Contacts of the strand formed by residues 236 - 241 (chain A) in PDB entry 1B0K
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 ALA 236 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PRO* 4.2 1.3 - - - -
201A LYS* 3.4 21.1 - - + +
203A ILE* 3.5 36.6 - - + -
233A GLY 3.1 10.4 + - - +
234A THR 4.3 3.4 - - - +
235A GLY* 1.3 78.0 - - - +
237A ILE* 1.3 61.7 + - - +
238A VAL* 5.9 0.2 - - + -
265A ALA* 3.5 7.3 - - - +
266A THR* 2.9 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER* 3.9 36.8 - - - +
43A VAL* 4.2 16.4 - - + -
177A ILE* 4.6 2.0 - - + -
179A ILE* 5.2 2.0 - - + -
197A LEU* 5.9 0.4 - - + -
200A PRO* 3.7 28.5 - - + -
201A LYS 3.0 9.3 + - - +
202A VAL* 3.4 5.4 - - + +
203A ILE 3.1 22.5 + - - -
236A ALA* 1.3 75.8 - - - +
238A VAL* 1.3 71.3 + - - +
239A GLU* 3.6 1.7 + - - +
266A THR* 4.2 9.9 - - + -
267A THR* 3.5 39.7 - - + +
268A SER* 4.3 2.5 - - - +
269A VAL* 4.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ILE* 3.6 22.4 - - + +
205A VAL* 3.8 20.2 - - + -
224A VAL* 5.6 2.5 - - + -
228A LEU* 5.4 0.9 - - + -
233A GLY* 5.7 0.2 - - - -
237A ILE* 1.3 72.0 - - - +
239A GLU* 1.3 57.9 + - - +
240A TYR* 3.4 33.6 + - + +
260A GLY* 5.9 1.1 - - - -
263A ILE* 4.4 16.6 - - + -
265A ALA* 4.0 21.8 - - + -
267A THR 3.1 6.9 + - - -
268A SER* 3.2 32.8 - - - +
269A VAL 3.3 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 3.2 12.5 + - - -
38A LEU* 2.9 45.1 + - + +
39A SER* 3.0 19.0 + - - +
202A VAL* 3.8 15.7 - - + +
203A ILE 2.9 10.6 + - - +
204A GLY* 3.4 4.2 - - - -
205A VAL 3.1 21.0 + - - -
237A ILE* 3.6 1.0 + - + -
238A VAL* 1.3 70.6 - - - +
240A TYR* 1.3 71.0 + - - +
241A HIS* 3.4 4.2 + - + -
269A VAL* 3.8 12.6 - - + -
301A PRO* 3.5 11.1 - - + +
307A TYR* 3.1 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 3.7 30.3 - - + -
207A LEU* 4.4 10.8 - - + -
220A VAL* 4.8 9.6 - - + -
221A ILE* 3.8 16.6 - - - +
224A VAL* 4.3 10.9 - - + +
238A VAL* 3.4 31.8 - - + +
239A GLU* 1.3 77.8 - - - +
241A HIS* 1.3 63.6 + - - +
245A VAL* 4.6 0.9 - - + -
256A ILE* 3.4 32.5 + - + +
257A CYS* 4.9 0.2 - - - -
268A SER* 4.1 17.1 + - - -
269A VAL 3.0 20.4 + - - +
270A PHE* 3.6 39.7 - + + -
271A PRO* 3.3 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLY 3.8 9.4 - - - -
205A VAL 3.0 26.4 + - - +
206A LYS* 3.2 23.6 - - + +
207A LEU* 2.8 23.2 + - - +
239A GLU* 3.4 8.3 + - + -
240A TYR* 1.3 76.5 - - - +
242A GLY* 1.4 63.9 + - - +
245A VAL* 3.5 16.2 - - - +
271A PRO* 4.8 7.0 - - + -
301A PRO* 5.2 9.4 - - + -
307A TYR* 3.2 45.3 + + - +
310A VAL* 5.3 3.4 - - + +
----------------------------------------------------------
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