Contacts of the helix formed by residues 215 - 234 (chain A) in PDB entry 1F7U
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 215 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ALA 4.0 1.6 + - - -
212A LEU 4.1 3.6 - - - -
213A VAL 3.5 0.4 - - - -
214A LYS* 1.3 85.0 - - + +
216A PRO* 1.3 76.6 - - - +
217A ILE* 3.9 8.1 + - - +
218A HIS* 2.9 39.9 + - + +
219A HIS* 3.2 22.5 + - - +
276A LYS* 3.8 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LEU* 3.7 21.5 - - + +
213A VAL 4.8 1.8 - - - +
214A LYS 4.3 1.1 - - - +
215A ASP* 1.3 90.6 - - - +
217A ILE* 1.3 60.9 + - + +
218A HIS 2.9 0.7 + - - -
219A HIS* 3.7 0.3 - - - +
220A LEU* 2.7 46.0 + - + +
272A PHE* 3.5 57.4 - - + +
273A SER 4.8 0.4 - - - +
276A LYS* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE 4.9 9.9 - - - +
155A ALA 5.3 1.3 - - - +
156A LYS* 4.3 6.7 - - - +
157A PRO* 4.1 33.1 - - + +
158A PHE* 5.7 2.0 - - + -
215A ASP* 3.7 7.1 + - - +
216A PRO* 1.3 79.8 - - + +
218A HIS* 1.3 57.3 + - - +
220A LEU* 4.1 7.6 - - - +
221A PHE* 3.0 26.2 + - - +
273A SER* 4.2 20.4 - - - +
276A LYS* 4.2 22.9 - - + -
277A TYR* 3.8 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PRO* 5.7 2.2 - - - -
214A LYS* 6.5 0.7 - - + -
215A ASP* 2.9 33.8 + - + +
216A PRO 2.9 1.6 + - - -
217A ILE* 1.3 73.2 - - - +
219A HIS* 1.3 70.8 + - + +
221A PHE* 2.9 20.5 + + - +
222A ASP* 3.0 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PHE* 3.9 11.4 - + - -
206A TYR 3.9 9.6 - - - -
207A GLY* 3.9 5.3 - - - -
208A ASN* 3.0 44.8 + - + -
211A ALA* 3.9 11.4 - - + +
212A LEU* 3.9 36.3 - - + -
215A ASP 3.2 13.7 + - - +
216A PRO 3.9 0.9 - - - +
218A HIS* 1.3 83.2 - - + +
220A LEU* 1.3 63.6 + - - +
222A ASP* 3.1 16.3 + - + +
223A VAL* 3.0 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE 5.3 7.6 - - - +
155A ALA* 4.8 5.1 - - - +
199A LEU* 3.3 21.3 - - + +
203A PHE* 4.4 9.6 - - + -
212A LEU* 3.9 12.8 - - + -
216A PRO* 2.7 43.0 + - + +
217A ILE* 4.3 5.8 - - - +
219A HIS* 1.3 73.4 - - - +
221A PHE* 1.3 60.3 + - - +
223A VAL* 3.7 4.9 - - + +
224A TYR* 3.1 17.2 + - - +
269A PHE* 3.5 69.3 - - + +
272A PHE* 5.7 0.2 - - + -
273A SER* 4.6 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ALA 3.8 15.9 - - - +
156A LYS* 4.7 9.4 - - + -
157A PRO* 3.5 36.8 - - + -
217A ILE 3.0 20.6 + - - +
218A HIS* 2.9 11.7 + - - +
220A LEU* 1.3 75.7 - - - +
222A ASP* 1.3 67.0 + - - +
224A TYR* 3.0 9.2 + + + +
225A VAL* 2.8 55.7 + - + +
410A THR* 6.5 1.3 - - + -
417A PHE* 4.5 18.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A HIS* 3.0 40.3 + - - +
219A HIS* 3.5 17.2 + - + +
221A PHE* 1.3 81.1 - - - +
223A VAL* 1.3 54.0 + - + +
225A VAL* 3.1 9.3 + - - +
226A ARG* 2.7 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU* 4.3 10.3 - - + +
202A GLY* 3.2 39.5 - - - +
203A PHE* 3.4 14.6 - - + +
206A TYR* 4.4 15.8 - - + +
219A HIS* 3.0 47.5 + - + +
220A LEU* 3.7 8.7 - - + +
222A ASP* 1.3 77.2 - - + +
224A TYR* 1.3 53.4 + - - +
226A ARG* 3.7 5.5 - - - +
