Contacts of the helix formed by residues 224 - 240 (chain C) in PDB entry 3SKU
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 ILE 224 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 5.5 0.9 - - + -
29C THR* 3.8 8.7 - - - -
30C ASP* 3.2 36.3 - - - +
36C ARG* 3.1 41.1 - - + +
132C GLN* 5.5 1.8 - - + -
133C PRO* 4.1 5.6 - - + -
222C ARG 5.4 0.4 - - - +
223C PHE* 1.3 76.0 - - - +
225C PRO* 1.3 80.3 - - + +
226C GLU* 3.0 7.0 + - + +
227C ASN* 3.0 42.6 + - - +
228C GLN 3.4 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ARG* 3.7 14.8 - - - +
113C MET* 4.6 12.1 - - - -
115C TYR* 5.6 1.8 - - - +
133C PRO* 4.1 9.4 - - + -
143C ALA* 4.9 0.3 - - - +
144C VAL* 4.0 16.6 - - + +
148C ASN* 3.7 28.3 - - - +
223C PHE 3.9 0.8 - - - +
224C ILE* 1.3 89.7 - - + +
226C GLU* 1.3 65.5 + - - +
228C GLN* 3.1 21.0 + - + +
229C ARG* 3.3 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.5 33.7 - - + +
146C GLU* 2.9 25.0 - - - +
224C ILE* 3.0 7.9 + - + +
225C PRO* 1.3 78.2 - - - +
227C ASN* 1.3 63.6 + - - +
229C ARG* 2.7 56.2 + - - +
230C THR* 3.6 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLN 5.8 0.7 - - - -
28C LEU* 2.8 47.4 + - + +
223C PHE* 3.6 30.3 - - + -
224C ILE* 3.0 37.0 + - - +
226C GLU* 1.3 72.5 - - - +
228C GLN* 1.3 68.7 + - - +
230C THR* 2.9 20.0 + - - -
231C VAL* 3.0 17.6 + - + +
129E PHE* 5.1 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C TRP* 3.3 39.1 - - - +
139C ASP* 3.6 25.6 + - - +
142C SER 3.6 10.1 + - - +
143C ALA* 3.2 26.2 - - + -
222C ARG* 4.2 3.5 - - - +
223C PHE* 3.7 36.2 + - + +
224C ILE 3.4 7.7 + - - +
225C PRO* 3.1 14.3 + - + +
227C ASN* 1.3 77.0 - - - +
229C ARG* 1.3 52.2 + - - +
230C THR 2.7 5.7 + - - -
231C VAL* 2.9 5.9 + - - +
232C ALA* 2.7 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ALA* 4.1 13.9 - - + -
144C VAL* 3.4 33.2 + - - +
145C SER* 2.8 34.1 + - - +
146C GLU* 3.6 19.5 - - - +
148C ASN* 4.3 2.2 - - - +
152C LEU* 5.6 9.6 - - + -
154C HIS* 4.5 2.4 + - - -
225C PRO* 3.3 12.5 + - - +
226C GLU* 2.7 66.1 + - - +
227C ASN 3.2 0.2 - - - -
228C GLN* 1.3 78.3 - - - +
230C THR* 1.3 56.7 + - - +
232C ALA* 4.2 4.1 + - - +
233C VAL* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 3.2 50.0 - - + +
28C LEU* 5.0 7.4 - - - +
226C GLU* 3.6 10.7 + - - -
227C ASN* 2.9 14.1 + - - -
228C GLN 2.7 4.2 + - - -
229C ARG* 1.3 71.5 - - - +
231C VAL* 1.3 62.6 + - + -
232C ALA 3.1 1.6 - - - -
233C VAL* 2.7 31.8 + - + +
234C TYR* 2.8 15.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C SER 5.1 2.8 - - - +
223C PHE* 4.8 15.9 - - + -
227C ASN* 3.0 13.3 + - + +
228C GLN* 2.9 7.8 + - - +
230C THR* 1.3 76.8 - - + +
232C ALA* 1.3 58.9 + - - +
233C VAL 3.2 4.0 + - - -
234C TYR* 3.4 11.6 + - - -
235C SER* 3.9 8.1 + - - -
236C LEU 5.2 0.5 + - - -
128E THR 4.3 6.3 - - - +
129E PHE 3.2 16.4 - - - +
130E PRO 2.8 30.5 - - - +
