Contacts of the strand formed by residues 227 - 239 (chain C) in PDB entry 1OPO
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 VAL 227 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C THR* 3.6 33.7 - - + -
94C VAL 3.5 5.2 - - - +
95C LYS* 4.6 7.4 - - + +
142C ALA* 4.6 12.6 - - + +
143C CYS* 5.6 1.9 - - - +
226C THR* 1.3 76.9 - - - +
228C VAL* 1.3 63.8 + - - +
229C GLY* 3.9 12.8 - - - +
230C GLU* 5.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C VAL* 2.7 17.9 + - + +
95C LYS 4.9 0.4 - - - -
96C GLY* 3.9 9.6 - - - +
139C TYR* 3.4 20.6 + - + +
141C PRO* 3.7 0.7 - - - +
142C ALA* 2.7 25.4 + - - +
143C CYS* 3.7 21.8 + - + -
147C THR* 4.8 7.2 - - + -
151C VAL* 5.3 1.3 - - + -
181C ALA* 4.1 3.8 - - + -
221C PHE* 3.6 39.3 - - + -
226C THR* 3.8 16.6 - - - +
227C VAL* 1.3 77.1 - - - +
229C GLY* 1.3 56.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C THR* 3.7 1.0 - - - -
94C VAL* 2.7 35.0 + - - +
139C TYR* 4.1 8.5 - - - -
140C SER 3.2 14.1 - - - -
142C ALA* 3.9 9.2 - - - -
227C VAL* 3.8 6.7 - - - +
228C VAL* 1.3 81.6 - - - +
230C GLU* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 4.1 13.5 - - + +
92C SER 3.5 8.7 - - - +
93C THR* 4.6 12.2 + - - +
94C VAL* 4.2 2.2 - - - -
138C LYS 3.6 0.7 - - - +
139C TYR* 3.4 6.1 - - - -
140C SER* 2.9 40.7 + - - +
142C ALA* 5.8 4.4 - - + +
227C VAL* 5.4 4.3 - - + -
229C GLY* 1.3 80.4 - - - +
231C LEU* 1.3 64.6 + - - +
232C PHE* 3.8 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 3.2 7.8 - - - +
91C LEU* 2.7 37.8 + - + -
92C SER* 2.8 23.7 + - - +
94C VAL* 4.1 11.2 - - + -
107C TRP* 4.3 17.5 - - + -
137C VAL* 4.1 15.9 - - + -
138C LYS 3.3 15.9 - - - +
139C TYR* 3.7 24.9 - - + -
151C VAL* 6.1 0.4 - - + -
153C LEU* 4.2 20.4 - - + -
214C ILE* 6.3 0.7 - - + -
216C LEU* 4.1 25.6 - - + -
230C GLU* 1.3 76.2 - - - +
232C PHE* 1.3 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C THR* 3.9 19.1 - - + -
89C GLU 3.2 18.2 - - - +
90C LEU* 3.8 22.0 - - + -
91C LEU* 4.5 2.2 - - - -
136C THR 3.7 0.3 - - - +
137C VAL* 3.3 6.9 - - - +
138C LYS* 2.9 52.7 + - + +
140C SER* 4.0 19.5 - - - -
230C GLU* 3.8 40.6 - - + -
231C LEU* 1.3 75.9 - - - +
233C ILE* 1.3 61.0 + - - +
234C GLN 4.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LYS 3.7 1.4 - - - +
88C THR* 3.1 5.6 - - - +
89C GLU* 2.8 46.5 + - + +
90C LEU 5.1 0.9 - - - +
91C LEU* 3.4 36.6 - - + -
116C VAL* 3.0 48.9 - - + +
117C PHE* 6.0 0.7 - - + -
135C LEU* 4.1 18.6 - - + -
136C THR 3.4 8.1 - - - +
137C VAL* 4.4 8.1 - - + -
214C ILE* 4.9 5.4 - - + -
232C PHE* 1.3 73.1 - - - +
234C GLN* 1.3 62.0 + - - +
235C TYR* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LYS 3.6 4.3 - - - +
88C THR* 3.4 24.1 + - + +
134C ALA 3.9 0.7 - - - +
135C LEU* 3.5 4.3 + - - +
136C THR* 2.8 47.9 + - - +
138C LYS* 3.2 40.1 + - + +
233C ILE* 1.3 73.6 - - - +
235C TYR* 1.3 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C MET* 3.9 22.4 - - + +
86C SER* 3.0 26.2 - - - -
87C LYS* 3.0 61.6 + - + +
89C GLU* 4.0 18.8 + - + -
116C VAL 5.2 0.9 - - - -
117C PHE* 3.7 33.4 - + + -
120C LEU* 3.7 27.2 + - + +
132C ILE* 5.9 0.4 - - + -
134C ALA* 3.3 6.3 - - - +
135C LEU* 3.7 17.7 - - + -
233C ILE* 4.6 12.1 - - + -
234C GLN* 1.3 78.4 - - - +
236C THR* 1.3 70.3 + - - +
237C ILE* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 236 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C THR* 4.7 11.7 - - - +
85C MET 3.1 7.2 - - - +
86C SER* 2.8 24.1 + - - +
132C ILE* 3.7 2.3 - - - -
133C THR* 2.8 46.8 + - + +
134C ALA* 2.9 25.2 + - - +
235C TYR* 1.3 75.3 + - - +
237C ILE* 1.3 62.4 + - - +
238C VAL* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C MET 3.9 0.5 - - - +
84C THR* 3.1 4.3 - - - -
85C MET* 2.9 35.2 + - + +
111C PRO* 4.6 9.4 - - + -
117C PHE* 4.0 19.7 - - + -
120C LEU* 3.8 26.9 - - + -
130C TYR* 4.2 7.6 - - + -
131C ARG 3.5 14.4 - - - +
132C ILE* 3.9 22.9 - - + -
235C TYR* 4.1 15.9 - - + -
236C THR* 1.3 78.3 - - - +
238C VAL* 1.3 88.2 + - - +
239C LEU* 4.1 17.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C SER* 4.4 11.7 - - - +
83C MET 3.2 12.3 - - - +
84C THR* 3.8 22.9 - - + -
130C TYR* 3.1 4.9 - - - -
131C ARG* 2.8 60.9 + - + +
133C THR* 4.1 19.5 - - + +
236C THR* 5.7 1.1 - - + -
237C ILE* 1.3 83.4 - - - +
239C LEU* 1.3 67.5 + - - +
240C SER* 4.6 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C SER* 3.1 5.4 - - - -
83C MET* 2.8 37.6 + - + +
85C MET* 5.3 3.8 - - - -
111C PRO* 4.9 7.2 - - + -
120C LEU* 4.0 23.8 - - + -
123C LEU* 3.9 29.6 - - + -
124C ALA* 4.1 11.4 - - - -
127C PHE* 3.9 24.9 - - + -
129C LYS 3.5 4.7 - - - +
130C TYR* 3.9 22.4 - - + -
198C ILE* 4.2 13.0 - - + -
237C ILE* 4.1 11.9 - - + +
238C VAL* 1.3 72.1 - - - +
240C SER* 1.3 62.6 + - - +
----------------------------------------------------------
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