Contacts of the helix formed by residues 191 - 209 (chain D) in PDB entry 3M0V
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 ASN 191 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B GLU* 6.0 1.6 - - - -
311B ASP* 3.0 32.8 + - - +
315B ARG* 4.6 3.3 + - - +
365B GLN* 3.6 26.2 + - - +
190D SER* 1.3 73.3 - - - +
192D PHE* 1.3 65.4 + - - +
193D THR* 3.2 11.4 + - - -
194D ARG* 2.9 55.3 + - + +
195D ALA* 3.0 21.7 + - - +
198D ARG* 5.4 2.4 - - - +
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Residues in contact with PHE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ASN* 4.2 5.6 - - - -
265B GLU* 3.7 22.0 - - + -
266B MET* 3.6 35.6 - - + +
269B ALA* 3.8 13.9 - - + -
270B ARG* 3.3 20.6 + - - +
308B GLU* 3.2 36.0 + - - +
184D SER* 4.8 1.6 - - - -
188D GLY 6.1 1.1 - - - -
190D SER* 3.5 13.2 + - - -
191D ASN* 1.3 71.2 + - - +
193D THR* 1.3 62.9 + - - +
195D ALA* 3.6 4.8 + - - +
196D PHE 3.2 16.6 + - - -
228D TYR* 3.5 31.0 - + - -
229D SER* 3.5 27.6 - - - -
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Residues in contact with THR 193 (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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269B ALA* 3.9 25.5 + - - +
270B ARG* 4.5 2.4 + - - +
272B ILE* 6.0 0.2 - - - +
273B GLN* 3.5 31.7 + - + +
308B GLU* 5.1 1.0 + - - -
315B ARG* 3.6 37.1 + - - +
191D ASN* 3.2 8.5 + - - -
192D PHE* 1.3 75.0 - - - +
194D ARG* 1.3 62.4 + - + +
196D PHE* 3.2 3.5 + - - +
197D GLU* 2.9 45.9 + - - +
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Residues in contact with ARG 194 (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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315B ARG* 3.8 28.3 - - - +
362B SER* 5.9 1.0 + - - -
365B GLN* 5.5 2.5 - - - -
366B GLU* 5.0 9.0 - - - -
191D ASN* 2.9 40.6 + - + +
193D THR* 1.3 73.9 - - + +
195D ALA* 1.3 64.6 + - - +
197D GLU* 3.2 23.2 + - - +
198D ARG* 2.9 44.4 + - + +
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Residues in contact with ALA 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D SER* 3.4 15.8 - - - +
190D SER* 4.7 11.7 - - - -
191D ASN 3.0 18.1 + - - +
192D PHE* 3.8 5.2 - - - +
194D ARG* 1.3 76.2 - - - +
196D PHE* 1.3 64.0 + - - +
198D ARG* 3.2 25.1 + - - +
199D TYR* 3.0 18.5 + - - +
231D VAL* 4.3 19.5 - - + -
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Residues in contact with PHE 196 (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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270B ARG* 3.5 38.8 - - - +
273B GLN* 3.4 24.2 - - - +
274B PHE* 3.9 20.9 - + - -
192D PHE 3.2 6.1 + - - +
193D THR 3.2 4.0 + - - +
195D ALA* 1.3 78.2 - - - +
197D GLU* 1.3 57.9 + - - +
199D TYR* 3.2 4.6 + + - -
200D LEU* 2.9 57.6 + - + +
231D VAL* 3.9 20.6 - - + +
237D THR* 3.5 29.4 - - + -
240D LEU* 4.3 7.2 - - + -
241D ILE* 3.5 27.4 - - + -
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Residues in contact with GLU 197 (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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273B GLN* 4.3 14.9 + - - +
193D THR* 2.9 36.0 + - + +
194D ARG* 3.2 31.8 + - - +
196D PHE* 1.3 77.2 - - - +
198D ARG* 1.3 62.1 + - + +
200D LEU* 3.3 9.8 + - - +
201D SER* 3.0 23.7 + - - -
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Residues in contact with ARG 198 (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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366B GLU* 4.2 10.9 + - - -
146D LEU 3.4 8.4 - - - +
147D SER* 2.8 30.5 + - - -
148D HIS 3.5 16.9 + - - -
149D THR* 3.6 28.5 - - - +
154D ARG* 3.8 23.9 - - - +
190D SER* 5.5 3.4 - - - +
191D ASN* 5.0 4.9 + - - +
194D ARG* 2.9 39.3 + - - +
195D ALA* 3.2 32.7 + - - +
197D GLU* 1.3 76.5 - - + +
199D TYR* 1.3 62.4 + - - +
201D SER* 3.3 6.9 + - - -
202D ALA* 3.0 19.4 + - - +
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Residues in contact with TYR 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D LEU* 3.7 18.2 - - + -
147D SER* 3.8 9.8 - - - -
178D VAL* 5.0 6.1 + - + +
180D ILE* 3.6 33.0 - - + -
195D ALA 3.0 13.4 + - - +
196D PHE* 3.5 20.0 - + - +
198D ARG* 1.3 77.2 - - - +
200D LEU* 1.3 62.3 + - + +
202D ALA* 3.3 1.9 + - - +
203D MET* 2.9 70.5 + - + +
218D SER* 3.7 10.6 - - - -
231D VAL* 4.0 11.2 - - + -
232D VAL* 3.6 17.6 - - + +
241D ILE* 3.2 37.5 - - + +
