Contacts of the helix formed by residues 209 - 228 (chain A) in PDB entry 4BPU
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 HIS 209 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A TYR* 3.8 29.6 - + - -
207A LYS 3.7 4.6 + - - -
208A ILE* 1.3 72.2 - - - +
210A PRO* 1.3 79.9 - - + +
211A PHE* 3.2 14.4 + - - +
212A ILE* 2.7 43.2 + - + +
213A ARG 3.1 8.3 + - - -
168B ALA 4.0 6.4 + - - +
169B SER* 3.6 21.9 - - - +
198B ARG* 3.5 41.7 - - + +
200B VAL 2.8 25.1 + - - -
201B TYR* 4.8 5.2 - + - -
202B LEU 5.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ILE 3.5 4.2 - - - +
209A HIS* 1.3 91.0 - - + +
211A PHE* 1.3 56.4 + - - +
213A ARG* 3.5 24.2 - - + +
214A LYS* 2.8 53.7 + - - +
165B GLU* 3.9 18.8 - - - +
168B ALA* 4.1 7.4 - - + -
169B SER* 3.3 26.5 - - - +
201B TYR* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 4.6 8.3 - - + -
142A ILE* 5.7 0.9 - - + -
144A ARG* 3.6 25.0 + - - +
145A ALA* 3.8 8.5 - - + -
149A ASP* 3.9 1.5 + - - +
188A TYR* 3.7 46.4 - + + +
189A LEU* 3.4 50.5 - - + -
191A LEU* 4.2 8.3 - - + -
209A HIS* 3.0 12.3 + - - +
210A PRO* 1.3 77.7 - - - +
212A ILE* 1.3 65.6 + - + +
214A LYS* 3.8 1.2 - - - +
215A SER* 2.7 49.4 + - - -
302A PHE* 3.6 20.9 - + - -
198B ARG* 4.1 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LEU* 3.7 31.9 - - + -
204A LEU* 3.9 25.8 - - + -
207A LYS 6.0 0.4 - - - +
208A ILE* 3.8 12.1 - - + -
209A HIS* 2.7 33.7 + - + +
211A PHE* 1.3 78.4 - - + +
213A ARG* 1.3 54.4 + - - +
215A SER* 3.1 5.2 + - - -
216A ILE* 2.8 57.8 + - + +
298A LEU* 4.1 10.1 - - + -
198B ARG* 4.0 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ILE* 3.7 18.3 + - + +
209A HIS 3.1 7.9 + - - +
210A PRO* 3.5 27.3 - - + +
212A ILE* 1.3 78.9 - - - +
214A LYS* 1.3 85.2 + - - +
216A ILE* 3.2 8.2 + - - +
217A ASN* 2.9 48.3 + - - +
294A TRP* 6.5 1.1 - - + -
164B GLN* 6.0 0.8 - - - +
165B GLU* 3.2 35.1 + - - +
168B ALA* 5.2 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ARG* 3.4 47.0 - - - +
148A GLU* 4.3 8.8 + - - +
149A ASP* 4.2 8.3 + - - +
210A PRO* 2.8 34.2 + - - +
211A PHE 4.0 0.7 - - - +
213A ARG* 1.3 99.7 - - - +
215A SER* 1.3 61.5 + - - +
217A ASN* 3.6 9.3 + - - +
218A ILE* 3.2 29.5 + - - +
165B GLU* 4.4 2.8 + - - -
201B TYR* 4.2 18.6 + - - -
202B LEU 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 3.5 28.7 + - - +
144A ARG* 5.1 1.5 + - - +
211A PHE* 2.7 35.0 + - - -
212A ILE* 3.4 6.5 - - - -
214A LYS* 1.3 75.2 - - - +
216A ILE* 1.3 60.5 + - - +
218A ILE* 3.1 7.3 + - - +
219A ILE* 2.9 33.5 + - - +
298A LEU* 4.9 2.2 - - - -
302A PHE* 3.8 26.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
204A LEU* 4.8 1.3 - - + -
208A ILE* 4.9 2.5 - - + -
212A ILE* 2.8 41.9 + - + +
213A ARG* 3.6 8.3 - - - +
215A SER* 1.3 71.7 - - - +
217A ASN* 1.3 59.3 + - - +
219A ILE* 2.8 11.4 + - - +
220A LYS* 2.7 42.9 + - + +
294A TRP* 3.7 63.5 - - + +
297A MET* 4.6 7.2 - - + -
298A LEU* 4.0 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ARG* 2.9 39.2 + - - +
214A LYS* 3.9 8.0 - - - +
215A SER 3.3 0.2 - - - -
216A ILE* 1.3 77.2 - - - +
218A ILE* 1.3 63.4 + - - +
220A LYS* 3.5 39.2 + - - +
221A LYS* 3.5 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A MET* 4.7 4.0 - - - +
140A ARG* 3.9 45.1 - - + +
141A ILE* 3.9 37.2 - - + -
144A ARG* 4.2 18.8 - - + -
214A LYS 3.2 16.7 + - - +
215A SER* 3.1 7.7 + - - +
217A ASN* 1.3 77.9 - - + +
219A ILE* 1.3 63.6 + - - +
221A LYS* 3.2 10.4 + - + +
