Contacts of the helix formed by residues 210 - 225 (chain D) 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 THR 210 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283C TYR* 4.0 14.4 - - + +
284C MET* 3.7 26.2 - - - +
287C GLY* 3.4 27.0 + - - -
208D VAL 4.4 1.8 + - - +
209D GLY* 1.3 78.3 - - - +
211D PRO* 1.3 75.7 - - - +
212D GLY 4.5 1.0 + - - -
213D ILE* 2.9 32.3 + - - +
214D MET* 3.0 9.2 + - - +
240D GLN* 3.6 17.0 - - - +
244D ASN* 3.1 9.2 + - - +
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Residues in contact with PRO 211 (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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29C LEU* 6.4 0.9 - - + -
246C LEU* 4.2 17.7 - - + -
284C MET* 3.7 33.7 - - + -
288C LEU* 3.7 17.0 - - + -
210D THR* 1.3 90.0 - - + +
212D GLY* 1.3 56.0 + - - +
214D MET* 3.5 1.5 + - + -
215D LYS* 3.0 24.1 + - - +
240D GLN* 4.3 1.6 - - - +
243D ALA* 4.6 9.2 - - + +
244D ASN* 3.2 12.9 - - - +
247D MET* 3.3 33.1 - - + +
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Residues in contact with GLY 212 (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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287C GLY 5.5 2.0 - - - -
288C LEU* 3.3 19.1 - - - +
210D THR* 3.1 2.0 + - - -
211D PRO* 1.3 76.7 - - - +
213D ILE* 1.3 62.7 + - - +
215D LYS* 3.3 8.1 + - - +
216D ASP* 2.9 39.3 + - - +
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Residues in contact with ILE 213 (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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287C GLY* 4.7 9.6 + - - +
172D LEU* 4.0 36.1 - - + +
179D LYS* 4.6 17.5 - - - +
180D ILE 5.9 3.4 - - - +
182D PRO* 5.7 0.5 - - - +
208D VAL 5.6 0.4 - - - +
209D GLY* 4.5 3.4 - - - -
210D THR* 2.9 32.3 + - - +
212D GLY* 1.3 78.0 - - - +
214D MET* 1.3 62.6 + - - +
216D ASP* 3.5 9.4 + - - +
217D MET* 3.1 23.8 + - + +
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Residues in contact with MET 214 (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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172D LEU* 4.0 25.0 - - + +
202D LEU 5.8 0.9 - - - +
210D THR 3.0 10.7 + - - +
211D PRO* 3.6 10.3 - - + +
213D ILE* 1.3 77.3 - - - +
215D LYS* 1.3 61.9 + - - +
217D MET* 3.4 13.9 + - + +
218D LEU* 3.0 57.2 + - + +
232D VAL* 3.8 17.3 - - + -
234D CYS* 3.5 28.3 - - - -
244D ASN* 3.4 31.2 - - + +
247D MET* 3.9 10.8 - - + -
248D ALA* 4.1 1.1 - - + +
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Residues in contact with LYS 215 (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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211D PRO 3.0 17.9 + - - +
212D GLY* 3.3 7.8 + - - +
214D MET* 1.3 78.2 - - - +
216D ASP* 1.3 66.3 + - - +
218D LEU* 4.1 0.5 - - - +
219D SER* 2.9 32.1 + - - -
247D MET* 3.9 19.1 - - + -
251D MET* 3.6 40.4 - - - +
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Residues in contact with ASP 216 (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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182D PRO* 3.7 25.7 - - + +
212D GLY* 2.9 23.0 + - - +
213D ILE* 3.9 11.4 - - - +
215D LYS* 1.3 81.0 - - - +
217D MET* 1.3 63.2 + - - +
219D SER* 3.5 5.4 - - - -
220D ALA* 3.1 18.5 + - - +
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Residues in contact with MET 217 (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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171D ALA* 3.6 20.9 - - + +
172D LEU* 3.7 22.2 - - + -
182D PRO* 4.2 13.1 - - + +
185D VAL* 3.7 23.8 - - + -
202D LEU* 3.4 45.5 - - + +
213D ILE* 3.1 17.3 + - + +
214D MET* 3.7 22.2 - - + +
216D ASP* 1.3 73.8 - - - +
218D LEU* 1.3 68.3 + - + +
220D ALA* 3.2 4.0 + - - +
221D VAL* 2.9 34.2 + - - +
232D VAL* 4.9 0.4 - - + -