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Residues in contact with LEU 200 (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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273B GLN* 4.1 12.8 - - - +
274B PHE* 4.8 6.5 - - + -
196D PHE* 2.9 62.3 + - + +
197D GLU* 3.7 7.4 - - - +
199D TYR* 1.3 80.0 - - + +
201D SER* 1.3 56.7 + - - +
203D MET* 3.9 3.4 - - - +
204D ALA* 3.0 27.9 + - - +
241D ILE* 4.0 26.9 - - + +
244D THR* 4.4 25.2 - - + +
245D LEU* 4.1 7.1 - - + +
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Residues in contact with SER 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D ARG* 6.1 1.6 - - - -
197D GLU 3.0 17.2 + - - -
198D ARG* 3.6 7.2 - - - -
200D LEU* 1.3 78.5 - - - +
202D ALA* 1.3 61.2 + - - +
204D ALA* 3.3 19.3 + - - +
205D GLU* 3.3 17.9 + - - +
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Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D LEU* 3.3 37.0 - - + +
154D ARG* 4.9 8.3 - - + +
158D VAL* 3.8 21.5 - - + +
198D ARG 3.0 8.9 + - - +
199D TYR 3.7 2.2 - - - +
201D SER* 1.3 73.2 - - - +
203D MET* 1.3 61.8 + - - +
204D ALA 3.0 1.1 - - - -
205D GLU* 2.9 26.1 + - - +
206D ILE* 3.1 15.3 + - - +
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Residues in contact with MET 203 (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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146D LEU* 3.8 22.4 - - + -
178D VAL* 4.1 21.5 - - + -
199D TYR* 2.9 58.9 + - + +
200D LEU* 4.0 2.9 - - - +
202D ALA* 1.3 77.3 - - - +
204D ALA* 1.3 56.8 + - - +
206D ILE* 3.2 11.0 + - - +
207D TYR* 2.9 29.6 + - - +
216D LEU* 3.9 29.3 - - + +
218D SER* 4.2 15.3 - - - -
241D ILE* 4.7 0.4 - - + -
245D LEU* 3.7 25.8 - - + +
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Residues in contact with ALA 204 (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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200D LEU 3.0 15.2 + - - +
201D SER* 3.3 14.4 - - - +
202D ALA 3.0 0.4 - - - -
203D MET* 1.3 78.1 - - - +
205D GLU* 1.3 56.0 + - - +
207D TYR* 3.4 4.6 + - - +
208D LYS* 2.9 31.1 + - - +
245D LEU* 3.7 13.4 - - + +
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Residues in contact with GLU 205 (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 ALA* 5.7 3.9 - - - +
158D VAL* 4.0 28.5 - - + +
162D LEU* 4.6 4.3 - - - +
201D SER* 3.3 17.9 + - - +
202D ALA* 2.9 13.4 + - - +
204D ALA* 1.3 77.1 - - + +
206D ILE* 1.3 65.0 + - - +
208D LYS* 3.3 17.5 + - - +
209D GLY* 3.3 15.6 + - - -
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Residues in contact with ILE 206 (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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146D LEU* 4.8 3.8 - - + -
158D VAL* 3.2 48.2 - - + +
161D ASN* 3.4 20.0 - - + -
162D LEU* 4.4 8.5 - - + +
165D ILE* 4.6 7.6 - - + +
176D LEU* 4.0 26.9 - - + -
178D VAL* 5.3 0.4 - - + -
202D ALA 3.1 13.3 + - - +
203D MET* 3.2 19.5 + - - +
205D GLU* 1.3 72.5 - - - +
207D TYR* 1.3 67.3 + - - +
209D GLY* 2.9 14.0 + - - -
210D LEU* 3.0 11.5 + - + +
216D LEU* 4.1 15.7 - - + -
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Residues in contact with TYR 207 (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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203D MET 2.9 17.7 + - - +
204D ALA* 3.5 9.6 - - - +
205D GLU 3.3 0.2 - - - -
206D ILE* 1.3 78.1 - - - +
208D LYS* 1.3 63.1 + - - +
210D LEU* 3.0 26.8 + - + +
216D LEU* 4.2 13.9 - - + +
245D LEU* 3.6 42.8 - - + -
246D GLY* 3.9 0.4 - - - -
247D PRO* 3.3 16.2 - - + +
248D LYS* 3.1 48.8 + - + +
249D ALA* 3.7 26.2 - - + -
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Residues in contact with LYS 208 (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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204D ALA 2.9 16.3 + - - +
205D GLU* 3.4 20.0 - - - +
206D ILE 3.1 0.2 - - - -
207D TYR* 1.3 80.5 - - - +
209D GLY* 1.3 59.3 + - - +
210D LEU 3.3 3.3 + - - +
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Residues in contact with GLY 209 (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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162D LEU* 4.2 16.2 - - - +
165D ILE* 4.1 12.4 - - - +
205D GLU 3.3 3.6 + - - -
206D ILE 2.9 10.4 + - - -
208D LYS* 1.3 79.3 - - - +
210D LEU* 1.3 62.5 + - - +
211D PRO* 3.6 8.1 - - - +
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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