Contacts of the strand formed by residues 256 - 267 (chain A) in PDB entry 2AEX
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 THR 256 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 4.4 0.9 - - + -
247A ILE 3.2 9.9 - - - +
248A HIS* 2.8 42.4 + - + +
249A PRO* 3.8 1.1 - - - +
254A ALA 3.9 0.8 + - - -
255A PRO* 1.3 73.5 - - - +
257A ILE* 1.3 67.5 + - - +
283A LEU* 3.5 7.0 - - - +
284A THR* 2.8 46.8 + - - -
389A ARG* 2.9 24.5 + - - +
392A TYR* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A SER* 5.8 0.2 - - - +
246A VAL* 3.4 6.4 - - - +
247A ILE* 2.9 51.3 + - + +
255A PRO 3.9 0.6 + - - -
256A THR* 1.3 76.2 - - - +
258A HIS* 1.3 71.9 + - - +
259A PHE* 5.0 3.6 - - + -
281A CYS* 3.7 14.8 - - - -
282A ASP 3.5 13.0 - - - +
283A LEU* 4.3 0.9 - - + -
284A THR* 6.1 0.2 - - - -
296A PHE* 3.7 22.0 - - + -
361A VAL* 4.5 10.1 - - + -
364A SER* 4.2 1.8 - - - +
365A TYR* 3.5 57.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A SER 3.3 21.1 - - - +
246A VAL* 3.8 12.1 - - + -
257A ILE* 1.3 77.3 - - - +
259A PHE* 1.3 68.9 + - - +
260A ASN* 3.3 24.6 + - - -
281A CYS* 3.3 0.5 - - - -
282A ASP* 2.7 64.4 + - - +
284A THR* 6.0 0.2 + - - -
323A PHE* 4.4 13.7 - + - -
332A ARG* 3.7 9.3 + - - +
338A PHE* 6.4 0.4 - + - -
392A TYR* 3.5 19.1 - - + +
500A CIT 2.7 32.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A THR* 4.0 20.6 - - + -
163A VAL* 3.8 28.5 - - + -
205A VAL* 4.5 5.6 - - + -
243A VAL* 4.1 16.6 - - + -
244A SER* 3.3 0.7 - - - -
245A SER* 2.9 63.8 + - - +
247A ILE* 4.7 4.9 - - + -
257A ILE* 5.0 6.3 - - + -
258A HIS* 1.3 81.7 + - - +
260A ASN* 1.3 69.7 + - - +
261A TYR* 4.1 11.0 - + + -
280A GLY 3.2 14.6 - - - +
281A CYS* 4.0 13.7 - - + -
361A VAL* 3.6 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL 3.1 11.9 - - - +
244A SER* 4.1 0.4 - - - +
258A HIS* 3.3 16.8 - - - -
259A PHE* 1.3 78.7 - - - +
261A TYR* 1.3 66.9 + - - +
262A ARG* 2.7 34.8 - - - +
279A GLY* 2.9 8.3 - - - -
280A GLY* 2.8 39.9 + - - +
338A PHE* 5.7 5.7 - - - -
500A CIT 2.8 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A MET* 4.0 9.8 - - + +
155A LEU* 5.9 0.9 - - + -
156A ILE* 5.4 0.4 - - + -
242A GLY* 3.1 2.3 - - - -
243A VAL* 2.9 41.6 + - + +
259A PHE* 4.1 19.7 - + + -
260A ASN* 1.3 88.7 - - - +
262A ARG* 1.3 60.7 + - - +
278A GLY 3.5 2.5 - - - -
279A GLY* 3.9 6.3 - - - -
280A GLY 3.6 28.1 + - - -
281A CYS* 3.6 14.4 - - - +
300A LEU* 5.1 0.9 - - - +
337A ILE* 4.0 6.6 - - - +
339A PHE* 3.8 16.2 - + - -
354A VAL* 4.0 24.5 - - + -
357A CYS* 3.3 36.0 + - + +