131E THR* 3.5 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ASP 5.0 4.7 - - - +
140C SER 4.5 5.9 - - - +
141C PHE* 3.8 17.6 - - - +
142C SER* 3.0 40.6 - - - +
143C ALA* 4.7 0.2 - - + -
154C HIS* 3.4 16.3 - - + +
228C GLN* 2.7 23.3 + - + +
229C ARG* 4.3 6.1 - - - +
231C VAL* 1.3 71.8 - - - +
233C VAL* 1.4 57.6 + - + +
236C LEU* 4.5 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 5.9 1.6 - - + -
154C HIS* 3.1 35.0 - - + +
229C ARG 3.1 16.2 - - - +
230C THR* 2.7 27.4 + - + +
232C ALA* 1.4 77.0 - - - +
234C TYR* 1.3 60.7 + - + +
235C SER 3.8 1.1 - - - -
236C LEU* 3.5 10.3 - - - +
237C LYS* 2.9 50.5 + - + +
241C TRP* 4.8 7.0 - - + -
244C PRO* 4.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 6.2 0.6 - - - -
25C LEU* 5.4 24.7 - - + -
230C THR* 2.8 23.7 + - + +
231C VAL* 3.4 10.1 + - - -
233C VAL* 1.3 72.9 - - + +
235C SER* 1.3 64.0 + - - +
236C LEU 3.1 1.6 - - - -
237C LYS* 3.0 24.3 + - + +
238C ILE* 3.1 39.7 + - + +
58E PRO* 5.5 6.6 - - - +
130E PRO* 3.3 49.6 - - + +
131E THR* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C LEU* 6.3 0.2 - - - -
231C VAL 3.9 6.5 + - - -
233C VAL 3.8 0.2 - - - -
234C TYR* 1.3 79.1 - - - +
236C LEU* 1.3 58.3 + - - +
238C ILE* 3.1 33.2 - - - +
239C ALA* 3.7 9.2 + - - +
131E THR* 3.0 39.7 + - - +
132E GLY* 4.3 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 236 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C SER 5.9 0.7 - - - +
141C PHE* 4.6 6.1 - - + -
154C HIS* 4.4 23.1 - - + -
155C ALA* 4.6 12.3 - - + +
191C TYR* 3.4 33.4 - - + +
192C ALA* 5.4 0.2 - - - -
193C LEU* 3.4 33.3 - - + +
231C VAL 5.2 0.4 + - - -
232C ALA 4.5 9.2 - - - +
233C VAL* 3.5 12.7 + - - +
234C TYR 3.1 0.2 - - - -
235C SER* 1.3 76.2 - - - +
237C LYS* 1.3 66.7 + - - +
239C ALA* 3.1 18.5 + - + +
240C GLY 3.2 7.3 + - - -
241C TRP* 3.5 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 6.5 1.3 - - + -
233C VAL* 2.9 37.9 + - + +
234C TYR* 3.0 15.9 + - + +
236C LEU* 1.3 74.3 - - - +
238C ILE* 1.3 56.3 + - + +
240C GLY* 2.7 29.1 + - - -
241C TRP* 3.3 21.2 + - + +
243C GLY 2.6 34.6 + - - +
244C PRO* 3.3 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C TYR* 3.1 35.0 + - + +
235C SER* 3.1 41.3 - - - +
237C LYS* 1.3 77.4 - - + +
239C ALA* 1.3 60.4 + - + +
240C GLY* 3.4 1.0 + - - -
131E THR* 4.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C TYR* 3.4 25.0 + - + -
193C LEU* 6.4 1.6 - - + -
235C SER 3.8 9.4 - - - +
236C LEU* 3.1 15.1 + - + +
237C LYS 2.9 0.8 + - - -
238C ILE* 1.3 82.6 - - + +
240C GLY* 1.3 56.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C TYR* 3.1 29.8 + - - -
236C LEU 3.2 1.8 + - - -
237C LYS 2.7 16.7 + - - -
238C ILE 4.3 1.1 - - - -
239C ALA* 1.3 74.5 - - - +
241C TRP* 1.3 64.3 + - - +
242C HIS* 3.8 5.7 + - - -
----------------------------------------------------------
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