Contacts of the helix formed by residues 214 - 231 (chain A) in PDB entry 3RK6
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 214 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 4.1 14.8 - - + -
199A TYR* 3.9 9.5 + - - +
202A LEU* 4.5 7.7 + - + +
204A ILE* 3.7 26.4 - - + +
213A ARG* 1.3 72.2 - - - +
215A ASP* 1.3 64.2 + - - +
216A ILE* 3.4 2.0 - - + -
217A LEU* 3.1 41.0 + - + +
218A GLN* 3.2 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ARG 3.5 8.3 + - - +
214A ALA* 1.3 66.5 - - - +
216A ILE* 1.3 67.3 + - - +
217A LEU 3.0 2.2 - - - -
218A GLN* 2.9 27.1 + - - +
219A VAL* 3.0 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 3.9 39.7 - - + +
168A ARG* 3.3 48.7 + - + +
214A ALA* 4.6 2.9 - - + -
215A ASP* 1.3 79.3 - - - +
217A LEU* 1.3 62.1 + - + +
219A VAL* 3.9 9.8 - - + +
220A GLY 3.0 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 3.9 24.9 - - + -
167A CYS* 4.7 6.3 - - + -
168A ARG* 4.3 7.9 - - - +
195A LEU* 4.2 35.3 - - + +
198A LEU* 3.9 22.4 - - + +
199A TYR* 3.6 38.8 - - + +
202A LEU* 4.6 1.6 - - + -
214A ALA* 3.1 23.5 + - + +
215A ASP 3.0 1.0 - - - -
216A ILE* 1.3 79.9 - - + +
218A GLN* 1.3 60.5 + - - +
219A VAL 3.2 0.4 - - - -
221A LEU* 2.9 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TYR* 2.8 41.9 + - + +
213A ARG* 5.4 3.4 - - - +
214A ALA 3.2 8.2 + - - +
215A ASP* 2.9 20.0 + - - +
217A LEU* 1.3 76.4 - - - +
219A VAL* 1.3 64.9 + - + +
221A LEU* 3.6 2.6 + - - +
222A ARG* 3.4 18.5 + - - +
251A LEU* 3.8 17.5 - - + +
254A ALA* 3.2 27.1 - - - +
255A TRP* 4.5 19.2 + - - +
260A LYS* 5.1 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ARG* 5.3 3.1 - - - +
171A TYR* 4.8 3.8 - - + +
215A ASP* 3.0 24.3 + - - +
216A ILE* 4.0 10.5 - - + +
218A GLN* 1.3 77.3 - - + +
220A GLY* 1.3 64.3 + - - +
222A ARG* 3.2 7.7 + - - +
223A GLU* 3.2 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ARG* 3.7 8.9 - - - +
171A TYR* 3.2 27.2 - - - -
195A LEU* 5.2 0.4 - - - -
216A ILE 3.0 18.8 + - - -
217A LEU 3.8 0.4 - - - -
219A VAL* 1.3 76.9 - - - +
221A LEU* 1.3 56.8 + - - +
223A GLU 3.2 1.2 + - - -
224A LEU* 2.8 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A VAL 4.3 1.1 - - - +
195A LEU* 4.1 15.7 - - + +
196A GLY* 3.9 28.5 - - - +
199A TYR* 3.7 37.5 - - + -
217A LEU 2.9 23.8 + - - +
218A GLN 3.9 4.5 - - - +
219A VAL 3.3 0.2 - - - -
220A GLY* 1.3 71.9 - - - +
222A ARG* 1.3 58.7 + - - +
224A LEU* 3.4 11.3 + - + +
225A LEU* 2.9 34.2 + - - +
243A LEU* 4.0 19.5 - - + +
247A THR* 4.1 16.2 - - - +
251A LEU* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A GLN 3.4 9.1 + - - +
219A VAL* 3.2 11.5 + - - +
221A LEU* 1.3 77.6 - - - +
223A GLU* 1.3 74.0 + - - +
225A LEU* 3.4 8.0 + - - +
226A ASN* 2.9 59.8 + - - +
255A TRP* 4.1 16.0 - - + +
262A ASP* 2.9 45.0 + - - +
265A GLU* 2.9 34.4 + - - +
266A ILE* 3.3 24.5 - - - +
269A ARG* 3.3 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR* 2.7 31.0 - - + +
