Contacts of the strand formed by residues 263 - 275 (chain A) in PDB entry 4U8T
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 263 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ILE* 4.3 11.9 - - + -
200A TRP 3.2 15.5 - - - +
201A SER* 3.8 6.1 - - - -
245A LEU* 3.6 8.7 - - - -
246A ARG 3.0 27.6 + - - +
249A LEU* 3.8 13.9 - - + +
251A THR* 3.8 18.7 - - + +
254A TRP* 3.9 10.3 - - + -
262A HIS* 1.3 77.9 - - - +
264A PHE* 1.3 61.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
199A ILE* 3.3 2.6 - - - -
200A TRP* 2.9 53.3 + + + -
201A SER* 4.4 0.9 - - - -
202A SER 4.6 0.2 - - - -
207A ASN* 3.8 15.3 - - - -
210A LEU* 3.5 34.8 - - + -
211A SER 6.2 0.2 - - - -
225A LEU* 4.0 4.9 - - + -
241A MSE 3.6 32.1 - - + -
243A SER* 3.6 10.1 - - - +
244A ASN 3.4 21.5 - - - +
245A LEU* 3.6 18.2 - - + -
249A LEU* 4.2 6.1 - - - -
263A ALA* 1.3 73.7 - - - +
265A LYS* 1.3 74.4 + - - +
266A VAL* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLY 3.3 11.4 - - - +
199A ILE* 4.3 2.5 - - + +
241A MSE 3.7 2.1 - - - -
242A SER* 2.8 39.0 + - - +
243A SER* 2.8 25.6 + - - +
246A ARG* 3.1 34.7 - - - +
249A LEU* 3.9 28.2 - - + +
264A PHE* 1.3 76.3 - - - +
266A VAL* 1.3 63.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
194A SER* 3.7 10.8 - - - +
198A GLY* 2.8 38.0 + - - +
199A ILE 3.6 13.5 - - - +
200A TRP* 3.8 12.1 - - + +
225A LEU* 3.9 12.3 - - + -
227A PHE* 5.5 0.4 - - + -
239A ALA* 4.3 8.3 - - + -
240A GLU 3.1 12.8 - - - +
242A SER* 3.7 4.9 + - - -
264A PHE* 3.7 24.7 - - + -
265A LYS* 1.3 80.3 - - - +
267A ARG* 1.3 64.3 + - - +
268A TRP* 3.8 14.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LYS* 4.7 9.5 - - - +
239A ALA* 3.5 0.8 - - - -
240A GLU* 2.9 61.5 + - - +
242A SER* 3.7 27.5 + - - +
266A VAL* 1.3 77.3 - - - +
268A TRP* 1.3 65.3 + - - +
269A ILE* 3.6 5.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 5.9 0.9 - - - +
191A VAL* 3.8 22.4 - - + -
194A SER* 3.2 32.7 + - - -
195A PHE* 3.7 43.1 - + + +
198A GLY* 5.2 1.3 - - - -
227A PHE* 3.6 44.0 - + + -
237A GLY* 4.0 7.4 - - - -
238A VAL 3.7 18.6 - - - -
239A ALA* 4.0 6.5 - - + +
266A VAL* 3.8 16.8 + - + +
267A ARG* 1.3 73.5 - - - +
269A ILE* 1.3 60.3 + - - +
270A VAL 3.5 24.5 - - - -
271A VAL* 4.0 9.6 - - + -
323A PHE* 4.1 11.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.9 14.3 - - - +
169A PRO* 3.3 31.2 - - + +
171A TRP 5.8 0.2 - - - +
172A ILE* 4.2 16.4 - - + -
224A TYR* 3.9 19.7 - - + -
238A VAL* 3.0 14.9 + - + +
240A GLU* 3.5 41.7 - - + +
267A ARG 4.1 3.6 - - - +
268A TRP* 1.3 77.7 - - - +
270A VAL* 1.3 77.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE 3.3 9.6 - - - +
168A ILE* 4.9 0.9 - - - -
169A PRO* 4.0 8.7 - - + -
172A ILE* 3.9 18.8 - - + -
237A GLY* 3.3 2.3 - - - -
238A VAL* 3.0 44.6 + - + +
268A TRP* 3.5 2.9 - - - -
269A ILE* 1.3 96.3 - - + +
271A VAL* 1.3 68.2 + - - +
272A ARG* 4.2 9.2 - - + +
313A PHE* 3.8 42.2 - - + +
314A LYS* 5.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ALA* 3.5 5.9 - - - +
167A ILE* 2.8 41.0 + - + +
195A PHE* 3.8 37.0 - - + -
236A CYS 4.0 3.1 - - - -
268A TRP* 4.0 9.9 - - + -
269A ILE 5.7 0.2 - - - -
270A VAL* 1.3 78.6 - - - +
272A ARG* 1.3 64.2 + - - +
322A SER* 3.7 14.1 - - - +
323A PHE* 3.7 25.4 - - + -
324A LEU* 3.7 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ALA* 4.6 2.0 - - + -
168A ILE* 3.8 21.4 - - + +
236A CYS* 3.2 25.1 + - - -
270A VAL* 4.0 12.3 - - + +
271A VAL* 1.3 77.4 - - - +
273A ASP* 1.3 84.0 + - - +
274A VAL* 4.2 8.2 - - + +
312A LEU 3.7 10.1 + - - -
313A PHE* 3.2 29.6 + - + +
315A TYR* 2.6 53.8 + - - +
320A VAL* 4.6 20.9 - - + +
321A GLN 3.6 11.4 - - - +
322A SER* 4.1 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ARG* 3.0 40.3 + - - -
235A PHE 3.4 3.4 - - - -
236A CYS* 3.9 14.9 - - - +
272A ARG* 1.3 95.9 + - - +
274A VAL* 1.3 59.4 + - - +
275A HIS* 5.4 8.9 + - + +
320A VAL* 6.1 0.2 - - - -
321A GLN* 2.9 46.9 + - + +
322A SER* 3.8 11.9 + - - -
323A PHE* 4.2 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ARG* 3.1 3.5 - - - +
235A PHE* 2.9 34.5 + - + +
272A ARG* 4.2 7.4 - - - +
273A ASP* 1.3 78.4 - - - +
275A HIS* 1.3 68.4 + - - +
278A SER* 4.3 9.9 - - - -
279A LEU* 3.7 33.8 - - + +
312A LEU* 4.1 23.6 - - + +
313A PHE* 3.7 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLY 3.8 11.2 - - - +
234A ARG* 4.0 21.7 + - + -
273A ASP* 5.4 7.7 + - + +
274A VAL* 1.3 79.4 - - - +
276A ASN* 1.3 66.9 + - - +
277A ARG* 3.8 41.9 + - + +
278A SER* 2.9 25.8 + - - +
279A LEU* 3.7 3.6 + - - +
321A GLN* 4.1 19.0 + - - -
----------------------------------------------------------
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