Contacts of the helix formed by residues 216 - 231 (chain A) in PDB entry 3BWC
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 ASP 216 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLN* 3.3 26.2 - - - +
211A GLU* 3.9 11.2 - - + +
212A SER 3.2 15.2 + - - +
215A LEU* 1.3 84.6 - - + +
217A LEU* 1.3 65.3 + - - +
218A GLU* 3.2 13.2 + - - +
219A LEU* 3.2 46.1 + - - +
220A ILE* 3.5 12.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
212A SER 3.5 4.5 + - - -
213A ILE* 3.4 25.3 + - + +
214A TRP 4.5 3.6 + - - +
216A ASP* 1.3 74.7 - - - +
218A GLU* 1.3 79.1 + - - +
220A ILE* 3.2 14.8 + - + +
221A GLU* 3.3 29.4 + - - +
296A PHE* 4.0 30.1 - - + +
297A ALA* 3.7 20.2 - - + -
299A HIS* 4.3 3.1 - - + -
300A ILE* 3.5 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ASP* 3.2 9.3 - - - +
217A LEU* 1.3 99.6 + - - +
219A LEU* 1.3 61.4 + - - +
221A GLU* 3.5 18.0 + - - +
222A LYS* 3.2 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLU* 3.6 19.1 - - + +
216A ASP* 3.2 36.6 + - - +
217A LEU 3.3 0.4 - - - -
218A GLU* 1.3 76.0 - - - +
220A ILE* 1.3 59.9 + - - +
222A LYS* 3.7 11.5 - - + +
223A MSE 2.9 57.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLY* 5.5 0.4 - - - -
211A GLU* 3.2 39.7 - - + +
212A SER 3.5 20.4 - - - +
213A ILE* 3.7 15.3 - - + +
216A ASP 3.5 9.8 + - - +
217A LEU* 3.2 9.6 + - - +
219A LEU* 1.3 75.4 - - - +
221A GLU* 1.3 54.5 + - - +
223A MSE 3.4 6.4 + - - +
224A SER* 2.8 35.9 + - - -
237A TYR* 3.6 28.3 - - + -
253A LEU* 4.8 6.4 - - + +
300A ILE* 3.4 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 3.3 25.5 + - - +
218A GLU* 3.7 18.1 - - - +
219A LEU 3.4 0.2 - - - -
220A ILE* 1.3 78.6 - - - +
222A LYS* 1.3 62.7 + - + +
224A SER* 3.4 6.2 + - - -
225A ARG* 3.0 38.0 + - - +
299A HIS* 2.7 40.5 + - + +
300A ILE* 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A GLU* 3.2 26.1 + - - +
219A LEU* 3.7 11.4 - - + +
221A GLU* 1.3 79.3 - - + +
223A MSE 1.3 56.6 + - - +
225A ARG* 3.3 23.0 + - - +
226A PHE* 2.8 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 5.6 6.3 - - + -
193A TYR* 4.9 6.3 - - + +
208A ASN* 4.2 18.2 - - - +
209A GLN 4.5 12.6 - - - +
210A GLY* 4.7 5.2 - - - -
211A GLU* 4.5 13.9 - - + +
219A LEU* 2.9 51.1 + - + +
220A ILE* 3.7 6.1 - - - +
222A LYS* 1.3 76.2 - - - +
224A SER* 1.3 56.3 + - - +
226A PHE* 3.8 11.1 - - + +
227A ILE* 3.0 44.3 + - + +
253A LEU* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ILE 2.8 19.0 + - - -
221A GLU* 3.6 8.1 - - - -
222A LYS 3.2 0.2 - - - -
223A MSE 1.3 78.2 - - - +
225A ARG* 1.3 60.5 + - - +
227A ILE* 3.6 0.9 + - - +
228A ARG* 3.3 26.2 + - - +
235A VAL* 3.2 36.8 + - - +
253A LEU* 4.3 16.9 - - - +
300A ILE* 4.3 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLU* 3.0 31.4 + - - +
222A LYS* 4.0 24.3 + - - +
224A SER* 1.3 73.6 - - - +
226A PHE* 1.3 61.0 + - - +
228A ARG* 3.1 24.1 + - + +
229A GLU* 2.8 57.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PHE 4.7 2.0 - - - -
189A GLY* 3.5 26.2 - - - -
190A GLU* 3.6 27.6 - - + -
193A TYR* 3.3 34.3 - + + -
222A LYS 2.8 20.5 + - - +
223A MSE 3.8 12.8 - - + +
225A ARG* 1.3 76.9 - - - +
227A ILE* 1.3 57.2 + - + +
229A GLU* 3.4 14.5 + - + +
230A THR* 2.7 43.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
193A TYR* 4.1 29.6 - - + +
208A ASN* 5.1 3.8 - - + +
223A MSE 3.0 28.9 + - + +
224A SER* 3.8 4.0 - - - +
226A PHE* 1.3 83.5 - - + +
228A ARG* 1.3 63.9 + - - +
230A THR* 3.4 14.3 + - - -
232A PHE* 3.4 40.7 + - + -
235A VAL* 4.5 9.4 - - + -
253A LEU* 3.7 29.8 - - + -
255A CYS* 4.1 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A SER* 3.3 14.3 + - - +
225A ARG* 3.1 30.8 + - + +
227A ILE* 1.3 77.4 - - - +
229A GLU* 1.3 64.4 + - + +
231A GLY* 3.2 12.3 + - - -
232A PHE* 3.5 22.8 - - + +
233A ALA 4.2 14.1 - - - +
234A SER* 4.6 1.6 - - - +
235A VAL* 3.2 50.7 + - + +
236A GLN* 5.7 0.8 - - - +
300A ILE 4.7 7.7 + - - -
302A ASN* 5.5 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LYS* 4.5 4.0 + - - -
225A ARG* 2.8 45.6 + - + +
226A PHE* 3.8 16.1 + - - +
228A ARG* 1.3 73.9 - - + +
230A THR* 1.3 64.6 + - - +
231A GLY* 3.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLU* 4.4 3.6 + - + +
193A TYR* 3.5 20.7 - - + +
194A LYS* 3.2 70.6 + - + +
197A LEU* 3.7 7.3 - - + +
226A PHE* 2.7 32.6 + - - -
227A ILE* 3.4 13.0 - - - -
228A ARG 3.2 0.4 - - - -
229A GLU* 1.3 77.1 - - - +
231A GLY* 1.3 56.4 + - - +
232A PHE* 4.7 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 3.4 18.5 - - - +
228A ARG 3.2 5.3 + - - -
229A GLU 3.2 4.3 - - - -
230A THR* 1.3 79.8 - - - +
232A PHE* 1.3 67.7 + - - +
233A ALA* 3.6 2.1 + - - -
257A LYS* 4.9 3.1 - - - +
----------------------------------------------------------
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