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Residues in contact with LEU 218 (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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202D LEU* 3.5 30.1 - - + -
214D MET* 3.0 32.5 + - + +
215D LYS 4.1 2.2 - - - +
217D MET* 1.3 80.3 - - + +
219D SER* 1.3 54.8 + - - +
221D VAL* 3.2 2.4 + - + +
222D MET* 2.7 51.3 + - + +
230D LEU* 5.0 7.0 - - + -
232D VAL* 4.3 4.3 - - + -
248D ALA* 3.4 40.2 - - + -
251D MET* 4.0 13.9 - - + -
253D VAL* 3.8 22.2 - - + -
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Residues in contact with SER 219 (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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215D LYS* 2.9 28.0 + - - -
216D ASP* 3.5 7.6 - - - -
217D MET 3.2 0.2 - - - -
218D LEU* 1.3 79.5 - - - +
220D ALA* 1.3 62.4 + - - +
222D MET* 3.5 9.1 + - - +
223D GLN* 3.2 32.3 + - - +
251D MET* 5.5 3.5 - - - -
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Residues in contact with ALA 220 (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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182D PRO* 3.6 39.5 - - + +
183D ALA* 4.4 3.1 - - - +
186D ALA* 3.8 11.4 - - + +
216D ASP 3.1 4.3 + - - +
217D MET 3.8 3.8 - - - +
219D SER* 1.3 74.7 - - - +
221D VAL* 1.3 67.9 + - - +
223D GLN* 3.1 26.0 + - - +
224D GLU* 4.0 2.6 + - - +
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Residues in contact with VAL 221 (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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182D PRO 4.8 0.4 - - - +
185D VAL* 3.8 12.6 - - + -
186D ALA* 3.8 25.8 - - - +
189D THR* 3.8 29.2 - - + +
202D LEU* 4.6 4.9 - - + -
217D MET* 2.9 37.2 + - - +
218D LEU* 3.7 6.7 - - - +
220D ALA* 1.3 76.2 - - - +
222D MET* 1.3 58.5 + - - +
224D GLU* 3.1 5.5 + - - +
225D VAL* 3.0 27.1 + - + +
230D LEU* 3.8 24.9 - - + -
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Residues in contact with MET 222 (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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218D LEU* 2.7 37.7 + - + +
219D SER* 3.7 9.2 - - - +
220D ALA 3.2 0.2 - - - -
221D VAL* 1.3 70.3 - - - +
223D GLN* 1.3 65.5 + - - +
224D GLU 3.1 0.9 + - - -
225D VAL 3.7 18.3 + - - +
226D PRO* 5.5 0.3 - - - +
227D LEU* 3.7 41.3 - - + -
230D LEU* 4.3 8.5 - - + -
251D MET* 3.9 29.8 - - - +
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Residues in contact with GLN 223 (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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219D SER* 3.2 26.9 + - - +
220D ALA* 3.1 15.6 + - - +
222D MET* 1.3 80.8 - - - +
224D GLU* 1.3 66.7 + - + +
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Residues in contact with GLU 224 (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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183D ALA 5.4 0.2 - - - +
186D ALA* 3.9 25.2 - - + +
187D GLU* 4.6 3.1 + - - -
190D LYS* 2.8 60.0 + - + +
220D ALA 4.8 2.4 - - - +
221D VAL 3.1 5.5 + - - +
222D MET 4.5 0.2 - - - -
223D GLN* 1.3 89.9 - - + +
225D VAL* 1.3 60.8 + - + +
226D PRO* 4.1 2.5 - - - +
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Residues in contact with VAL 225 (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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186D ALA 5.1 0.7 - - - +
189D THR* 4.0 14.1 - - + -
190D LYS* 3.7 35.2 - - + +
193D TYR* 4.0 17.0 - - + -
200D ILE* 4.6 1.3 - - + -
221D VAL* 3.0 11.7 + - + +
222D MET* 3.7 21.0 - - - +
224D GLU* 1.3 83.9 - - + +
226D PRO* 1.3 79.0 - - + +
227D LEU 3.3 1.6 + - - -
229D ALA* 4.0 10.3 - - + -
230D LEU* 3.5 30.6 - - + +
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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