Contacts of the strand formed by residues 239 - 245 (chain B) in PDB entry 1MS4
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 LYS 239 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLU* 3.4 7.8 - - - +
236B TRP* 2.9 42.6 + - - +
237B GLU* 3.9 17.7 + - - +
238B GLY* 1.3 83.0 - - - +
240B LEU* 1.3 71.2 + - - +
241B ILE* 3.5 4.7 + - + +
255B GLU* 3.3 42.2 + - + +
256B SER 3.7 10.8 - - - +
257B SER* 3.4 22.2 - - - +
324B ASN* 5.4 2.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
183B ILE* 3.8 29.2 - - + -
185B ALA* 5.2 2.0 - - + -
191B VAL* 4.1 20.6 - - + -
207B ILE* 3.9 28.9 - - + -
233B ALA* 5.3 4.5 - - + -
234B LEU 3.5 5.6 - - - +
235B GLU* 4.4 13.7 + - + +
239B LYS* 1.3 74.1 - - - +
241B ILE* 1.3 60.8 + - - +
242B ILE* 4.0 14.8 - - + -
254B TYR 3.7 0.2 - - - +
255B GLU* 3.1 6.9 - - - +
256B SER* 2.7 41.2 + - - +
259B MET* 4.2 30.3 - - + +
260B GLY 4.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ALA* 3.1 4.6 - - - +
234B LEU* 2.8 44.7 + - + -
236B TRP* 3.5 36.3 - - + +
239B LYS* 4.0 10.5 - - + +
240B LEU* 1.3 78.5 - - - +
242B ILE* 1.3 62.1 + - - +
253B VAL* 3.6 26.5 - - + -
254B TYR 3.2 4.0 - - - +
255B GLU* 4.2 23.1 - - + +
266B ALA* 5.8 0.2 - - + -
270B LEU* 4.7 4.3 - - + -
289B PHE* 3.8 20.0 - - + -
300B MET* 4.3 11.9 - - + -
324B ASN* 4.4 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PRO* 4.5 5.8 - - + -
207B ILE* 3.9 24.7 - - + -
231B PRO* 3.8 28.5 - - + -
232B VAL 3.6 4.5 - - - +
233B ALA* 4.1 6.5 - - + -
240B LEU* 4.3 11.4 - - + +
241B ILE* 1.3 74.4 - - - +
243B ASN* 1.3 59.3 + - - +
244B THR* 4.0 7.1 + - + -
253B VAL* 3.4 3.0 - - - -
254B TYR* 2.7 50.9 + - + +
256B SER* 4.3 15.7 - - - -
263B TRP* 3.7 44.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B PRO* 3.8 0.7 - - - +
232B VAL* 2.8 36.8 + - + +
241B ILE 3.9 0.6 + - - -
242B ILE* 1.3 70.5 - - - +
244B THR* 1.3 59.9 + - - +
251B ARG* 2.8 45.2 + - - +
253B VAL* 3.7 20.9 - - + +
274B TRP* 3.6 17.6 - - - -
289B PHE* 3.7 26.4 - - + -
302B PHE* 3.2 30.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B SER* 4.0 12.6 - - - +
228B CYS* 3.4 38.3 - - + +
229B SER 3.9 6.1 - - - -
231B PRO* 4.4 2.7 - - + -
242B ILE* 4.1 15.5 - - + +
243B ASN* 1.3 76.2 + - - +
245B ARG* 1.3 61.4 - - - +
246B VAL* 3.8 1.6 - - - +
251B ARG* 3.4 29.7 + - - +
252B LEU 2.8 31.5 + - - +
254B TYR* 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLY 3.6 0.2 - - - +
228B CYS* 3.5 4.5 - - - -
229B SER* 2.7 59.5 + - - +
230B GLU* 3.0 30.6 + - + +
244B THR* 1.3 71.1 - - - +
246B VAL* 1.3 62.2 + - - +
247B ASP* 2.8 36.2 + - - +
251B ARG* 3.7 10.7 - - - +
284B GLY* 3.3 19.7 + - - +
285B SER* 3.3 30.3 - - - +
312B TRP* 4.0 15.8 - - - +
314B ARG* 3.5 10.9 - - - +
342B TYR* 2.9 27.5 + - - -
----------------------------------------------------------
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