Contacts of the strand formed by residues 196 - 206 (chain A) in PDB entry 4EJX
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 ARG 196 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LYS* 4.9 4.0 - - - +
194A ILE* 3.4 5.2 - - - +
195A ASP* 1.3 84.1 - - + +
197A GLU* 1.3 64.4 + - - +
198A PHE* 3.4 29.3 - - + -
253A GLY 5.8 0.4 + - - -
255A SER* 2.9 37.1 + - - -
256A MET* 3.8 8.8 - - - +
257A CYS* 5.1 7.1 - - - +
260A ASP* 3.1 24.5 + - - +
261A ARG 3.3 2.4 + - - -
262A VAL* 3.4 10.6 - - + +
263A LYS 2.9 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TRP* 3.5 19.5 - - - -
79A LYS* 2.7 30.6 + - - +
189A GLU 4.6 0.7 - - - +
190A LYS* 3.2 32.2 - - - +
191A GLU* 3.1 28.5 + - - +
194A ILE* 3.7 13.2 - - + -
196A ARG* 1.3 79.7 - - - +
198A PHE* 1.3 64.5 + - - +
199A VAL* 5.8 0.9 - - - -
263A LYS* 3.8 11.0 - - + -
265A TYR* 4.3 13.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TRP* 3.5 40.8 - + + -
196A ARG* 3.4 39.3 - - + -
197A GLU* 1.3 76.3 - - - +
199A VAL* 1.3 64.4 + - - +
200A VAL* 4.0 0.6 + - + -
253A GLY 4.7 4.7 - - - -
254A LEU* 3.7 21.5 - - + -
255A SER 3.7 24.2 - - - -
256A MET* 4.5 8.3 - - + -
262A VAL* 3.6 21.5 - - + -
263A LYS 3.1 7.8 + - - +
264A TRP* 3.6 31.0 - + + -
265A TYR* 3.1 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TRP* 2.9 33.2 - - + -
71A LEU* 3.8 13.5 - - + +
74A LEU* 4.4 5.8 - - + -
77A ILE* 5.2 10.8 - - + -
177A PRO* 3.5 31.0 - - + -
179A ILE* 4.5 20.2 - - + -
197A GLU 5.6 1.1 - - - +
198A PHE* 1.3 74.5 - - - +
200A VAL* 1.3 68.3 + - - +
244A ASN* 3.5 13.8 + - - +
265A TYR* 3.7 9.2 - - + +
267A PHE* 3.6 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PHE* 4.9 1.3 - - + +
199A VAL* 1.3 81.1 - - - +
201A MET* 1.3 61.0 + - - +
202A PHE* 3.2 35.6 + - + -
243A VAL* 3.7 10.5 - - + -
244A ASN* 3.7 8.7 - - - +
251A LEU* 5.7 1.8 - - + -
254A LEU* 5.7 5.2 - - + -
264A TRP* 3.7 32.8 - - + -
265A TYR 2.9 10.4 + - - +
266A LEU* 2.9 47.4 - - + +
267A PHE* 2.9 6.8 + - - -
317A LEU* 4.4 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 3.8 19.5 - - + -
74A LEU* 3.4 35.2 - - + -
175A ILE* 4.1 15.0 - - - -
200A VAL* 1.3 73.4 - - - +
202A PHE* 1.3 62.4 + - - +
203A SER* 3.7 22.9 - - - +
205A VAL* 4.7 0.9 - - + -
242A SER 4.6 1.8 - - - +
243A VAL* 3.0 5.9 - - - -
244A ASN* 2.6 53.1 + - - +
267A PHE* 3.3 39.5 - - + +
269A MET* 4.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL* 3.2 28.3 - - + -
201A MET* 1.3 68.8 - - - +
203A SER* 1.3 61.6 + - - +
242A SER 3.8 2.2 - - - -
243A VAL* 3.7 18.2 - - + +
266A LEU* 4.0 4.7 - - + -
267A PHE 3.3 5.1 + - - +
268A GLY* 3.3 4.9 - - - -
269A MET 3.2 21.5 + - - -
276A HIS* 3.6 29.0 + + + +
278A ALA* 3.5 24.9 - - + -
297A LEU* 3.3 23.1 - - + -
317A LEU* 3.6 35.7 - - + -
318A SER 4.9 0.2 - - - -
319A CYS* 4.8 12.6 - - + -
329A LEU* 3.3 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ILE* 5.6 0.9 - - - +
201A MET* 3.6 23.8 + - - -
202A PHE* 1.3 74.8 - - - +
204A VAL* 1.3 54.9 + - - +
205A VAL* 2.8 29.7 + - - +
240A MET 2.9 1.3 - - - +
242A SER* 2.8 39.5 + - - +
269A MET* 2.6 38.1 + - - +
270A GLY* 4.2 1.9 + - - -
274A ASP* 3.8 1.3 + - - -
276A HIS* 4.1 2.7 - - - -
329A LEU* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A SER* 1.3 67.4 - - - +
205A VAL* 1.3 67.2 + - - +
206A ASP* 2.9 10.2 + - - +
239A ARG* 3.9 19.2 - - + +
240A MET 3.0 7.2 - - - -
241A TYR* 3.4 50.5 - - + +
270A GLY* 5.5 1.6 - - - -
273A VAL* 5.1 4.5 - - + +
274A ASP* 2.8 28.9 + - - +
276A HIS* 3.7 5.8 - - + -
324A HIS* 3.2 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 4.2 8.3 - - - +
50A LYS* 4.0 11.4 - - - +
73A PHE* 3.8 23.1 - - + -
170A ILE* 4.3 7.6 - - + +
171A ALA* 3.6 34.5 - - - +
201A MET* 4.7 0.2 - - + -
203A SER* 2.8 38.9 + - - +
204A VAL* 1.3 67.5 - - - +
206A ASP* 1.3 61.0 + - - +
207A GLU* 3.5 4.8 + - - +
238A ASN 3.5 2.3 - - - +
240A MET* 2.7 35.4 + - + +
242A SER* 3.6 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA* 3.3 21.7 - - + +
204A VAL 2.9 8.4 + - - +
205A VAL* 1.3 71.8 - - - +
207A GLU* 1.3 58.7 + - - +
208A ASN* 3.0 31.2 + - - +
209A PHE* 3.2 47.0 + - + -
238A ASN 4.2 2.0 - - - -
239A ARG* 3.4 32.9 + - + +
271A ASN* 5.4 3.6 + - + +
----------------------------------------------------------
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