Contacts of the strand formed by residues 228 - 240 (chain A) in PDB entry 5TJB
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 LEU 228 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.1 25.8 - - + -
167A GLN* 4.4 16.2 - - + +
168A ARG 3.5 9.9 - - - +
169A TYR* 4.0 2.5 - - + -
223A LEU* 5.2 4.5 - - + -
224A LYS 2.6 19.2 + - - +
225A PHE* 3.3 24.2 + - + +
226A HIS 5.3 0.2 - - - +
227A LYS* 1.3 72.0 - - - +
229A VAL* 1.3 57.4 + - - +
230A ASN* 3.1 31.9 - - - +
231A VAL* 3.7 16.2 - - + -
262A PHE* 5.7 1.1 - - + +
264A ASN* 2.8 27.9 + - + +
267A HIS* 3.2 13.2 + - - -
271A ILE* 4.2 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ARG* 2.6 28.1 + - + +
169A TYR* 3.8 15.7 - - - +
170A TYR* 3.8 33.7 - - + +
188A VAL* 4.4 15.5 - - + -
228A LEU* 1.3 73.4 - - - +
230A ASN* 1.3 67.5 + - - +
264A ASN* 2.9 31.2 + - - +
265A LYS* 3.3 32.1 + - + +
267A HIS* 4.4 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ARG* 3.0 58.8 + - - +
228A LEU* 3.1 15.1 - - - +
229A VAL* 1.3 90.9 - - - +
231A VAL* 1.3 68.9 + - - +
232A THR* 3.9 10.2 - - - +
261A THR* 4.7 5.7 - - + +
262A PHE 3.2 17.7 - - - +
263A ASP* 4.2 11.4 + - - +
264A ASN 4.2 0.9 - - - +
265A LYS* 4.3 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 5.2 2.2 - - + -
129A ILE* 4.0 22.4 - - + -
165A LEU* 4.1 17.0 - - + -
166A CYS 3.2 14.4 - - - +
167A GLN* 3.9 11.2 - - + -
221A LEU* 6.0 0.4 - - + -
223A LEU* 4.1 14.6 - - + -
228A LEU* 3.7 22.2 - - + -
230A ASN* 1.3 83.8 + - - +
232A THR* 1.3 69.9 + - - +
261A THR* 4.1 0.2 - - - +
262A PHE* 2.9 49.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA 3.4 2.0 + - - +
165A LEU* 3.6 2.6 - - - +
166A CYS* 2.9 40.8 + - - +
168A ARG* 3.2 33.6 + - - +
230A ASN* 3.9 8.9 + - - +
231A VAL* 1.3 79.3 - - - +
233A ILE* 1.3 65.6 + - - +
234A HIS* 4.1 2.4 + - - +
259A LEU* 4.0 18.1 - - + +
260A ILE 3.1 6.7 - - - -
261A THR* 3.8 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ILE* 3.9 15.9 - - + +
132A ALA* 3.8 27.4 - - + -
133A VAL* 4.1 4.3 - - + -
163A LEU* 3.7 35.2 - - + -
164A ALA 3.4 3.1 - - - -
165A LEU* 3.5 27.4 - - + -
232A THR* 1.3 73.4 - - - +
234A HIS* 1.3 62.0 + - - +
235A PHE* 4.0 13.0 - - + -
258A VAL 3.7 1.6 - - - +
259A LEU* 3.6 4.0 - - - -
260A ILE* 2.9 42.7 + - + +
262A PHE* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLY 4.0 0.5 - - - +
163A LEU* 3.4 1.6 - - - +
164A ALA* 2.8 48.0 + - + +
166A CYS* 6.5 0.2 - - - -
232A THR* 5.5 2.7 - - - +
233A ILE* 1.3 75.8 - - - +
235A PHE* 1.3 70.9 + - - +
236A ARG* 4.3 23.3 - - + -
257A SER* 3.2 25.2 + - - -
258A VAL 3.4 11.0 - - - -
259A LEU* 4.2 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 3.7 36.6 - + - -
132A ALA* 5.6 1.3 - - + -
136A TYR* 3.6 32.5 - + + -
162A GLY 3.7 16.6 - - - +
163A LEU* 3.6 23.1 - - + -
233A ILE* 4.0 16.8 - - + -
234A HIS* 1.3 85.1 + - - +
236A ARG* 1.3 62.2 + - - +
237A LEU* 4.1 15.0 - - + -
257A SER* 3.8 0.3 - - - -
258A VAL* 2.8 68.4 + - + +
260A ILE* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 5.0 3.3 + - - -
149A TYR* 4.3 0.9 - - - -
150A VAL* 3.5 64.9 + - + +
151A ARG 4.0 14.5 + - - -
162A GLY 4.5 8.7 + - - +
234A HIS* 4.3 14.4 + - + -
235A PHE* 1.3 80.7 - - - +
237A LEU* 1.3 71.6 + - - +
255A THR* 4.5 13.0 - - + -
256A PHE 3.1 12.8 - - - +
257A SER* 3.9 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 3.6 37.5 - - + -
105A PHE* 4.5 2.7 - - + -
136A TYR* 4.5 9.4 - - + -
139A LEU* 3.6 34.5 - - + -
147A TYR* 4.0 20.6 - - + -
148A ALA 3.5 7.0 - - - +
149A TYR* 4.5 6.5 - - + -
150A VAL* 4.6 0.2 - - - -
235A PHE* 4.1 27.6 - - + -
236A ARG* 1.3 83.1 - - - +
238A LYS* 1.3 61.9 + - - +
254A TYR 3.8 0.7 - - - +
255A THR* 3.4 3.4 - - - -
256A PHE* 2.7 41.8 + - + +
258A VAL* 4.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ARG 3.8 0.7 - - - +
147A TYR* 3.4 0.9 - - - -
148A ALA* 2.6 55.6 + - + +
149A TYR 5.6 0.9 - - - +
150A VAL* 3.7 19.9 - - + +
237A LEU* 1.3 74.5 - - - +
239A THR* 1.3 69.2 + - - +
240A ILE* 6.0 1.3 - - + -
253A CYS* 3.9 31.7 - - - +
254A TYR 3.5 3.1 - - - +
255A THR* 3.5 23.1 + - - +
282A GLN* 4.1 10.9 + - - -
284A CYS* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 4.8 6.1 - - + -
97A ASN* 4.8 0.9 - - - +
146A ARG* 2.9 28.0 + - - +
147A TYR* 3.9 16.7 - - + -
238A LYS* 1.3 79.8 - - - +
240A ILE* 1.3 83.5 + - - +
253A CYS* 3.7 4.0 - - - -
254A TYR* 2.8 41.2 + - + +
256A PHE* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 4.2 6.1 - - - -
238A LYS* 6.0 1.8 - - + -
239A THR* 1.3 97.3 + - - +
241A ASN* 1.3 62.8 + - - +
242A LEU* 3.5 31.2 + - + +
251A PRO* 3.3 25.6 - - + +
252A ASP 3.7 4.0 - - - +
253A CYS* 3.2 26.0 - - - -
254A TYR* 5.1 0.2 - - - -
284A CYS* 3.7 16.2 - - - -
----------------------------------------------------------
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