Contacts of the helix formed by residues 220 - 233 (chain A) in PDB entry 5K6S
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 GLY 220 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 3.5 21.0 + - - -
179A ARG* 4.0 2.7 - - - -
218A HIS* 3.0 15.4 + - - -
219A ASN* 1.3 80.0 - - - +
221A ILE* 1.3 63.4 + - - +
222A ALA 3.2 2.9 - - - -
223A GLU* 3.4 12.7 + - - +
224A LEU* 3.1 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ILE* 4.5 4.5 - - + -
208A PHE* 3.8 33.3 - - + -
211A PHE* 3.7 33.2 - - + -
218A HIS* 3.4 40.4 - - + +
219A ASN 3.5 2.0 - - - -
220A GLY* 1.3 77.1 - - - +
222A ALA* 1.3 63.2 + - - +
224A LEU* 3.5 2.3 + - - +
225A LEU* 3.1 26.3 + - + +
254A LEU* 4.7 3.1 - - + -
263A TYR* 3.6 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASN 5.1 1.3 + - - +
220A GLY* 3.2 0.8 - - - -
221A ILE* 1.3 79.1 - - - +
223A GLU* 1.3 73.9 + - - +
225A LEU* 3.1 6.5 + - - +
226A GLU* 3.0 19.4 + - - +
262A VAL* 4.1 12.6 - - + +
263A TYR* 3.7 28.3 - - + +
266A GLN* 3.6 23.7 - - - +
----------------------------------------------------------
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 PHE* 4.1 11.9 - - + -
176A PRO* 5.0 2.9 - - - +
179A ARG* 3.1 56.1 + - + +
180A ASP* 4.7 2.4 + - - +
183A LYS* 3.8 24.5 - - + +
219A ASN 3.7 2.4 - - - +
220A GLY* 3.4 22.5 + - - +
222A ALA* 1.3 82.1 - - - +
224A LEU* 1.3 63.3 + - - +
226A GLU* 3.3 11.5 + - - +
227A ILE* 3.2 26.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
168A LEU* 4.0 18.2 - - + -
171A PHE* 3.9 26.7 - - + -
186A LEU* 4.3 7.9 - - + -
204A ILE* 4.3 18.8 - - + -
207A ILE* 4.0 36.6 - - + -
208A PHE* 4.0 20.0 - - + -
218A HIS* 4.5 5.6 - - + -
220A GLY 3.1 24.5 + - - +
221A ILE* 3.8 4.3 - - - +
223A GLU* 1.3 75.0 - - - +
225A LEU* 1.3 63.8 + - - +
227A ILE* 3.2 6.8 + - + +
228A LEU* 3.0 29.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
208A PHE* 3.7 21.8 - - + -
221A ILE* 3.1 22.4 + - + +
222A ALA 3.5 6.3 - - - +
224A LEU* 1.3 76.3 - - - +
226A GLU* 1.3 57.7 + - - +
228A LEU* 3.2 7.2 + - + -
229A GLY* 2.9 25.1 + - - -
251A LEU* 3.8 28.3 - - + -
254A LEU* 4.1 6.1 - - + -
263A TYR* 3.6 34.5 - - + +
266A GLN* 3.7 13.4 - - + +
267A LEU* 3.8 21.1 - - + +
269A TYR* 5.9 0.2 - - - -
270A CYS* 3.2 16.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LYS* 3.3 39.1 + - + +
222A ALA 3.0 11.4 + - - +
223A GLU* 3.5 13.6 - - - +
224A LEU 3.2 0.2 - - - -
225A LEU* 1.3 76.8 - - - +
227A ILE* 1.3 61.2 + - - +
229A GLY* 3.6 1.8 + - - -
230A SER* 3.5 14.2 + - - -
266A GLN* 4.2 25.3 + - + +
269A TYR* 6.0 2.3 - - - -
667B LYS 4.9 5.5 - - - +
668B LYS* 4.9 9.7 - - + +
