Contacts of the helix formed by residues 238 - 252 (chain B) in PDB entry 1SOZ
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 PHE 238 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 5.7 0.2 - - - +
143B ILE* 4.4 16.2 - - + -
144B ASN 3.6 15.3 - - - -
145B ALA* 3.9 13.9 - - + -
147B ARG 3.6 21.3 - - - -
149B PRO* 4.2 11.0 - - + -
212B LEU* 3.2 46.8 - - + +
213B MET* 3.1 34.2 + - + +
214B GLY* 4.5 2.0 - - - -
236B ILE 3.5 1.7 + - - -
237B PRO* 1.3 71.8 - - + +
239B GLN* 1.3 94.8 + - + +
241B ALA* 3.0 9.5 + - - +
242B THR* 2.7 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ALA* 2.9 34.6 + - - +
147B ARG 4.8 2.4 + - - -
149B PRO* 6.3 0.4 - - + -
237B PRO* 3.1 4.1 + - + -
238B PHE* 1.3 110.1 - - + +
240B LEU* 1.3 63.5 + - - +
242B THR* 3.2 12.2 + - - +
243B LYS* 2.9 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B THR* 4.5 7.4 - - + -
187B GLN* 3.7 36.6 - - + +
188B ASN* 4.5 5.2 - - + +
236B ILE* 3.2 27.4 - - + -
237B PRO* 3.0 21.3 + - + +
239B GLN* 1.3 79.3 - - - +
241B ALA* 1.3 56.9 + - - +
243B LYS* 3.4 11.6 + - + +
244B ILE* 3.0 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 5.6 1.8 - - + -
92B ILE* 3.5 15.7 - - + +
127B LEU* 4.0 19.4 - - + +
212B LEU* 5.9 0.2 - - + -
215B ILE* 4.0 28.0 - - + -
236B ILE* 4.2 4.9 - - + +
237B PRO 3.0 10.9 + - - +
238B PHE* 3.0 11.7 + - - +
240B LEU* 1.3 76.5 - - - +
242B THR* 1.3 57.5 + - - +
244B ILE* 3.5 1.2 + - - +
245B MET* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 4.3 14.0 - - - +
92B ILE* 5.1 0.4 - - - -
143B ILE* 4.7 10.6 - - - +
238B PHE* 2.7 26.2 + - - +
239B GLN* 3.5 15.5 - - - +
241B ALA* 1.3 72.2 - - - +
243B LYS* 1.3 69.7 + - + +
245B MET* 3.5 12.9 + - + +
246B ASP* 3.3 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B GLN* 2.9 45.3 + - - +
240B LEU* 3.9 11.9 - - + +
242B THR* 1.3 79.5 - - + +
244B ILE* 1.3 62.6 + - + +
246B ASP* 3.7 7.0 + - - +
247B LYS* 3.4 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ASP* 4.3 2.7 - - + -
125B THR* 4.0 21.3 - - + +
127B LEU* 3.7 36.6 - - + -
240B LEU* 3.0 41.7 + - + +
241B ALA 3.9 0.4 - - - +
243B LYS* 1.3 78.8 - - + +
245B MET* 1.3 59.2 + - - +
247B LYS* 3.3 10.4 + - + +
248B LEU* 2.9 32.7 + - + +
254B VAL* 4.0 24.7 - - + -
256B ARG* 4.2 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 3.3 49.8 - - + -
86B ASP* 4.5 9.0 - - - +
88B ARG* 5.2 1.1 - - - +
90B TYR* 4.4 8.1 - - - -
92B ILE* 3.8 11.7 - - + -
129B VAL* 3.9 23.1 - - + -
143B ILE* 6.3 0.4 - - + -
241B ALA 3.0 17.0 + - - +
242B THR* 3.9 13.2 - - + +
244B ILE* 1.3 73.6 - - - +
246B ASP* 1.3 70.9 + - - +
248B LEU* 2.9 2.9 + - - +
249B ILE* 2.7 53.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ARG* 5.2 3.6 + - - -
242B THR* 3.3 25.6 + - - +
243B LYS* 3.9 7.2 - - - +
245B MET* 1.3 90.2 - - - +
247B LYS* 1.3 57.9 + - + +
249B ILE* 3.8 9.0 - - - +
250B ARG* 2.8 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LYS* 3.4 24.6 + - - +
244B ILE* 3.3 15.9 + - + +
246B ASP* 1.3 80.7 - - + +
248B LEU* 1.3 58.5 + - - +
250B ARG* 4.5 4.9 - - - +
251B ASP* 2.9 34.7 + - - +
253B ARG 3.5 12.1 - - - +
254B VAL* 4.0 31.4 - - + -
255B ILE 5.5 5.6 + - - +
324B GLU* 2.7 37.8 + - - -
326B ARG* 5.8 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 3.4 11.4 - - + +
120B GLY 3.6 8.1 - - - +
121B SER* 3.5 40.4 - - - +
122B ASP 4.3 0.4 - - - +
127B LEU 4.0 8.5 - - - +
128B ALA* 4.4 0.4 - - - -
129B VAL* 3.8 25.6 - - + -
244B ILE* 2.9 24.7 + - + +
245B MET 2.9 8.3 + - - +
247B LYS* 1.3 74.8 - - - +
249B ILE* 1.3 61.0 + - - +
252B GLY* 2.9 28.0 + - - +
253B ARG* 3.2 38.1 - - - +
254B VAL* 3.7 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ARG* 3.9 21.3 - - - +
90B TYR* 3.5 62.8 - - + +
119B VAL* 4.1 6.8 - - + +
129B VAL* 4.4 5.4 - - + -
245B MET* 2.7 43.7 + - + +
246B ASP* 3.8 7.4 - - - +
248B LEU* 1.3 74.8 - - - +
250B ARG* 1.3 66.6 + - + +
252B GLY 4.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ASP* 2.8 22.0 + - - +
247B LYS* 3.8 4.0 - - - +
249B ILE* 1.3 81.6 - - + +
251B ASP* 1.3 76.0 + - - +
326B ARG* 5.8 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LYS* 2.9 19.8 + - - +
250B ARG* 1.3 91.8 + - - +
252B GLY* 1.3 58.0 + - - +
253B ARG* 3.0 37.4 + - - +
255B ILE* 3.9 15.4 + - + +
326B ARG* 3.2 40.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL 3.4 15.3 - - - +
120B GLY* 3.5 16.6 - - - -
121B SER 4.3 1.2 + - - -
248B LEU* 2.9 23.9 + - - -
249B ILE 4.4 1.0 + - - -
250B ARG 3.8 0.6 - - - -
251B ASP* 1.3 76.1 - - - +
253B ARG* 1.3 60.0 + - - +
----------------------------------------------------------
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