Contacts of the helix formed by residues 208 - 225 (chain A) in PDB entry 4O91
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 GLU 208 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A HIS* 3.2 55.9 - - + +
151A ALA* 6.0 2.9 - - + -
153A ILE* 3.5 23.0 - - + +
207A SER* 1.3 86.7 + - - +
209A LYS* 1.3 84.2 + - + +
210A CYS 3.1 2.6 + - - -
211A ASP* 3.2 11.0 + - - +
212A VAL* 3.8 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLU* 4.8 0.7 - - - +
207A SER* 3.0 15.3 - - - +
208A GLU* 1.3 92.0 - - + +
210A CYS* 1.3 62.4 + - - +
211A ASP 3.3 0.4 - - - -
212A VAL* 3.2 23.5 + - + +
213A PHE 3.3 1.4 + - - -
271A PRO* 3.4 30.4 + - + +
272A SER* 4.2 10.0 + - - +
274A ARG* 2.7 51.6 + - + +
275A PRO 4.0 10.4 - - - +
276A SER* 3.9 24.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE* 3.9 20.2 - - - -
155A ARG* 3.9 23.6 - - - -
197A ALA* 3.8 9.3 + - + +
199A GLU* 4.0 4.8 + - - +
200A VAL* 3.6 24.0 - - + -
206A TYR* 4.1 5.2 - - + -
207A SER 3.2 22.8 + - - +
208A GLU 3.1 1.6 - - - -
209A LYS* 1.3 74.9 - - - +
211A ASP* 1.3 77.9 + - - +
213A PHE* 3.2 13.5 + - - +
214A SER* 3.2 15.8 + - - -
274A ARG* 3.8 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 3.9 11.6 - - + +
145A HIS* 2.9 26.6 + - + +
153A ILE* 3.6 6.7 - - - +
154A HIS* 2.9 32.1 + - - +
155A ARG* 2.9 29.3 + - - -
157A LEU* 3.8 15.0 - - + +
208A GLU 3.2 9.3 + - - +
210A CYS* 1.3 76.5 - - - +
212A VAL* 1.3 58.3 + - - +
214A SER* 3.2 7.0 + - - -
215A TRP* 3.0 27.4 + - - +
277A MET* 3.8 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A HIS* 5.1 0.7 - - + -
208A GLU* 4.4 2.9 - - + +
209A LYS* 3.2 25.1 + - + +
210A CYS 3.1 0.8 - - - -
211A ASP* 1.3 75.8 - - - +
213A PHE* 1.3 64.0 + - - +
215A TRP* 3.2 3.3 + - - +
216A GLY 3.1 18.5 + - - -
266A CYS* 3.6 26.0 - - + +
274A ARG* 3.7 18.2 - - + -
275A PRO* 3.3 28.7 - - + +
277A MET* 4.0 34.1 - - + +
280A ILE* 4.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ALA 5.1 1.3 - - - -
195A TRP* 3.8 7.4 - - - -
196A MET 3.3 20.9 - - - -
197A ALA* 3.5 24.9 - - + -
198A PRO* 3.7 18.8 - - + -
209A LYS 3.3 2.4 + - - -
210A CYS 3.2 9.9 + - - +
212A VAL* 1.3 79.1 - - - +
214A SER* 1.3 62.5 + - - +
216A GLY* 3.3 3.6 + - - -
217A ILE* 3.2 44.7 + - + +
229A PHE* 6.1 1.1 - + - -
243A VAL* 4.0 19.7 - - + -
248A ARG* 3.7 12.6 - - - -
266A CYS 3.4 23.7 + - - +
267A TRP* 3.4 27.5 - - - -
274A ARG* 3.9 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ARG 5.6 2.9 + - - -
157A LEU* 3.5 34.6 + - - +
195A TRP* 2.7 26.9 + - - -
196A MET* 4.8 1.2 - - - -
197A ALA 4.9 0.2 + - - -
210A CYS 3.2 11.9 + - - -
211A ASP* 3.2 10.9 + - - -
213A PHE* 1.3 78.7 - - - +
215A TRP* 1.3 58.6 + - - +
217A ILE* 3.0 6.4 + - - +
218A ILE* 2.9 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A CYS* 2.8 48.5 + - + +
137A CYS* 4.1 16.6 - - + -
138A SER* 3.8 14.2 - - - -
157A LEU* 4.9 2.4 - - + +
211A ASP 3.0 13.9 + - - +
212A VAL* 3.2 7.4 + - - +
214A SER* 1.3 75.3 - - - +
216A GLY* 1.3 63.7 + - - +
218A ILE* 3.2 13.8 + - + +
219A LEU* 2.9 50.8 + - + -
262A LEU* 3.7 21.1 - - + -
263A MET* 5.4 0.2 - - - -
266A CYS* 3.8 24.5 - - - -
277A MET* 3.7 18.4 - - + -
280A ILE* 3.5 31.4 - - + -
284A MET* 3.8 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A VAL 3.1 10.9 + - - -
213A PHE 3.7 3.8 - - - -
214A SER 3.2 0.4 - - - -
215A TRP* 1.3 86.9 - - - +
217A ILE* 1.3 60.0 - - - +
219A LEU* 3.2 5.6 + - - +
220A TRP* 3.2 18.7 + - - +
263A MET* 4.1 6.4 - - - +
266A CYS* 3.9 17.0 - - - -
267A TRP* 3.6 16.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
194A ALA 3.5 18.4 - - - +
195A TRP* 3.5 25.4 - - + -
213A PHE* 3.2 41.5 + - + +
