Contacts of the strand formed by residues 225 - 234 (chain A) in PDB entry 4FLL
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 ILE 225 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A VAL* 3.4 6.6 - - - +
207A ASN* 2.9 47.9 + - - +
223A GLY 3.8 1.3 + - - +
224A ASP* 1.4 79.2 - - - +
226A VAL* 1.4 62.4 + - - +
244A THR* 4.0 8.7 - - + -
245A PHE 3.4 6.3 - - - +
246A PHE* 4.1 17.9 - - + -
250A VAL* 4.5 1.1 - - + -
254A ALA* 3.7 28.5 - - + -
257A LEU* 4.0 21.1 - - + -
258A VAL* 4.2 8.1 - - + -
362A ARG* 4.2 13.7 - - + +
363A SER 3.6 22.9 - - - +
364A ALA* 4.3 10.3 - - + -
504A NA 4.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 3.9 23.1 - - + -
172A THR* 4.7 2.2 - - + -
175A ILE* 5.6 1.1 - - + -
204A THR* 4.6 9.0 - - - -
205A SER 3.3 6.7 - - - +
206A VAL* 3.8 20.9 - - + -
220A LEU* 4.1 22.0 - - + -
225A ILE* 1.4 76.0 - - - +
227A ASN* 1.3 72.7 + - - +
228A VAL* 4.7 5.8 - - + -
244A THR* 4.1 3.4 - - - -
245A PHE* 2.7 43.6 + - + +
247A VAL* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A CYS 3.5 0.9 - - - +
204A THR* 3.3 5.5 - - - -
205A SER* 2.8 47.5 + - - +
210A ILE 5.9 0.7 - - - +
226A VAL* 1.3 76.5 - - - +
228A VAL* 1.4 67.3 + - - +
229A ASP* 3.7 6.8 + - - +
242A ASN* 2.9 32.4 + - - +
243A GLU 3.2 11.9 + - - -
244A THR* 3.2 12.2 + - + +
364A ALA* 6.1 0.9 - - - -
365A GLN* 2.9 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 3.4 9.5 - - + +
162A ALA* 3.8 16.6 - - + -
166A ILE* 4.2 16.4 - - + -
175A ILE* 4.4 12.8 - - + -
202A CYS* 4.4 11.4 - - - -
203A CYS 3.4 6.3 - - - +
204A THR* 4.5 7.9 - - + -
226A VAL* 4.1 5.6 + - + -
227A ASN* 1.4 77.2 + - - +
229A ASP* 1.4 64.4 + - - +
230A ILE* 3.8 26.2 - - + -
242A ASN* 3.2 20.1 - - - +
243A GLU 3.1 11.4 + - - -
245A PHE* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A PRO* 5.0 2.1 - - - +
202A CYS* 3.3 9.4 - - - +
203A CYS* 2.9 46.3 + - + +
212A HIS* 6.0 0.5 - - - -
227A ASN* 3.7 6.9 + - - +
228A VAL* 1.4 73.4 - - - +
230A ILE* 1.3 64.5 + - - +
231A THR 4.3 0.3 + - - -
240A ASP* 3.1 3.6 - - - +
241A LEU 3.1 2.1 - - - +
242A ASN* 2.8 27.9 + - + -
336A GLU* 4.2 0.3 - - - +
365A GLN* 4.5 3.3 + - - +
502A MN 2.1 36.8 + - - -
503A YZ6 2.8 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ALA* 3.8 15.0 - - - +
158A VAL* 4.0 6.3 - - + -
159A LEU* 3.8 33.2 - - + -
179A VAL* 3.6 41.7 - - + -
201A SER 5.6 0.4 - - - -
202A CYS* 3.9 6.3 - - + -
228A VAL* 3.8 14.4 - - + -
229A ASP* 1.3 72.9 - - - +
231A THR* 1.3 69.2 + - - +
232A LEU* 3.3 27.6 - - + -
239A GLY 3.8 0.5 - - - +
240A ASP* 3.4 1.0 - - - +
241A LEU* 2.9 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A CYS* 5.0 0.2 - - - -
190A PRO* 3.7 3.3 - - - +
191A SER* 2.9 42.5 + - - +
192A PRO* 3.4 13.7 - - - +
201A SER 4.8 1.8 + - - +
229A ASP 4.2 1.2 + - - -
230A ILE* 1.3 73.4 + - - +
232A LEU* 1.3 68.2 + - - +
238A HIS* 4.2 4.9 - - + -
239A GLY 3.1 21.5 - - - +
240A ASP* 2.8 26.4 + - + -
309A PHE* 3.5 30.5 - - + -
503A YZ6 3.5 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 3.2 14.7 - - + +
154A LEU* 3.6 33.9 - - + +
155A ALA* 3.7 7.0 - - + +
158A VAL* 3.8 13.0 - - + -
183A CYS* 3.5 28.5 - - - -
186A ARG* 4.9 0.9 - - - -
188A CYS* 3.8 27.8 - - + -
189A TYR 3.5 2.9 - - - -
191A SER* 3.1 7.5 + - - -
230A ILE* 3.3 29.6 - - + -
231A THR* 1.3 75.2 - - - +
233A TYR* 1.3 59.5 - - - +
238A HIS* 3.1 5.0 - - - -
239A GLY 2.9 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLN* 3.7 34.1 + - + +
114A ARG 3.6 7.4 + - - -
115A PRO* 3.4 41.1 - - + +
116A ASP 5.1 0.5 + - - -
188A CYS* 3.4 6.6 - - - -
189A TYR* 2.9 38.5 + - + +
191A SER* 3.5 10.3 - - - +
232A LEU* 1.3 73.1 - - - +
234A ARG* 1.3 59.4 - - - +
236A GLY* 3.4 36.2 + - - -
237A TYR 3.2 12.3 - - - -
238A HIS* 3.3 36.3 - + + +
307A LYS 4.6 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLN* 6.1 3.6 - - - +
147A GLY* 5.1 1.0 - - - +
150A LEU* 4.2 19.8 - - + +
151A VAL* 3.8 17.7 - - + +
154A LEU* 4.3 6.0 - - + +
186A ARG 4.2 5.8 + - - -
187A ASN* 3.4 40.4 + - - +
188A CYS* 3.6 20.0 - - - -
233A TYR* 1.3 75.0 - - - +
235A ASN* 1.4 108.0 + - - +
236A GLY 3.0 3.6 + - - -
237A TYR* 2.8 25.9 + - - +
----------------------------------------------------------
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