669B LEU* 4.0 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 4.2 5.4 - - + -
183A LYS* 3.4 39.7 - - + +
186A LEU* 3.9 34.5 - - + +
187A HIS* 4.3 18.6 - - + +
190A TYR* 5.5 2.7 - - + -
200A ILE* 6.3 1.1 - - + -
204A ILE* 5.3 4.0 - - + -
223A GLU 3.3 15.5 - - - +
224A LEU* 3.2 11.1 + - + +
226A GLU* 1.3 74.9 - - - +
228A LEU* 1.3 69.0 + - + +
230A SER* 3.0 15.4 + - - -
231A ILE* 3.2 26.4 + - + +
669B LEU* 4.0 9.6 - - + -
672B ILE* 5.5 1.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
201A ARG* 6.3 1.8 - - + -
204A ILE* 3.7 32.8 - - + -
208A PHE* 3.5 25.6 - - + -
224A LEU 3.0 16.6 + - - +
225A LEU* 3.2 15.9 + - + +
227A ILE* 1.3 80.0 - - + +
229A GLY* 1.3 56.8 + - - +
231A ILE* 2.9 18.1 + - + +
232A ILE* 2.8 39.8 + - + +
246A PHE* 3.4 36.1 - - + -
251A LEU* 4.9 0.7 - - + -
270A CYS* 4.2 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU 2.9 15.0 + - - -
226A GLU* 3.6 3.1 + - - -
227A ILE 3.3 0.2 - - - -
228A LEU* 1.3 75.8 - - - +
230A SER* 1.3 60.2 + - - +
232A ILE* 4.1 6.4 - - - +
233A ASN* 3.2 25.8 + - - +
269A TYR* 4.1 27.0 - - - -
270A CYS* 3.7 14.1 - - - -
273A GLN* 4.5 1.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
187A HIS* 3.1 21.2 + - - -
226A GLU 3.5 6.9 + - - -
227A ILE 3.0 12.9 + - - -
229A GLY* 1.3 76.3 - - - +
231A ILE* 1.3 60.3 + - - +
233A ASN* 4.0 5.0 + - - +
234A GLY 4.1 0.9 + - - -
669B LEU* 4.0 18.4 - - - -
670B SEP 2.4 30.7 + - - -
671B PRO* 3.4 8.4 - - - +
672B ILE* 2.8 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A TYR* 3.4 58.6 - - + +
200A ILE* 6.0 0.4 - - + -
201A ARG* 5.0 10.8 - - + -
204A ILE* 5.7 2.5 - - + -
227A ILE* 3.3 25.6 - - + +
228A LEU* 2.9 22.1 + - + +
230A SER* 1.3 78.2 - - - +
232A ILE* 1.3 65.6 + - + +
233A ASN 3.2 0.2 - - - -
234A GLY* 3.1 13.3 + - - -
235A PHE* 3.6 30.0 + - + -
672B ILE* 3.7 15.5 - - + +
674B GLU* 5.7 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 2.8 31.9 + - + +
229A GLY* 4.1 3.4 - - - +
231A ILE* 1.3 72.9 - - + +
233A ASN* 1.3 63.1 + - - +
234A GLY 3.1 1.4 + - - -
235A PHE* 3.2 44.9 + - + +
246A PHE* 5.1 3.6 - - + -
251A LEU* 4.5 2.7 - - + -
270A CYS* 4.0 28.5 - - + +
273A GLN* 3.8 22.7 - - + +
274A PHE* 3.4 43.3 - - + +
277A LYS* 3.3 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLY 3.2 16.0 + - - +
230A SER* 4.1 7.2 - - - +
231A ILE 3.2 0.8 - - - -
232A ILE* 1.3 78.3 - - - +
234A GLY* 1.3 56.6 + - - +
235A PHE 3.5 0.4 - - - -
269A TYR* 4.3 7.5 + - - +
273A GLN* 2.5 34.9 + - - +
277A LYS* 3.1 19.5 + - - +
671B PRO* 3.3 28.5 - - + +
----------------------------------------------------------
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