +
230D GLU* 4.0 7.6 - - + +
232D GLU* 1.3 73.8 - - - +
234D GLU* 1.3 54.0 + - - +
236D VAL* 3.0 6.1 + - - +
237D ASN* 2.8 35.2 + - - +
259D SER* 3.7 35.7 - - - +
260D SER* 4.2 13.6 - - - +
263D VAL* 4.2 9.3 - - + +
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Residues in contact with GLU 234 (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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234B GLU* 3.5 13.0 - - - +
237B ASN* 3.9 13.5 - - - +
238B ARG* 3.6 19.5 + - + +
241B THR* 3.4 30.7 - - + +
201D ASN* 2.9 28.9 + - - +
230D GLU 3.2 19.4 + - - +
231D VAL* 4.1 4.7 - - - +
233D ALA* 1.3 79.5 - - - +
235D ALA* 1.3 57.5 + - - +
237D ASN* 3.2 5.2 - - - +
238D ARG* 2.9 50.0 + - - -
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Residues in contact with ALA 235 (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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168D MET* 3.3 29.0 - - + +
199D ALA* 3.5 14.4 - - - -
200D GLU 3.4 33.7 - - - +
201D ASN 3.5 2.2 - - - +
231D VAL 3.4 6.0 + - - +
232D GLU 3.1 1.0 + - - +
234D GLU* 1.3 78.3 - - - +
236D VAL* 1.3 59.5 + - - +
238D ARG* 3.7 5.6 - - - +
239D ALA* 2.8 25.3 + - - +
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Residues in contact with VAL 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ALA* 3.7 21.1 - - + +
232D GLU* 3.0 17.2 + - + +
233D ALA* 3.0 10.1 + - - +
235D ALA* 1.3 75.6 - - - +
237D ASN* 1.3 63.0 + - - +
239D ALA* 3.4 3.9 + - - +
240D ILE* 3.1 40.7 + - + +
252D ILE* 3.7 27.8 - - + -
260D SER* 4.4 13.9 - - - +
263D VAL* 4.0 7.9 - - + -
264D ILE* 3.8 22.2 - - + -
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Residues in contact with ASN 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ALA 4.8 0.5 - - - +
234B GLU* 4.0 16.3 - - - +
237B ASN* 3.2 34.2 - - - +
233D ALA 2.8 16.2 + - - +
234D GLU 3.2 9.9 - - - +
236D VAL* 1.3 74.8 - - - +
238D ARG* 1.3 57.8 + - - +
240D ILE* 3.5 5.2 + - - +
241D THR* 2.8 31.3 + - - -
263D VAL* 3.9 27.6 - - + +
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Residues in contact with ARG 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ASP* 4.6 6.9 + - - -
201B ASN* 4.3 2.0 - - - +
204B ILE* 5.8 0.2 - - + -
234B GLU* 3.3 38.6 - - + +
238B ARG* 3.5 13.9 - - - +
168D MET* 2.7 38.3 + - + +
175D GLN* 5.8 3.8 - - - +
176D LEU 5.6 2.4 + - - -
178D ASP* 3.0 44.0 + - - +
181D ILE* 5.6 0.8 - - - +
201D ASN* 4.0 15.0 - - - +
234D GLU* 2.9 42.1 + - - +
235D ALA* 3.7 8.1 - - - +
237D ASN* 1.3 70.3 + - - +
239D ALA* 1.3 66.5 + - - +
241D THR* 3.2 4.3 + - - -
242D ILE* 3.2 26.3 + - + +
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Residues in contact with ALA 239 (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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168D MET* 4.1 14.6 - - - +
181D ILE* 5.8 3.6 - - + -
185D LEU* 4.6 2.3 - - - +
197D VAL* 4.2 22.9 - - + -
199D ALA* 4.9 0.2 - - + -
235D ALA 2.8 22.6 + - - +
236D VAL* 3.8 6.7 - - - +
238D ARG* 1.3 72.4 - - - +
240D ILE* 1.3 57.2 + - - +
242D ILE* 3.2 12.5 + - - +
243D ALA* 3.0 27.4 + - - +
250D LEU* 3.7 14.0 - - + +
252D ILE* 4.6 0.9 - - + -
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Residues in contact with ILE 240 (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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236D VAL* 3.1 29.7 + - + +
237D ASN* 3.7 4.7 - - - +
239D ALA* 1.3 71.1 - - - +
241D THR* 1.3 67.3 + - - +
243D ALA* 3.9 0.4 - - - +
244D ASN* 2.9 48.4 + - - +
250D LEU* 3.4 21.7 - - + +