174A LYS* 3.6 22.6 + - - +
219A VAL* 3.3 18.6 - - + +
220A GLY 3.2 1.7 + - - +
222A ARG* 1.3 95.5 - - - +
224A LEU* 1.3 65.0 + - - +
226A ASN* 3.3 19.1 + - - +
227A ALA* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR* 4.0 6.3 - - + -
174A LYS* 3.6 19.7 - - + -
188A PHE* 3.6 32.1 - - + -
191A PHE* 4.1 12.1 - - + -
192A VAL* 4.1 28.5 - - + -
195A LEU* 3.8 28.0 - - + -
220A GLY 2.8 22.3 + - - +
221A LEU* 3.7 14.8 - - + +
223A GLU* 1.3 72.5 - - - +
225A LEU* 1.3 66.5 + - - +
227A ALA* 3.3 4.5 + - - +
228A LEU* 2.9 30.8 + - + +
243A LEU* 5.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU 2.9 24.3 + - - +
222A ARG* 3.6 7.9 - - - +
224A LEU* 1.3 75.5 - - - +
226A ASN* 1.3 63.4 + - - +
228A LEU* 3.1 5.6 + - + +
229A PHE* 2.9 35.0 + - + -
240A ALA* 3.8 27.6 - - + +
243A LEU* 3.7 24.9 - - + -
244A LEU* 3.9 39.7 - - + -
251A LEU* 4.7 11.4 - - + -
255A TRP* 5.1 1.6 - - + -
266A ILE* 4.0 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ARG* 2.9 56.3 + - - +
223A GLU* 3.5 28.5 + - - +
224A LEU 3.2 0.2 - - - -
225A LEU* 1.3 76.6 - - - +
227A ALA* 1.3 61.6 + - - +
229A PHE* 3.4 3.2 + - - -
230A SER* 3.0 29.2 + - - -
266A ILE* 4.0 1.7 - - - +
269A ARG* 3.2 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LYS* 3.9 34.1 - - + +
175A ASP* 4.2 11.0 + - - +
178A ALA* 3.5 10.5 - - + +
188A PHE* 4.6 4.5 - - + -
223A GLU 3.0 13.9 + - - +
224A LEU* 3.3 8.9 + - - +
226A ASN* 1.3 76.4 - - - +
228A LEU* 1.3 60.8 + - - +
230A SER* 3.5 4.0 + - - -
231A ASN* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PHE* 3.7 22.4 - - + -
189A HIS* 3.9 11.2 - - + -
192A VAL* 4.1 16.4 - - + -
224A LEU 2.9 24.8 + - - +
225A LEU* 3.7 8.5 - - + +
227A ALA* 1.3 75.6 - - - +
229A PHE* 1.3 64.3 + - - +
231A ASN 3.2 20.6 - - - +
232A PRO* 4.0 2.6 - - - +
236A ASN* 3.6 48.8 - - - +
237A LEU* 4.2 2.8 - - - +
239A CYS* 4.0 11.0 - - + -
240A ALA* 3.9 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 2.9 43.7 + - + +
226A ASN* 4.1 5.2 - - - +
228A LEU* 1.3 77.2 - - - +
230A SER* 1.3 59.8 + - - +
231A ASN 3.4 0.7 + - - -
232A PRO* 3.7 18.4 - - - +
237A LEU* 3.7 18.2 - - + -
240A ALA* 3.6 27.8 - - + -
244A LEU* 4.1 9.4 - - + -
266A ILE* 4.2 15.5 - - + -
269A ARG* 4.2 27.6 - - + +
270A ILE* 3.5 33.9 - - + -
273A VAL* 3.8 20.0 - - + +
287A LEU* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ASN 3.0 19.0 + - - -
227A ALA* 3.8 7.9 - - - -
228A LEU 3.3 0.4 - - - -
229A PHE* 1.3 74.9 - - - +
231A ASN* 1.3 69.7 + - - +
232A PRO* 3.6 7.0 - - - +
269A ARG* 4.1 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASP* 4.6 2.4 - - - +
178A ALA* 3.4 31.9 - - - +
179A LYS* 3.4 40.5 + - - +
227A ALA* 2.8 23.6 + - - +
228A LEU 3.2 6.9 - - - +
229A PHE 3.3 0.2 - - - -
230A SER* 1.3 87.9 + - - +
232A PRO* 1.4 51.9 - - - +
233A MET* 2.8 21.9 + - + +
236A ASN* 3.0 20.6 + - - +
----------------------------------------------------------
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