Contacts of the helix formed by residues 236 - 241 (chain B) in PDB entry 1SMN
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 236 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A TYR* 4.1 15.0 - - + +
230A LEU* 4.5 7.1 - - + +
233A LYS* 3.8 22.7 - - + -
234A PRO 3.7 23.1 - - - +
235A GLY* 4.6 2.7 - - - -
236A VAL* 4.0 20.7 - - + +
184B HIS* 3.5 35.9 - - + +
185B TYR 3.4 1.8 + - - +
234B PRO 5.0 0.9 - - - +
235B GLY* 1.3 76.3 - - - +
237B LEU* 1.3 67.1 + - - +
238B PRO* 3.1 4.5 - - - -
239B GLU* 2.9 26.2 + - - +
240B LEU* 4.1 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 4.1 20.0 - - + -
174B ILE* 3.8 39.0 - - + +
176B ILE* 3.9 29.2 - - + -
184B HIS* 3.8 21.5 - - + +
185B TYR* 3.1 26.2 + - - +
186B ALA* 3.9 7.0 - - + -
236B VAL* 1.3 78.4 - - - +
238B PRO* 1.4 64.8 - - + +
240B LEU* 2.9 33.8 + - + +
241B MET* 3.6 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ALA* 3.6 22.2 - - + -
187B ALA 5.4 0.7 - - - +
188B PHE* 4.0 11.0 - - + -
204B ARG* 3.6 37.2 - - + +
235B GLY 3.5 13.0 - - - +
236B VAL* 3.1 6.7 - - - -
237B LEU* 1.4 93.0 - - + +
239B GLU* 1.3 56.7 + - - +
240B LEU 3.0 0.2 - - - -
241B MET* 2.8 30.1 + - + +
242B GLY 3.4 0.2 + - - -
243B CYS* 3.0 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER* 3.3 42.8 - - - +
230A LEU* 4.0 14.8 - - + -
233A LYS* 3.9 24.8 - - + +
204B ARG* 3.7 7.8 + - - -
235B GLY 4.9 0.5 - - - +
236B VAL* 2.9 20.6 + - - +
238B PRO* 1.3 77.4 - - - +
240B LEU* 1.3 58.7 + - - +
241B MET 3.2 1.1 + - - -
242B GLY* 3.6 8.1 + - - -
243B CYS 3.2 14.7 - - - +
244B LYS* 3.2 6.3 - - - -
245B ASN* 2.6 42.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
181A ALA 3.5 23.3 - - - +
226A VAL* 4.7 11.9 - - + -
229A SER* 3.8 18.2 - - - +
230A LEU* 4.3 22.9 - - + -
129B GLN* 5.0 1.6 - - - +
133B LEU* 4.3 9.8 - - + +
136B ARG* 3.2 53.0 + - - +
139B ILE* 4.5 11.9 - - + -
176B ILE* 5.0 0.2 - - + -
184B HIS* 4.2 11.9 - - + -
236B VAL 5.1 0.4 - - - +
237B LEU* 2.9 23.1 + - + +
239B GLU* 1.3 77.0 - - - +
241B MET* 1.3 60.1 + - - +
242B GLY 3.3 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.7 28.0 - - + -
129B GLN* 3.6 32.9 - - + +
130B GLU* 3.7 31.2 - - + +
133B LEU* 4.0 20.9 - - + -
174B ILE* 4.5 6.5 - - + -
188B PHE* 4.4 13.7 - - - -
200B PHE* 3.7 20.8 - - + -
237B LEU* 3.6 22.0 - - - +
238B PRO* 2.8 23.6 + - + +
240B LEU* 1.3 81.0 - - - +
242B GLY* 1.3 58.3 + - - +
243B CYS 3.5 0.4 - - - -
----------------------------------------------------------
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