Contacts of the helix formed by residues 213 - 226 (chain B) in PDB entry 1MKD
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 ARG 213 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B SER* 2.9 27.5 + - - +
211B GLY 4.0 5.5 + - - +
212B ASN* 1.3 83.2 + - - +
214B PRO* 1.3 66.5 - - - +
215B LEU 3.3 2.0 - - - -
216B THR* 3.3 3.9 + - - -
217B VAL* 3.0 28.5 + - + +
244B MET* 3.0 64.1 + - + +
247B GLU* 3.3 27.0 - - - +
248B ASP* 2.8 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 4.5 6.5 - - + +
206B ILE* 4.5 5.6 - - + -
207B ALA* 3.9 27.4 - - + +
210B SER* 3.4 6.9 - - - +
212B ASN* 3.3 5.2 - - - +
213B ARG* 1.3 90.2 - - - +
215B LEU* 1.3 56.8 + - - +
217B VAL* 4.5 3.4 - - + -
218B ILE* 2.8 42.4 + - + +
247B GLU* 3.1 7.9 - - - +
259B ASN* 3.2 28.3 - - - +
260B ILE* 4.1 10.8 - - + -
263B ALA* 3.7 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PRO* 1.3 80.3 - - - +
216B THR* 1.3 57.6 + - - +
219B MET* 2.8 54.6 + - + +
243B LEU* 5.1 3.8 - - + +
246B LEU* 4.0 18.4 - - + -
247B GLU* 3.0 28.5 + - + +
250B TYR* 3.8 33.7 - - + -
259B ASN* 3.9 7.9 - - + +
262B ALA* 3.9 6.1 - - + -
263B ALA* 3.6 26.9 - - - +
266B VAL* 3.9 12.8 - - + -
295B ALA* 4.0 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ARG* 3.9 12.4 - - - -
215B LEU* 1.3 71.5 - - - +
217B VAL* 1.3 66.4 + - + +
220B HIS* 3.0 27.5 + - + +
240B ILE* 4.6 12.1 - - + -
243B LEU* 3.4 45.9 + - + +
244B MET* 3.6 30.8 + - + +
247B GLU* 2.6 29.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 4.6 11.4 - - + -
193B LEU* 3.4 37.5 - - + -
206B ILE* 4.5 7.6 - - + -
210B SER* 3.7 21.5 - - - -
213B ARG* 3.0 26.1 + - + +
214B PRO* 3.9 4.5 - - + +
216B THR* 1.3 79.3 - - + +
218B ILE* 1.3 52.3 + - - +
220B HIS* 3.6 4.8 + - - +
221B THR* 2.7 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 4.2 17.3 - - + -
196B VAL* 4.8 4.0 - - + -
201B LEU* 4.1 17.5 - - + -
203B VAL* 4.0 18.2 - - + -
206B ILE* 4.3 12.1 - - + -
214B PRO 2.8 25.6 + - - +
215B LEU 4.2 0.7 - - - +
217B VAL* 1.3 68.9 - - - +
219B MET* 1.3 65.8 + - - +
221B THR* 3.1 7.6 + - - -
222B ILE* 2.9 44.1 + - + +
263B ALA* 3.9 26.0 - - + +
266B VAL* 4.7 3.1 - - + -
267B GLN* 4.1 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 2.8 42.2 + - + +
218B ILE* 1.3 72.9 - - - +
220B HIS* 1.3 63.4 + - - +
222B ILE* 3.2 4.7 + - - +
223B PHE* 2.9 57.4 + - + -
239B LEU* 5.4 0.9 - - + -
242B TYR* 6.2 0.9 - - + -
243B LEU* 3.5 33.7 - - + -
246B LEU* 5.8 0.4 - - + -
266B VAL* 3.6 24.5 - - + -
291B ILE* 3.8 15.5 - - + +
292B PHE* 4.6 11.2 - - + -
295B ALA* 3.6 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B THR* 3.0 19.8 + - + +
217B VAL* 3.6 5.1 + - - +
219B MET* 1.3 77.3 - - - +
221B THR* 1.3 63.4 + - - +
223B PHE* 3.2 7.5 + - - +
224B GLN* 3.0 67.9 + - + +
229B LEU* 4.7 0.4 - - + -
236B VAL* 4.0 13.8 - - + +
239B LEU* 4.2 13.2 - - + -
240B ILE* 3.5 28.8 - - + +
243B LEU* 3.9 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 3.7 37.5 - - + +
196B VAL* 4.8 11.9 - - - +
217B VAL* 2.7 19.5 + - + +
218B ILE* 3.1 15.4 + - - -
220B HIS* 1.3 80.9 - - - +
222B ILE* 1.3 56.0 + - - +
224B GLN* 3.5 9.4 + - + +
225B GLU* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL* 3.6 20.2 - - + -
218B ILE* 2.9 38.7 + - + +
219B MET* 3.7 4.9 - - - +
221B THR* 1.3 75.8 - - - +
223B PHE* 1.3 62.9 + - + +
225B GLU* 3.5 5.4 - - - +
226B ARG* 2.8 29.6 + - - +
266B VAL* 3.8 18.2 - - + -
267B GLN* 4.0 5.4 - - - -
270B HIS* 3.4 47.8 - - + +
291B ILE* 4.0 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B MET* 2.9 56.2 + - + +
220B HIS 3.6 7.6 - - - +
222B ILE* 1.3 76.3 - - + +
224B GLN* 1.3 60.7 + - - +
227B ASP* 2.9 23.4 + - - -
228B LEU* 3.0 36.6 + - + -
229B LEU* 4.0 11.6 + - + -
234B ILE* 3.7 25.8 - - + -
239B LEU* 3.8 33.7 - - + -
288B LEU* 3.7 25.8 - - + -
291B ILE* 4.1 14.6 - - + -
292B PHE* 5.7 3.4 - - + -
345B ILE* 5.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B HIS* 3.0 53.5 + - + +
221B THR* 3.5 12.1 - - + +
223B PHE* 1.3 75.2 - - - +
225B GLU* 1.3 57.6 + - - +
227B ASP* 2.8 26.1 + - - +
229B LEU* 3.1 23.5 - - - +
236B VAL* 4.9 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL* 4.4 10.2 - - + +
197B ASN* 3.4 37.1 + - - +
221B THR 2.9 19.1 + - - +
222B ILE* 3.5 8.5 - - - +
224B GLN* 1.3 78.1 - - - +
226B ARG* 1.3 59.5 + - + +
227B ASP* 3.6 1.2 + - - +
270B HIS* 4.1 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ILE* 2.8 20.5 + - - +
225B GLU* 1.3 74.4 - - + +
227B ASP* 1.3 71.0 + - - +
228B LEU* 3.0 22.2 + - + +
231B THR* 4.7 2.3 + - - -
270B HIS* 2.8 45.0 + - + -
273B LEU* 3.5 16.4 - - - +
274B SER* 2.9 28.6 + - - +
284B ASP* 5.6 2.1 - - - +
287B ILE* 3.9 33.1 - - - +
291B ILE* 3.6 25.4 - - - +
----------------------------------------------------------
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