Contacts of the helix formed by residues 216 - 228 (chain D) in PDB entry 4K9N
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 ALA 216 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D VAL* 2.9 22.2 + - + +
214D ALA* 4.2 13.0 - - + -
215D ASN* 1.3 76.8 - - - +
217D ASN* 1.3 64.1 + - - +
218D ALA 3.4 2.5 - - - -
219D ASP* 3.2 13.0 + - - +
220D CYS* 2.9 22.2 + - - -
318D ILE* 4.3 9.2 - - + +
319D GLY* 4.3 5.4 - - - +
322D ALA* 3.7 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D VAL* 3.3 18.3 - - - +
212D ASP* 3.0 30.1 + - - +
215D ASN* 3.2 9.2 - - - +
216D ALA* 1.3 81.7 + - - +
218D ALA* 1.3 59.2 + - - +
220D CYS* 3.0 5.2 + - - +
221D VAL* 2.9 31.2 + - - +
240D CYS 3.5 11.1 + - - -
241D PRO* 3.5 28.6 + - - +
242D PHE* 4.2 3.4 - - - +
243D PRO* 5.5 3.8 - - + -
391D ASN 5.1 0.6 + - - -
392D PRO* 3.7 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D ASN* 4.8 4.1 + - - +
216D ALA 3.4 0.4 - - - -
217D ASN* 1.3 79.4 - - - +
219D ASP* 1.3 65.1 + - - +
221D VAL* 3.3 11.4 + - - +
222D MET* 3.0 21.3 + - - +
392D PRO* 5.7 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D ASN 5.3 1.6 - - - +
216D ALA* 3.2 15.5 + - - +
217D ASN 3.2 0.6 - - - -
218D ALA* 1.3 81.4 - - - +
220D CYS* 1.3 57.7 + - - +
222D MET* 3.3 7.6 + - - +
223D LEU* 2.9 24.5 + - - +
319D GLY 4.6 2.3 - - - +
322D ALA* 3.9 21.1 - - + +
323D SER* 3.5 31.9 + - - -
326D ALA* 3.3 17.0 - - + +
327D ASN* 4.7 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ILE* 5.1 2.0 - - + +
207D LEU* 3.8 36.8 - - + -
211D VAL* 3.8 22.9 - - - -
216D ALA 2.9 17.2 + - - +
217D ASN* 3.0 10.1 + - - +
219D ASP* 1.3 73.9 - - - +
221D VAL* 1.3 61.2 + - - +
223D LEU* 3.6 8.3 - - + +
224D ALA* 2.9 29.8 + - - +
231D VAL* 5.4 0.2 - - - +
242D PHE* 3.8 5.7 - - + -
273D ILE* 4.4 10.5 - - - -
322D ALA* 4.3 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D ASN 2.9 20.3 + - - +
218D ALA* 3.4 12.1 - - - +
219D ASP 3.3 0.2 - - - -
220D CYS* 1.3 76.6 - - - +
222D MET* 1.3 63.5 + - - +
224D ALA* 3.3 1.0 + - - +
225D GLU* 2.9 47.5 + - - +
242D PHE* 3.6 14.1 - - + -
243D PRO* 3.6 33.7 - - + -
246D HIS* 3.7 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D ALA 3.0 12.7 + - - +
219D ASP* 3.3 12.8 + - - +
221D VAL* 1.3 76.6 - - - +
223D LEU* 1.3 58.3 + - - +
225D GLU* 3.3 11.4 + - - +
226D ARG* 2.9 61.0 + - + +
326D ALA* 3.4 30.3 - - + +
327D ASN* 3.5 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D LEU* 5.2 0.7 - - + -
205D ILE* 4.3 12.6 - - + -
219D ASP 2.9 17.7 + - - +
220D CYS* 3.6 9.4 - - - +
222D MET* 1.3 77.4 - - - +
224D ALA* 1.3 57.5 + - - +
226D ARG* 3.4 3.2 + - - +
227D LEU* 3.0 44.3 + - + +
271D LEU* 4.0 15.0 - - + -
273D ILE* 3.8 28.5 - - + -
322D ALA* 5.3 3.4 - - - +
325D LEU* 4.1 22.2 - - + +
326D ALA* 4.1 10.3 - - + +
329D VAL* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ILE* 3.8 12.5 - - + +
220D CYS 2.9 16.6 + - - +
221D VAL 3.7 3.8 - - - +
223D LEU* 1.3 78.4 - - - +
225D GLU* 1.3 53.2 + - - +
227D LEU* 4.9 0.2 - - - -
228D LYS* 2.8 28.4 + - - -
229D ALA 3.0 15.7 + - - +
231D VAL* 3.6 31.2 - - + -
242D PHE* 4.0 9.4 - - + -
246D HIS* 5.2 0.2 - - + -
248D CYS* 4.0 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D VAL* 2.9 31.0 + - - +
222D MET* 3.8 8.3 - - - +
224D ALA* 1.3 73.6 - - - +
226D ARG* 1.3 62.8 + - - +
228D LYS* 2.9 33.2 + - - +
246D HIS* 2.9 36.4 + - + +
331D GLU* 4.4 2.0 - - - +
336D LEU* 4.4 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D MET* 2.9 50.2 + - + +
223D LEU 3.7 1.1 - - - +
225D GLU* 1.3 78.9 - - - +
227D LEU* 1.3 56.0 + - - +
228D LYS* 3.7 1.2 + - - -
326D ALA 4.4 6.7 + - - +
327D ASN* 5.9 0.8 + - - +
329D VAL* 3.7 42.6 + - + -
330D GLU 3.5 2.9 - - - +
331D GLU* 3.2 44.2 + - - +
332D SER* 2.7 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D LEU* 4.0 44.4 - - + +
198D ASN* 4.7 2.9 - - - +
203D PRO* 4.2 9.4 - - + +
205D ILE* 4.4 14.1 - - + -
223D LEU* 3.0 41.3 + - + +
226D ARG* 1.3 76.5 - - - +
228D LYS* 1.3 70.1 + - - +
229D ALA* 3.1 15.7 + - + +
271D LEU* 5.3 2.0 - - + -
329D VAL* 4.2 20.0 - - + -
330D GLU 4.6 5.2 - - - +
332D SER* 4.2 1.8 - - - -
334D ARG* 2.8 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D PRO* 6.1 0.2 - - - +
224D ALA 2.8 11.6 + - - -
225D GLU 2.9 20.0 + - - +
226D ARG 3.2 2.8 + - - -
227D LEU* 1.3 79.9 - - - +
229D ALA* 1.3 56.6 + - - +
230D PRO* 4.2 2.4 - - - +
331D GLU* 2.8 35.2 + - - -
332D SER* 3.2 20.0 + - - +
333D SER 5.3 0.2 - - - -
334D ARG* 3.3 39.2 + - + +
335D GLN 3.8 14.4 - - - +
336D LEU* 3.8 28.3 - - + +
337D PRO* 3.5 22.2 - - - +
----------------------------------------------------------
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