Contacts of the helix formed by residues 215 - 232 (chain J) in PDB entry 1S9C
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 215 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185J ALA* 3.7 29.2 - - + +
188J TYR* 3.4 30.8 - + + +
189J ARG* 3.6 13.9 - - + +
193J ASP* 3.2 43.7 + - + +
195J ASN 5.2 0.2 + - - -
198J HIS* 3.3 50.5 + + + +
214J LEU* 1.3 75.5 - - - +
216J GLY* 1.3 67.6 + - - +
217J LEU* 4.2 3.6 - - + +
218J CYS* 3.0 17.4 + - + +
219J THR* 3.4 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198J HIS* 4.8 2.6 - - - -
214J LEU 3.4 4.1 + - - -
215J HIS* 1.3 71.8 - - - +
217J LEU* 1.3 61.7 + - - +
218J CYS 3.1 0.3 + - - -
219J THR* 3.2 10.0 + - - -
220J PHE* 3.0 20.1 + - - +
246J PHE* 3.4 27.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J TYR* 4.4 2.9 + - - -
62J VAL* 3.4 33.2 - - + -
66J GLN* 3.2 32.1 - - + +
89J HIS* 4.1 20.4 - - + +
92J GLN* 4.0 15.7 - - + -
142J PHE* 5.1 1.1 - - + -
188J TYR* 3.3 22.8 + - + +
193J ASP* 5.9 0.4 - - - +
215J HIS* 3.2 2.7 - - + +
216J GLY* 1.3 74.7 - - - +
218J CYS* 1.3 57.9 + - - +
220J PHE* 3.1 17.7 - - + +
221J GLY* 2.9 22.5 + - - -
246J PHE* 3.8 20.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 218 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J GLY 3.2 27.1 - - - -
34J VAL* 3.5 2.7 - - - +
184J GLN* 4.1 1.8 - - - -
188J TYR* 3.8 36.3 - - + -
214J LEU* 4.0 22.2 - - + -
215J HIS* 3.0 13.2 + - + +
217J LEU* 1.3 75.8 - - - +
219J THR* 1.3 65.9 + - - +
220J PHE 3.0 1.3 - - - -
221J GLY* 3.0 2.9 + - - -
222J PHE* 2.9 42.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 219 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214J LEU* 3.9 12.2 + - - +
215J HIS 3.4 8.9 + - - -
216J GLY* 3.2 10.2 + - - -
218J CYS* 1.3 79.0 - - - +
220J PHE* 1.3 64.2 + - - +
222J PHE* 3.2 4.7 + - - +
223J SER* 3.1 23.7 + - - -
250J VAL* 3.9 15.9 - - + +
256J LEU* 3.7 35.9 - - + -
271J THR* 4.1 4.5 - - + -
280J VAL* 3.9 16.8 - - + -
281J ILE* 3.6 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 220 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J TYR* 5.0 1.1 - - - -
59J THR* 3.6 24.7 - - + -
62J VAL* 3.6 20.6 - - + -
92J GLN* 4.1 19.3 - - + -
94J LEU* 5.3 0.4 - - + -
216J GLY 3.0 14.5 + - - +
217J LEU* 3.1 27.6 - - + +
219J THR* 1.3 77.4 - - - +
221J GLY* 1.3 57.6 + - - +
223J SER* 4.0 1.4 - - - -
224J ALA* 2.9 33.9 + - + +
242J VAL* 3.0 34.3 - - + -
244J ALA* 3.6 33.0 - - + -
246J PHE* 4.1 11.7 - + + -
269J PHE* 5.2 7.2 - + - -
281J ILE* 3.7 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 221 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J TYR* 3.9 10.5 - - - -
34J VAL* 3.2 27.1 - - - +
59J THR* 4.0 10.0 + - - -
217J LEU 2.9 13.3 + - - -
218J CYS 3.0 0.8 + - - -
220J PHE* 1.3 75.6 - - - +
222J PHE* 1.3 52.3 + - - +
224J ALA* 3.4 1.5 + - - +
225J ARG* 2.8 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 222 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J VAL 3.2 26.0 - - - -
35J GLY* 3.5 24.0 - - - -
178J ASP* 3.7 36.3 - - + -
179J THR 4.8 6.5 - - - -
180J THR* 4.5 9.9 - - - -
184J GLN* 3.7 25.6 - - + -
214J LEU* 5.1 1.3 - - + -
218J CYS* 2.9 41.9 + - - -
219J THR* 3.2 8.1 - - - +
221J GLY* 1.3 73.9 - - - +
223J SER* 1.3 66.6 + - - +
225J ARG* 2.9 21.8 + - - +
226J ARG* 2.9 18.5 + - - +
256J LEU* 3.6 22.9 - - + -
258J THR* 5.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 223 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219J THR 3.1 9.5 + - - -
220J PHE 4.0 2.2 - - - -
222J PHE* 1.3 79.1 - - - +
224J ALA* 1.3 65.0 + - - +
226J ARG* 3.0 4.9 + - - +
227J VAL* 2.9 27.6 + - - +
256J LEU* 5.5 0.2 - - - +