214A SER 3.0 7.8 + - - +
216A GLY* 1.3 73.8 - - - +
218A ILE* 1.3 63.6 + - - +
220A TRP* 3.2 7.4 + - - +
221A GLU* 2.9 20.7 + - - +
228A PRO* 3.8 21.3 - - + -
229A PHE* 4.7 4.5 - - + -
248A ARG* 5.3 0.2 - - - -
249A PRO* 3.9 22.4 - - + -
267A TRP* 3.7 22.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
112A LEU* 4.5 5.6 - - + -
134A CYS* 4.5 9.2 - - - -
137A CYS* 4.9 8.5 - - + -
157A LEU* 3.9 12.8 - - + -
158A LYS* 3.9 23.3 - - - +
159A PRO* 4.3 10.8 - - + -
162A LEU* 3.9 27.6 - - + -
195A TRP* 4.0 14.6 - - + -
214A SER 2.9 21.2 + - - +
215A TRP* 3.2 11.9 + - + +
217A ILE* 1.3 77.5 - - - +
219A LEU* 1.3 60.2 + - - +
221A GLU* 3.1 7.8 + - - +
222A VAL* 2.9 38.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
130A ALA 5.4 0.2 - - - +
131A MET* 4.2 17.3 - - - -
134A CYS* 3.6 32.3 - - + -
215A TRP* 2.9 40.9 + - + +
216A GLY* 3.2 10.1 + - - +
218A ILE* 1.3 74.5 - - - +
220A TRP* 1.3 62.7 + - - +
222A VAL* 3.3 5.5 - - + +
223A ILE* 3.3 38.3 + - + +
259A ILE* 4.3 11.2 - - + +
262A LEU* 4.9 3.6 - - + -
263A MET* 3.7 36.3 - - + +
284A MET* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLY 3.2 9.1 + - - +
217A ILE* 3.4 9.2 - - - +
219A LEU* 1.3 79.8 - - - +
221A GLU* 1.3 64.1 + - + +
223A ILE* 3.3 1.9 + - - +
224A THR* 2.9 53.8 + - + +
226A ARG* 3.5 36.6 - - + -
227A LYS 4.4 1.8 - - - -
228A PRO* 3.7 29.2 - - + -
229A PHE 5.3 1.1 - - - -
249A PRO* 3.4 22.1 - - + +
250A PRO* 2.8 51.9 + - + -
252A ILE* 3.5 24.6 - - + +
263A MET* 3.8 16.3 - - - +
267A TRP* 3.9 15.7 - + + -
478A VAL* 4.4 4.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
113A TYR* 5.3 0.9 - - - -
116A LEU* 4.0 7.2 - - + +
117A HIS* 2.8 29.7 + - - +
159A PRO* 3.4 23.0 - - - +
195A TRP* 2.8 36.5 + - - -
217A ILE 2.9 11.5 + - - +
218A ILE* 3.1 10.1 + - - +
220A TRP* 1.3 88.2 - - + +
222A VAL* 1.3 57.8 + - + +
224A THR* 3.5 1.7 + - - -
225A ARG* 2.7 31.9 + - - -
226A ARG 3.3 14.8 + - - +
227A LYS* 4.7 0.9 - - - +
228A PRO* 3.5 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.1 25.4 - - + -
116A LEU* 4.1 16.2 - - + -
125A TYR* 2.5 35.5 + - - +
130A ALA* 3.8 26.4 - - + +
133A TRP* 4.4 11.0 - - + -
134A CYS* 3.7 22.2 - - - -
218A ILE* 2.9 24.0 + - + +
219A LEU* 3.3 12.8 - - + +
221A GLU* 1.3 76.7 - - + +
223A ILE* 1.3 66.2 + - + +
482A VAL* 4.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ALA* 4.7 6.3 - - + -
131A MET* 4.8 5.4 - - - -
219A LEU* 3.3 30.7 - - + +
220A TRP 3.3 3.7 + - - +
221A GLU 3.2 0.6 - - - -
222A VAL* 1.3 84.7 - - + +
224A THR* 1.3 57.0 + - - +
252A ILE* 3.9 19.5 - - + -
255A LEU* 4.0 13.7 - - + -
259A ILE* 4.1 7.6 - - + -
263A MET* 3.9 20.0 - - + -
480A PRO* 4.1 13.7 - - + -
481A TYR* 2.8 22.9 + - - +
482A VAL* 3.3 18.8 + - + -
484A PHE* 4.1 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TRP* 2.9 36.4 + - + +
221A GLU 3.5 1.2 + - - -
223A ILE* 1.3 77.3 - - + +
225A ARG* 1.3 69.8 + - - +
226A ARG* 3.2 36.2 + - - +
252A ILE* 3.7 33.0 - - + -
468A HIS* 5.1 2.6 + - - -
478A VAL* 4.0 10.1 - - + -
479A GLU 4.4 8.4 - - - +
480A PRO* 4.4 0.7 - - - -
481A TYR* 3.5 14.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
115A VAL 2.9 25.3 + - - -
116A LEU* 3.1 26.7 + - + +
117A HIS* 3.8 13.2 + - - -
122A LEU* 3.6 18.7 - - - +
123A PRO* 2.7 30.5 + - - +
125A TYR* 3.4 33.5 - - + +
221A GLU 2.7 20.4 + - - -
222A VAL 3.9 0.6 + - - -
223A ILE 3.5 2.0 - - - -
224A THR* 1.3 75.9 - - - +
226A ARG* 1.3 57.5 + - - +
302A CYS* 3.9 9.5 - - - -
468A HIS* 3.7 32.1 + - + -
470A LEU* 6.1 0.7 - - - +
481A TYR* 2.9 41.6 + - + -
----------------------------------------------------------
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