263D VAL* 3.4 29.4 - - + +
264D ILE* 4.4 7.4 - - + -
267D ALA* 3.8 21.8 - - + -
272D THR* 3.4 17.7 - - + -
274D VAL* 4.6 7.0 - - + -
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Residues in contact with THR 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ILE* 3.6 21.3 - - + -
230B GLU* 4.2 21.4 + - + +
231B VAL* 4.6 9.6 - - + -
234B GLU* 3.4 30.1 - - + +
237D ASN* 2.8 19.6 + - - -
238D ARG 3.2 9.8 + - - -
240D ILE* 1.3 78.5 - - - +
242D ILE* 1.3 61.1 + - - +
244D ASN* 3.4 6.2 + - - +
245D GLN* 3.2 24.8 + - + +
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Residues in contact with ILE 242 (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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204B ILE* 3.7 22.4 - - + -
168D MET* 6.3 0.7 - - + -
178D ASP* 3.6 38.6 - - + +
181D ILE* 3.6 22.0 - - + -
182D TYR* 3.5 34.3 - - + +
185D LEU* 4.2 11.9 - - + -
238D ARG* 3.2 15.3 + - + +
239D ALA* 3.6 7.9 - - - +
241D THR* 1.3 73.0 - - - +
243D ALA* 1.3 55.8 + - - +
245D GLN* 3.4 3.5 + - - +
246D THR* 2.4 42.2 + - + +
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Residues in contact with ALA 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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185D LEU* 3.8 10.9 - - + +
239D ALA 3.0 16.8 + - - +
240D ILE* 3.9 2.7 - - - +
242D ILE* 1.3 76.4 - - - +
244D ASN* 1.3 58.1 + - - +
246D THR* 3.3 6.5 - - - -
247D ASN* 2.9 23.6 + - - -
248D CYS 3.0 29.0 + - - +
250D LEU* 3.6 26.0 - - + -
272D THR* 5.6 3.1 - - + -
273D VAL 5.5 0.4 - - - +
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Residues in contact with ASN 244 (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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230B GLU* 5.7 8.9 - - + +
240D ILE* 2.9 35.2 + - - +
241D THR* 3.8 6.2 - - - +
243D ALA* 1.3 75.4 - - - +
245D GLN* 1.3 75.8 + - - +
247D ASN* 3.4 11.1 + - - +
272D THR* 3.0 43.8 + - - +
273D VAL 4.7 0.7 + - - -
485D ARG* 5.2 3.3 + - - -
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Residues in contact with GLN 245 (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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204B ILE* 3.9 29.2 - - + -
208B GLU* 3.9 30.7 - - + +
211B ARG* 5.1 4.2 + - - -
225B LEU 5.3 1.6 - - - +
228B PRO* 3.7 29.2 - - + +
230B GLU* 4.5 15.4 + - - +
231B VAL* 4.5 7.2 - - + -
182D TYR* 4.9 1.1 - - + -
241D THR 3.2 17.1 + - - +
242D ILE* 3.9 4.9 - - - +
244D ASN* 1.3 89.6 + - - +
246D THR* 1.3 64.7 + - + +
247D ASN* 3.7 0.5 + - - +
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Residues in contact with THR 246 (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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208B GLU* 5.4 0.4 - - - -
182D TYR* 3.7 50.7 - - + +
185D LEU* 3.8 13.2 - - - +
186D SER* 3.9 14.6 - - - +
189D ARG* 3.1 28.9 + - - +
242D ILE* 2.4 29.5 + - + +
243D ALA* 3.3 11.6 + - - -
245D GLN* 1.3 75.5 - - - +
247D ASN* 1.3 68.7 + - - +
248D CYS* 3.3 5.1 + - - -
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Residues in contact with ASN 247 (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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189D ARG* 3.5 9.4 - - - +
243D ALA 2.9 9.5 + - - -
244D ASN* 3.4 7.6 + - - +
245D GLN 3.4 3.6 - - - +
246D THR* 1.3 80.9 - - - +
248D CYS* 1.3 56.9 + - - +
482D ILE* 3.1 56.1 + - - +
485D ARG* 3.4 37.0 + - - +
486D SER* 3.5 16.0 + - - +
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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