258J THR* 2.8 28.1 + - - +
269J PHE* 3.6 18.6 - - - -
271J THR* 2.7 34.8 + - - +
281J ILE* 5.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J THR* 3.5 30.5 - - + +
220J PHE* 2.9 21.5 + - + +
221J GLY 3.7 2.0 - - - +
223J SER* 1.3 76.5 - - - +
225J ARG* 1.3 63.1 + - - +
227J VAL* 3.2 10.2 + - - +
228J LEU* 3.0 22.9 + - - +
239J PHE* 3.9 16.9 - - + -
242J VAL* 5.0 4.9 - - + -
269J PHE* 4.9 7.5 - - + -
286J VAL* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 225 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J VAL* 2.5 34.4 + - + -
35J GLY* 3.1 23.3 + - - -
36J ALA* 3.6 20.0 - - - +
43J ASP* 4.4 11.6 + - - +
46J PHE* 5.2 5.6 - - + -
57J LEU* 4.0 37.0 - - + -
59J THR* 5.7 0.2 + - - -
178J ASP* 3.1 25.1 + - - -
221J GLY 2.8 22.6 + - - +
222J PHE* 2.9 18.9 + - - +
224J ALA* 1.3 74.0 - - - +
226J ARG* 1.3 74.3 + - - +
228J LEU* 3.4 12.2 - - + +
229J GLN* 3.2 25.9 + - - +
234J ASN* 4.7 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 226 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176J LEU* 3.2 41.7 - - + +
177J THR 2.9 25.5 + - - +
178J ASP* 2.5 31.8 + - - +
222J PHE 2.9 18.4 + - - +
223J SER* 3.0 10.3 + - - +
225J ARG* 1.3 87.0 - - - +
227J VAL* 1.3 60.6 + - - +
229J GLN* 2.4 41.8 + - - +
230J GLN* 2.8 32.2 + - - +
258J THR* 4.6 7.4 - - - +
260J MET* 4.4 7.6 - - + -
173K ASP* 4.4 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223J SER 2.9 18.7 + - - +
224J ALA* 3.5 7.9 - - - +
226J ARG* 1.3 75.1 - - - +
228J LEU* 1.3 66.2 + - - +
231J PHE* 2.9 25.4 + - + +
232J ALA* 4.0 0.9 + - - +
258J THR* 4.8 1.1 - - + -
260J MET* 3.8 28.7 - - + -
267J ILE* 3.9 22.7 - - + -
269J PHE* 4.2 18.2 - - + -
286J VAL* 3.1 41.7 - - + -
288J LEU* 5.2 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J PHE* 3.8 28.9 - - + -
57J LEU* 3.9 17.0 - - + -
58J PRO* 4.2 11.9 - - + -
224J ALA 3.0 13.0 + - - +
225J ARG* 3.4 11.2 - - - +
226J ARG 3.1 0.2 - - - -
227J VAL* 1.3 77.4 - - - +
229J GLN* 1.3 57.3 + - - +
232J ALA* 3.2 28.7 + - + +
234J ASN* 3.1 25.4 + - - +
235J ASP 3.9 31.4 - - - +
236J VAL* 4.1 5.8 - - + +
239J PHE* 4.0 26.2 - - + -
288J LEU* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 229 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J ASP* 4.0 18.4 + - - +
42J LYS* 5.7 3.2 - - - +
43J ASP* 4.3 11.3 + - - -
176J LEU* 4.2 1.5 - - + +
225J ARG* 3.2 11.5 + - - +
226J ARG* 2.4 51.3 + - - +
228J LEU* 1.3 79.8 - - - +
230J GLN* 1.3 71.7 + - + +
233J ASP* 3.9 12.2 + - - -
234J ASN* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 230 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174J ALA* 3.6 17.4 - - + +
176J LEU* 3.7 22.4 - - + +
226J ARG 2.8 16.2 + - - +
229J GLN* 1.3 84.1 + - - +
231J PHE* 1.3 92.2 + - + +
232J ALA 3.7 0.4 + - - -
233J ASP 4.9 0.7 + - - -
260J MET* 4.1 7.6 - - + -
176K LEU* 3.8 2.3 - - - +
230K GLN* 3.0 41.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 231 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173J ASP* 4.5 11.9 - - + -
174J ALA* 4.4 12.3 - - + -
227J VAL 2.9 11.2 + - - +
230J GLN* 1.3 103.8 - - + +
232J ALA* 1.3 60.8 + - - +
233J ASP* 3.8 0.9 - - - -
238J ARG* 3.9 9.8 + - - -
260J MET* 3.5 32.3 - - + -
262J LYS* 3.7 32.8 - - + -
267J ILE* 3.6 44.9 - - + -
288J LEU* 3.2 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228J LEU* 3.2 24.8 + - + +
231J PHE* 1.3 80.5 - - - +
233J ASP* 1.3 74.0 + - - +
234J ASN 3.3 0.9 - - - -
235J ASP* 2.9 19.1 + - - +
238J ARG* 3.5 27.3 + - + +
288J LEU* 3.9 25.6 - - + -
----------------------------------------------------------
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