227A ILE* 2.7 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ALA* 4.4 7.6 - - + +
156A LYS* 3.3 39.9 + - + -
195A GLN* 3.8 21.1 - - - +
198A LEU* 3.3 24.0 - - + +
199A LEU* 3.4 26.9 - - + +
220A LEU 3.1 11.4 + - - +
221A PHE* 3.0 18.4 + + - +
223A VAL* 1.3 78.2 - - - +
225A VAL* 1.3 63.3 + - + +
227A ILE* 3.0 4.7 - - - +
228A ASN* 2.6 61.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PHE* 2.8 55.6 + - + +
222A ASP* 3.4 8.5 - - - +
224A TYR* 1.3 80.3 - - + +
226A ARG* 1.3 62.6 + - - +
228A ASN* 3.3 7.3 + - - +
229A LYS* 3.2 48.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A TYR* 3.4 49.5 + - + -
222A ASP 2.7 20.1 + - - +
223A VAL* 3.7 5.2 - - - +
225A VAL* 1.3 75.7 - - - +
227A ILE* 1.3 60.6 + - - +
229A LYS* 3.3 50.7 + - - +
230A ASP* 2.9 21.7 + - - +
233A GLU* 4.8 11.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
198A LEU* 3.6 42.6 - - + +
201A VAL* 4.3 2.7 - - + -
202A GLY* 3.7 29.4 - - - +
205A ARG* 4.4 12.3 - - - +
206A TYR* 4.6 4.2 - - + -
223A VAL* 2.7 22.7 + - + +
224A TYR* 3.0 27.6 - - + +
226A ARG* 1.3 72.4 - - - +
228A ASN* 1.3 62.7 + - - +
230A ASP* 3.3 24.1 + - - +
231A ILE* 3.5 13.0 + - - +
244A THR* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 2.9 23.4 - - - +
224A TYR* 2.6 67.3 + - - +
225A VAL* 3.6 7.5 - - - +
226A ARG 3.3 0.4 - - - -
227A ILE* 1.3 76.3 - - - +
229A LYS* 1.3 58.1 + - + +
231A ILE* 3.2 15.2 - - - +
232A GLU* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A VAL* 3.2 35.7 - - + +
226A ARG* 3.4 38.6 - - - +
227A ILE 3.2 0.2 - - - -
228A ASN* 1.3 77.8 - - + +
230A ASP* 1.3 56.7 + - - +
232A GLU* 4.0 15.5 - - - +
233A GLU* 2.7 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ARG* 5.5 3.6 - - - +
206A TYR* 2.6 40.8 + - - -
226A ARG* 2.9 27.1 + - - +
227A ILE* 3.3 19.8 + - + +
229A LYS* 1.3 78.3 - - - +
231A ILE* 1.3 53.1 + - - +
233A GLU* 4.6 6.2 - - - +
234A GLU* 2.6 39.7 + - - +
244A THR* 4.8 9.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
198A LEU* 4.1 19.3 - - + -
227A ILE 3.7 7.6 - - - +
228A ASN* 3.2 31.2 - - - +
230A ASP* 1.3 76.6 - - - +
232A GLU* 1.3 59.5 + - + +
233A GLU 3.5 0.2 - - - -
234A GLU* 3.5 16.4 - - - +
235A GLY* 4.4 5.7 + - - +
244A THR* 3.6 18.8 - - + -
245A ASN* 3.2 61.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ASN* 3.0 19.8 + - - +
229A LYS* 3.0 16.0 + - - +
231A ILE* 1.3 80.6 - - + +
233A GLU* 1.3 59.1 + - - +
235A GLY* 4.3 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ARG* 4.8 11.3 + - - -
229A LYS* 2.7 18.2 + - + +
230A ASP* 4.6 5.2 - - - +
232A GLU* 1.3 78.3 - - - +
234A GLU* 1.3 65.3 + - - +
235A GLY* 3.0 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ASP* 2.6 29.9 + - - +
231A ILE* 3.5 20.1 - - - +
233A GLU* 1.3 79.1 - - - +
235A GLY* 1.3 70.8 + - - +
237A SER* 2.8 30.4 + - - -
238A ILE* 4.7 8.3 - - + +
240A LEU* 5.0 3.6 - - - +
243A SER* 2.7 34.1 + - - +
244A THR* 3.6 16.1 + - - -
245A ASN* 4.4 6.6 + - - +
----------------------------------------------------------
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