Contacts of the helix formed by residues 239 - 252 (chain E) in PDB entry 1SMK
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 THR 239 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E PHE* 1.3 76.8 - - - +
240E GLN* 1.3 66.1 + - - +
241E GLU* 3.4 14.2 + - - +
242E GLU* 2.9 41.3 + - - +
243E ILE* 2.9 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 240 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E PHE 4.1 0.2 + - - -
239E THR* 1.3 72.4 - - - +
241E GLU* 1.3 62.7 + - - +
243E ILE* 3.8 11.4 - - + +
244E SER* 3.1 29.7 + - - -
331E TYR* 6.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 241 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239E THR* 3.4 13.5 + - - +
240E GLN* 1.3 80.5 - - - +
242E GLU* 1.3 98.8 + - - +
244E SER* 4.0 3.8 - - - -
245E TYR* 3.3 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E VAL* 3.5 32.1 - - + +
237E SER 4.4 3.1 - - - +
238E PHE* 3.6 19.8 - - + +
239E THR* 2.9 42.7 + - - +
241E GLU* 1.3 96.1 + - - +
243E ILE* 1.3 64.9 + - - +
245E TYR* 3.9 6.1 - - + +
246E LEU* 3.1 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E LEU* 3.6 24.0 - - + +
238E PHE* 3.3 33.7 - - + +
239E THR 2.9 20.1 + - - +
240E GLN* 3.8 8.3 - - + +
242E GLU* 1.3 77.4 - - - +
244E SER* 1.3 58.5 + - - +
247E THR* 2.8 34.0 + - - -
329E ASN* 5.4 10.3 - - - +
331E TYR* 3.2 34.8 - - + -
332E GLU* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 244 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E GLN* 3.1 21.9 + - - -
241E GLU* 4.0 4.5 - - - -
243E ILE* 1.3 76.1 - - - +
245E TYR* 1.3 63.4 + - - +
248E ASP* 3.1 23.6 + - - +
331E TYR* 3.1 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 245 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E VAL* 4.3 13.0 - - + -
241E GLU* 3.3 18.4 + - - +
242E GLU* 3.9 6.3 - - + +
243E ILE 3.4 0.2 - - - -
244E SER* 1.3 78.2 - - - +
246E LEU* 1.3 82.8 + - + +
248E ASP* 3.1 13.2 + - - +
249E ARG* 2.9 64.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E PHE* 3.4 32.5 - - + +
201E VAL* 4.0 6.5 - - + +
204E VAL* 3.4 41.5 - - + -
229E LEU* 3.9 25.6 - - + -
238E PHE* 4.3 21.5 - - + -
242E GLU 3.1 22.7 + - - +
245E TYR* 1.3 84.6 - - + +
247E THR* 1.3 66.9 + - - +
248E ASP 3.0 1.3 - - - -
249E ARG* 4.0 2.4 - - + +
250E ILE* 3.0 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 247 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E LEU* 5.3 4.5 - - + -
227E PRO* 3.9 26.4 + - + +
229E LEU* 3.8 9.9 - - - +
243E ILE 2.8 22.6 + - - -
246E LEU* 1.3 77.3 - - - +
248E ASP* 1.3 60.1 + - - +
250E ILE* 4.0 0.7 - - - +
251E GLN* 2.8 57.7 + - - +
331E TYR* 3.1 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 248 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E SER 3.1 14.1 + - - +
245E TYR* 3.1 17.9 + - - +
246E LEU 3.0 0.4 - - - -
247E THR* 1.3 75.6 - - - +
249E ARG* 1.3 76.5 + - - +
251E GLN* 3.0 8.8 + - - -
252E ASN* 2.9 47.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 249 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E PHE* 3.2 39.8 - - + +
203E GLU* 2.9 29.3 + - - +
245E TYR* 2.9 51.6 + - + +
246E LEU* 4.1 4.3 - - - +
248E ASP* 1.3 78.6 - - - +
250E ILE* 1.3 53.0 + - - +
252E ASN* 3.1 4.3 + - - -
253E GLY* 2.7 37.9 + - - -
256E GLU* 2.9 40.4 + - - +
89F SER* 5.0 4.4 + - - -
90F HIS* 4.7 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E ASP* 4.1 21.5 - - - +
196E ARG* 4.8 6.2 + - + -
197E ALA* 3.7 23.1 - - + +
200E PHE* 3.5 27.8 - - + -
201E VAL* 4.8 0.9 - - + -
216E VAL* 5.0 0.4 - - + -
225E ILE* 3.7 30.3 - - + +
227E PRO* 3.6 30.3 - - + -
229E LEU* 4.6 8.3 - - + -
246E LEU* 3.0 36.8 + - + +
247E THR 4.0 3.6 - - - +
249E ARG* 1.3 78.3 - - - +
251E GLN* 1.3 60.9 + - - +
253E GLY* 3.6 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 251 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222E GLY* 2.8 37.0 + - - +
223E VAL* 3.2 39.7 + - - +
225E ILE* 2.8 42.3 + - + +
226E LEU* 5.0 4.9 - - - +
227E PRO* 4.5 2.0 - - + +
247E THR* 2.8 41.1 + - + +
248E ASP* 3.0 8.6 + - - +
250E ILE* 1.3 77.8 - - - +
252E ASN* 1.3 65.3 + - - +
253E GLY 3.5 1.0 + - - -
254E GLY 5.2 0.9 + - - -
335E GLY* 6.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 252 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222E GLY* 4.6 8.7 - - - -
223E VAL* 5.9 3.1 - - - +
248E ASP* 2.9 40.4 + - - +
249E ARG* 3.2 5.4 - - - +
251E GLN* 1.3 85.4 + - - +
253E GLY* 1.3 64.1 + - - +
254E GLY 3.1 2.9 - - - +
255E THR* 3.1 30.3 + - - +
256E GLU* 3.3 9.2 + - - +
----------------------------------------------------------
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