Contacts of the helix formed by residues 251 - 275 (chain A) in PDB entry 5XJY
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 SER 251 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 5.8 7.2 - - - -
247A SER 4.9 0.4 + - - -
248A PRO 4.1 6.5 + - - +
249A PHE 3.9 6.8 - - - +
250A PRO* 1.3 79.7 - - - +
252A LYS* 1.3 63.0 + - - +
253A GLU* 4.4 7.4 - - - -
254A LEU* 4.1 14.9 + - - +
255A ALA* 3.8 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PRO 4.2 0.2 + - - -
251A SER* 1.3 71.9 - - - +
253A GLU* 1.3 61.9 + - - +
254A LEU 3.2 2.2 - - - -
255A ALA* 3.0 22.2 + - + +
256A GLU* 3.3 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A THR* 5.1 15.0 + - + +
135A ILE* 5.6 8.7 - - + -
251A SER* 3.6 3.5 - - - -
252A LYS* 1.3 74.7 - - - +
254A LEU* 1.3 64.7 + - - +
256A GLU* 4.0 3.6 + - - +
257A ALA* 3.5 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 5.2 7.5 - - + +
131A THR* 4.9 14.9 + - - +
248A PRO* 5.0 7.6 - - + +
251A SER* 4.1 19.1 + - - +
252A LYS 3.2 0.6 - - - -
253A GLU* 1.3 79.1 - - - +
255A ALA* 1.3 52.9 + - - +
257A ALA* 3.1 5.0 + - - +
258A THR* 2.5 41.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PRO 5.0 7.6 - - - +
249A PHE* 5.9 0.9 - - - +
251A SER 3.8 12.7 + - - +
252A LYS* 3.0 16.3 + - + +
254A LEU* 1.3 78.5 - - - +
256A GLU* 1.3 57.6 + - - +
258A THR* 3.8 4.5 - - - -
259A LYS* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LYS 3.3 10.2 + - - +
253A GLU* 4.6 4.3 - - - +
255A ALA* 1.3 78.0 - - - +
257A ALA* 1.3 59.8 + - - +
259A LYS* 3.1 8.8 + - - +
260A THR* 3.0 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP* 5.2 2.8 - - - +
127A LYS* 5.3 11.4 - - + -
128A VAL* 3.7 28.6 - - + +
131A THR* 5.1 4.5 - - + +
253A GLU 3.5 18.4 + - - +
254A LEU* 3.1 5.9 + - - +
256A GLU* 1.3 79.2 - - - +
258A THR* 1.3 57.4 + - - +
260A THR* 3.2 9.4 + - - -
261A LEU* 2.9 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 4.2 10.5 - - - +
248A PRO* 6.5 0.9 - - - -
254A LEU* 2.5 23.7 + - - -
255A ALA* 3.8 4.9 - - - -
257A ALA* 1.3 70.7 - - - +
259A LYS* 1.3 58.1 + - - +
260A THR 3.3 0.2 - - - -
261A LEU* 3.3 11.8 - - - +
262A LEU* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ALA 2.9 19.8 + - - +
256A GLU* 3.1 10.7 + - - +
258A THR* 1.3 74.3 - - - +
260A THR* 1.3 60.9 + - - +
262A LEU* 3.3 5.5 + - - +
263A HIS* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP* 5.0 19.0 - - - +
256A GLU 3.0 11.9 + - - -
257A ALA* 3.2 11.9 + - - -
259A LYS* 1.3 72.3 - - - +
261A LEU* 1.3 60.0 + - - +
263A HIS* 4.1 5.6 - - - +
264A SER* 2.9 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A SER 6.1 0.4 - - - -
124A ASP* 5.9 2.2 - - - +
125A MET* 3.6 31.4 - - + -
128A VAL* 5.0 3.1 - - + -
257A ALA 2.9 8.4 + - - +
258A THR* 3.3 22.0 - - - +
259A LYS 3.2 0.2 - - - -
260A THR* 1.3 77.6 - - - +
262A LEU* 1.3 57.2 + - - +
264A SER* 3.2 3.7 + - - -
265A LEU* 2.9 37.7 + - + +
439A LEU* 5.9 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A THR 2.9 16.7 + - - +
259A LYS* 3.3 6.7 + - - +
261A LEU* 1.3 76.1 - - - +
263A HIS* 1.3 57.5 + - - +
265A LEU* 3.8 4.5 + - - +
266A GLY* 2.9 22.3 + - - -
439A LEU* 6.3 4.0 - - + -
448A PHE* 5.5 11.0 - - + -
449A TRP* 5.9 10.0 - - + +
452A GLN* 5.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LYS 2.9 17.2 + - - +
260A THR* 4.1 6.5 - - - +
262A LEU* 1.3 76.3 - - - +
264A SER* 1.3 58.5 + - - +
266A GLY* 3.0 3.1 + - - +
267A THR* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASP* 5.0 3.1 - - - +