358A ALA* 3.8 29.4 - - + -
361A VAL* 4.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A MET* 3.7 6.8 - - - +
241A MET 3.2 15.3 - - - +
242A GLY* 3.9 4.7 - - - -
260A ASN* 2.7 34.1 - - - +
261A TYR* 1.3 75.5 - - - +
263A TYR* 1.3 63.1 + - - +
276A TRP* 5.9 2.7 - - + +
277A PHE* 3.3 12.3 - - - +
278A GLY* 2.9 44.1 + - - +
279A GLY 3.5 9.3 - - - +
338A PHE* 5.3 5.3 - - - -
339A PHE 4.3 4.0 + - - -
340A ASP* 3.1 29.3 + - - +
354A VAL* 5.3 0.5 - - - +
407A LEU* 3.3 25.6 + - + +
408A PHE* 4.3 3.9 - - - +
409A THR 3.9 22.4 - - - +
410A PRO* 4.0 4.2 - - - +
500A CIT 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MET* 3.6 18.8 - - + +
149A LYS* 4.3 9.6 - - + -
152A MET* 3.7 27.8 - - + -
239A CYS* 5.3 2.2 - - - -
240A ALA* 3.4 3.1 - - - +
241A MET* 2.9 42.3 + - + +
262A ARG* 1.3 77.1 - - - +
264A PHE* 1.3 71.9 + - - +
265A GLU* 2.6 47.4 + - + +
275A TRP* 3.9 11.8 - + + +
276A TRP 3.5 8.1 - - - -
277A PHE* 3.4 39.5 - + + -
347A LYS* 3.2 23.0 + - + +
407A LEU 5.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 4.3 4.5 - - + -
222A MET* 3.5 18.4 - - + -
238A PHE* 3.6 28.7 - + + -
239A CYS 3.4 5.4 - - - -
240A ALA* 3.9 8.7 - - + -
263A TYR* 1.3 80.4 - - - +
265A GLU* 1.3 62.0 + - - +
266A VAL* 3.6 35.2 - - + -
275A TRP* 3.0 6.6 - - - +
276A TRP* 2.9 77.7 + + + +
408A PHE* 3.3 42.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASP* 4.7 1.7 - - - +
148A MET* 4.8 0.7 - - - +
149A LYS* 2.9 38.2 + - - +
238A PHE* 3.1 6.1 - - - +
239A CYS* 2.9 47.2 + - + +
263A TYR* 2.6 37.9 + - + +
264A PHE* 1.3 78.4 - - - +
266A VAL* 1.3 62.8 + - - +
267A GLU* 4.7 5.7 - - + +
273A LYS* 3.4 33.7 + - + +
274A GLN 3.2 9.9 - - - +
275A TRP* 4.0 4.0 - - + -
347A LYS* 3.9 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 4.1 11.7 - - + -
222A MET* 5.8 0.2 - - - -
229A LEU* 3.7 17.9 - - + -
236A LEU* 3.8 29.4 - - + +
237A PRO 3.3 12.6 - - - +
238A PHE* 4.1 1.3 - - + -
264A PHE* 3.6 21.3 - - + -
265A GLU* 1.3 75.4 - - - +
267A GLU* 1.3 75.5 + - - +
268A GLU* 3.7 1.8 + - + +
273A LYS* 3.4 5.5 - - - -
274A GLN* 2.8 55.0 + - + +
276A TRP* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LYS* 5.4 2.4 + - - -
232A LYS* 2.4 48.4 + - + +
236A LEU* 3.8 6.6 - - - +
237A PRO* 2.7 43.5 + - + +
238A PHE* 6.0 0.2 - - - -
265A GLU* 4.7 6.1 - - + +
266A VAL* 1.3 79.8 - - - +
268A GLU* 1.3 61.7 + - - +
272A ASN 3.9 5.4 - - - +
273A LYS* 4.0 26.9 + - - +
----------------------------------------------------------
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