222A TYR* 3.1 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A MET* 4.2 12.8 - - - -
141A ILE* 3.8 23.3 - - + -
215A SER 2.9 17.2 + - - +
216A ILE* 2.8 9.5 + - + +
218A ILE* 1.3 76.6 - - - +
220A LYS* 1.3 50.8 + - - +
222A TYR* 2.8 7.1 + - - +
223A PHE* 2.8 36.2 + - + -
297A MET* 4.0 24.7 - - + +
298A LEU* 4.0 26.9 - - + -
301A CYS* 3.7 41.5 - - + +
302A PHE* 4.1 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ILE* 2.7 18.6 + - + +
217A ASN* 3.5 32.9 + - - +
219A ILE* 1.3 72.2 - - - +
221A LYS* 1.3 63.2 + - - +
222A TYR 3.1 0.7 + - - -
223A PHE* 3.5 6.1 + - - -
224A GLU* 4.7 2.8 + - - +
293A GLU* 5.1 7.0 - - - -
294A TRP* 4.2 27.4 - - - +
297A MET* 3.7 21.1 - - + -
1411A GOL 3.8 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 4.6 15.0 - - - +
217A ASN 3.5 7.3 + - - +
218A ILE* 3.2 13.8 + - - +
219A ILE 3.1 0.8 + - - -
220A LYS* 1.3 78.6 - - - +
222A TYR* 1.3 92.9 + - + +
224A GLU 5.6 0.2 - - - -
340A ASP* 4.0 7.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A THR* 3.9 23.1 - - + +
136A THR* 4.0 10.8 - - + -
137A MET* 3.7 31.6 - - + -
140A ARG* 3.0 38.7 + - - -
218A ILE* 3.1 30.1 - - + -
219A ILE 2.8 1.8 + - - +
221A LYS* 1.3 105.8 + - + +
223A PHE* 1.3 68.6 + - - +
224A GLU 3.3 2.9 + - - -
225A GLU* 3.4 9.0 + - - +
226A TYR* 3.0 22.4 + - - +
340A ASP* 2.5 32.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A MET* 5.6 0.2 - - - -
219A ILE* 2.8 17.0 + - + +
220A LYS 3.5 2.3 + - - +
222A TYR* 1.3 78.2 - - - +
224A GLU* 1.3 57.5 + - - +
226A TYR* 4.8 1.8 - - - -
227A ALA* 2.8 55.4 + - + +
228A LEU* 3.6 15.3 + - + -
233A ILE* 4.1 13.7 - - + -
269A TRP* 3.4 50.0 - + - -
296A ILE* 5.2 1.1 - - + -
297A MET* 3.7 37.2 - - + -
300A TYR* 4.8 3.6 - - + -
301A CYS* 3.8 23.6 - - - -
1411A GOL 3.8 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LYS 4.7 2.3 + - - +
222A TYR 3.3 1.0 + - - -
223A PHE* 1.3 78.2 - - - +
225A GLU* 1.3 62.3 + - - +
228A LEU* 3.2 16.0 + - + +
229A VAL* 3.2 27.3 + - + +
266A LEU* 3.3 34.0 - - + +
1411A GOL 3.5 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A THR* 5.6 4.0 + - - -
222A TYR* 3.4 8.4 + - - +
224A GLU* 1.3 80.1 - - - +
226A TYR* 1.3 58.9 + - - +
229A VAL* 3.5 13.9 - - + +
230A ASN* 3.0 50.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL 3.9 14.5 + - - -
119A ARG* 4.0 2.1 - - - +
130A LYS 3.3 26.2 - - - -
131A CYS* 4.1 3.6 - - - -
133A THR* 4.0 26.9 - - + -
134A LEU* 3.2 40.3 - - + +
137A MET* 4.3 6.7 - - + -
222A TYR 3.0 18.6 + - - +
223A PHE 4.8 0.4 - - - -
225A GLU* 1.3 79.2 - - - +
227A ALA* 1.3 72.5 + - + +
230A ASN* 3.6 7.4 - - - +
231A GLN* 2.9 56.9 + - + +
233A ILE* 5.9 1.3 - - + -
300A TYR* 4.1 6.3 + + + -
301A CYS* 3.8 28.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
223A PHE* 2.8 50.9 + - + +
226A TYR* 1.3 90.8 - - + +
228A LEU* 1.3 59.8 + - - +
229A VAL 3.6 0.2 - - - -
231A GLN* 4.0 4.9 - - - -
232A ASP 2.9 20.9 + - - -
233A ILE* 3.0 27.0 + - + +
300A TYR* 5.7 0.9 - - + -
301A CYS* 4.9 0.4 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
223A PHE* 4.0 17.7 - - + -
224A GLU* 3.2 24.5 + - + +
227A ALA* 1.3 80.6 - - - +
229A VAL* 1.3 63.0 + - - +
232A ASP* 3.7 8.5 - - - +
233A ILE* 4.3 14.4 - - + -
234A LEU* 4.5 1.6 - - + -
265A SER* 3.3 33.5 + - - +
266A LEU* 3.6 32.1 + - + +
269A TRP* 3.6 50.9 - - + -
1411A GOL 4.1 4.9 - - - +
----------------------------------------------------------
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