120A THR* 6.1 0.2 - - - -
121A SER* 3.7 32.5 - - - -
124A ASP* 6.3 0.9 - - - -
125A MET* 6.5 0.4 - - - -
260A THR 2.9 21.3 + - - -
261A LEU* 3.7 5.2 - - - -
263A HIS* 1.3 76.1 - - - +
265A LEU* 1.3 59.9 + - - +
267A THR* 3.3 11.6 - - - +
268A LEU* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A SER* 5.5 4.5 - - - -
125A MET* 4.8 19.3 - - + -
261A LEU* 2.9 27.0 + - + +
262A LEU* 4.3 4.5 - - - +
264A SER* 1.3 79.3 - - - +
266A GLY* 1.3 58.9 - - - +
268A LEU* 4.4 10.5 - - + -
269A ALA* 2.9 31.4 + - - +
436A VAL* 4.5 31.2 - - + +
439A LEU* 5.4 7.2 - - + -
440A LEU* 5.4 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU 2.9 17.0 + - - -
263A HIS* 3.0 6.8 + - - -
265A LEU* 1.3 77.0 - - - +
267A THR* 1.3 56.3 + - - +
269A ALA* 3.2 5.4 + - - +
270A GLN* 2.9 27.8 + - - +
452A GLN* 4.4 25.7 - - - +
453A LEU* 5.9 0.4 - - - -
456A LEU* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TYR* 3.3 34.8 + - - +
263A HIS 3.0 13.7 + - - +
264A SER* 3.3 18.6 - - - +
266A GLY* 1.3 74.8 - - - +
268A LEU* 1.3 58.0 + - - +
270A GLN* 3.3 7.0 + - - +
271A GLU* 3.0 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 6.4 1.6 - - + -
115A TYR* 3.6 22.0 - - + +
119A ASP* 3.4 27.8 - - - +
121A SER* 3.5 22.7 - - - +
264A SER 2.9 17.9 + - - +
265A LEU* 4.4 9.9 - - + -
267A THR* 1.3 73.4 - - - +
269A ALA* 1.3 61.0 + - - +
271A GLU* 4.5 6.3 - - + +
272A LEU* 2.9 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU 2.9 23.9 + - - +
266A GLY* 3.2 5.8 + - - +
268A LEU* 1.3 77.5 - - - +
270A GLN* 1.3 58.0 + - - +
272A LEU* 5.0 1.8 - - - -
273A PHE* 3.0 32.2 + - - +
453A LEU* 5.2 15.0 - - + -
456A LEU* 4.7 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLY 2.9 13.8 + - - +
267A THR* 3.6 11.4 - - - +
268A LEU 3.3 0.2 - - - -
269A ALA* 1.3 77.5 - - - +
271A GLU* 1.3 59.0 + - + +
273A PHE* 4.2 1.9 - - - +
274A SER* 2.7 32.0 + - - -
452A GLN 5.5 0.2 - - - +
456A LEU* 3.7 33.1 - - + +
457A ASP* 5.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG* 4.6 3.6 - - - +
112A LEU* 4.5 13.5 - - + +
115A TYR* 3.1 58.3 - - - +
267A THR* 3.0 23.8 + - - +
268A LEU* 4.2 5.7 - - + +
270A GLN* 1.3 77.4 - - + +
272A LEU* 1.3 57.5 + - - +
274A SER* 2.7 32.9 + - - +
275A MET* 3.0 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 5.1 13.2 - - + +
268A LEU* 2.9 24.3 + - + +
269A ALA* 4.7 1.6 - - - +
271A GLU* 1.3 75.9 - - - +
273A PHE* 1.3 61.1 + - - +
275A MET* 4.4 11.8 + - - +
276A ARG 5.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ALA 3.0 19.9 + - - +
270A GLN* 4.3 1.8 - - - +
272A LEU* 1.3 79.7 - - - +
274A SER* 1.3 65.6 + - - +
275A MET 3.1 2.4 + - - -
276A ARG* 3.4 31.6 + - + +
456A LEU* 6.2 1.1 - - + -
457A ASP* 4.2 17.7 - - + -
458A TRP* 3.2 29.6 - - + -
459A THR* 3.6 19.5 - - - -
460A ALA* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG* 4.1 12.4 + - - -
270A GLN 2.7 19.3 + - - -
271A GLU* 2.7 28.5 + - - +
273A PHE* 1.3 77.3 - - - +
275A MET* 1.3 72.4 + - - +
276A ARG* 3.3 9.3 - - - +
457A ASP* 5.4 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 5.9 1.0 - - - +
108A ASP* 2.8 55.1 - - + +
111A ARG* 3.6 45.4 + - + +
112A LEU* 4.1 24.5 - - + -
271A GLU* 3.0 31.9 + - + +
272A LEU* 4.6 7.9 - - - +
273A PHE 3.1 1.0 + - - -
274A SER* 1.3 97.8 - - - +
276A ARG* 1.3 58.7 + - - +
277A SER* 2.7 17.9 + - - +
----------------------------------------------------------
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