Contacts of the helix formed by residues 244 - 265 (chain A) in PDB entry 6EBT
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 244 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE* 3.8 26.9 - - + +
228A ILE* 2.8 20.7 + - + +
230A LYS* 3.4 32.8 - - + +
242A LEU 3.7 1.6 + - - -
243A THR* 1.3 71.6 - - - +
245A GLY* 1.3 56.9 + - - +
247A GLU* 3.5 11.8 + - - +
248A PHE* 3.0 46.4 + - + -
345A LEU* 4.8 2.5 - - + -
355A GLU* 4.3 4.7 - - - +
356A LEU* 3.9 19.7 - - + -
440A ALA* 3.8 28.7 - - + -
445A ILE* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A SER* 2.6 50.3 + - - -
225A PHE* 2.9 18.7 + - - -
226A ALA* 4.2 2.5 - - - -
243A THR* 3.0 2.8 + - - -
244A LEU* 1.3 75.4 - - - +
246A GLN* 1.3 53.4 + - - +
248A PHE 3.2 0.3 + - - -
249A SER* 2.7 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 3.4 11.5 - - + +
243A THR* 2.8 51.5 + - - +
245A GLY* 1.3 76.4 - - - +
247A GLU* 1.3 62.2 + - - +
249A SER* 2.5 26.6 + - - -
250A GLY 3.3 3.6 + - - -
507A LEU* 3.6 26.5 + - - +
281B THR* 3.8 4.3 - - - +
312B PHE* 3.5 45.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LYS* 3.0 30.8 + - - +
233A ARG* 5.4 0.7 + - - -
242A LEU* 3.7 16.0 - - + +
243A THR 3.0 5.8 + - - +
244A LEU* 3.6 11.5 - - - +
245A GLY 3.3 0.2 - - - -
246A GLN* 1.3 76.4 - - - +
248A PHE* 1.3 62.4 + - - +
250A GLY* 3.2 11.1 + - - -
251A TYR* 3.6 35.2 + - + +
341A ASP* 5.2 0.7 - - - +
345A LEU* 3.3 24.7 - - - +
312B PHE* 5.1 7.0 - - - +
403B PHE* 4.2 12.0 - - - +
404B GLU* 2.5 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 4.0 25.8 - - + +
221A LYS* 4.0 24.7 - - + -
222A SER* 3.8 17.0 - - - -
225A PHE* 4.3 13.7 - + - -
244A LEU* 3.0 50.6 + - + +
245A GLY 3.7 4.0 - - - +
247A GLU* 1.3 75.6 - - + +
249A SER* 1.3 65.8 + - - +
250A GLY 3.1 2.5 - - - -
251A TYR* 3.0 32.5 + + - +
252A VAL* 2.9 24.6 + - - +
342A ILE* 4.5 7.9 - - + -
345A LEU* 5.0 0.9 - - + -
356A LEU* 4.1 24.5 - - + -
438A ILE* 4.5 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A SER* 3.3 10.3 + - - -
245A GLY 2.7 17.8 + - - -
246A GLN* 2.5 24.7 + - - -
248A PHE* 1.3 72.9 - - - +
250A GLY* 1.3 56.1 + - - +
252A VAL* 3.3 10.7 + - - +
253A GLN* 3.0 23.0 + - - +
310B ASN* 3.1 24.6 + - - -
312B PHE* 3.9 5.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLN 3.3 1.6 + - - -
247A GLU 3.2 9.1 + - - -
248A PHE 3.1 1.0 - - - -
249A SER* 1.3 79.9 + - - +
251A TYR* 1.3 67.3 + - - +
253A GLN* 3.3 3.3 + - - +
254A GLN* 3.0 29.6 + - - +
310B ASN* 3.7 17.7 - - - -
312B PHE* 4.3 4.7 - - - -
313B GLU* 3.8 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 4.2 11.2 - - + -
247A GLU* 3.7 34.0 + - + +
248A PHE* 3.0 49.1 + + - +
250A GLY* 1.3 75.7 - - - +
252A VAL* 1.3 64.2 + - - +
254A GLN* 3.2 14.9 + - - +
255A VAL* 3.0 28.5 + - - +
337A LYS* 4.0 10.5 - - - -
338A ILE* 3.8 38.4 - - + -
341A ASP* 2.7 43.8 + - + +
342A ILE* 4.5 10.3 - - + -
345A LEU* 4.0 4.0 - - + +
403B PHE 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A HIS* 3.4 31.0 - - + +
218A LEU* 3.5 14.3 - - + +
219A ASP* 3.4 47.6 - - + +
222A SER* 4.5 1.1 - - - -
248A PHE 2.9 18.6 + - - +
249A SER* 3.5 14.6 - - - +
251A TYR* 1.3 76.5 - - - +
253A GLN* 1.3 58.5 + - - +
255A VAL* 3.2 3.9 + - - -
256A LYS* 2.8 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A SER 3.0 14.0 + - - +
250A GLY 3.6 8.1 - - - +
251A TYR 3.3 0.2 - - - -
252A VAL* 1.3 77.9 - - - +
254A GLN* 1.3 58.3 + - - +
256A LYS* 3.2 34.4 + - - +
257A TYR* 2.8 66.2 + - + +
271B GLU* 5.2 0.2 + - - -
309B PRO* 3.5 20.8 - - - +
310B ASN* 3.9 20.3 + - + +
313B GLU* 3.8 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A GLY 3.0 20.2 + - - +
251A TYR* 3.2 16.1 + - - +
253A GLN* 1.3 74.7 - - - +
255A VAL* 1.3 59.1 + - - +
257A TYR* 3.4 5.4 + - - +
258A ALA* 2.8 28.6 + - - +
261A ARG* 4.6 0.7 + - - -
334A SER* 3.7 32.2 + - - +
337A LYS* 4.1 15.0 + - - +
338A ILE* 3.8 20.9 - - + +
313B GLU* 3.6 19.3 - - + -
316B ALA* 5.6 2.3 - - - +
317B ALA* 3.5 20.1 - - - +
319B ASP* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.4 42.8 - - + +
214A LEU* 4.2 10.8 - - + -
215A HIS* 3.7 18.6 - - + +
218A LEU* 3.8 15.7 - - + -
251A TYR 3.0 16.6 + - - +
252A VAL 3.8 3.6 - - - +
254A GLN* 1.3 73.6 - - - +
256A LYS* 1.3 66.5 + - - +
258A ALA* 3.2 6.8 + - - +
259A MET* 3.1 23.3 + - + +
334A SER* 5.8 0.7 - - - -
335A LEU* 4.4 4.9 - - + -
338A ILE* 3.6 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A HIS* 3.9 22.3 - - + +
252A VAL* 2.8 18.8 + - + +
253A GLN* 3.2 39.2 + - - +
255A VAL* 1.3 77.2 - - - +
257A TYR* 1.3 76.4 + - + +
259A MET* 3.3 10.2 + - - +
260A THR* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLN* 2.8 58.9 + - + +
254A GLN* 3.8 2.5 - - - +
256A LYS* 1.3 84.9 - - + +
258A ALA* 1.3 60.5 + - - +
260A THR* 3.2 10.4 + - + -
261A ARG* 2.8 56.5 + - - +
268B ARG* 3.6 29.4 - - + -
271B GLU* 2.7 37.9 + - - -
309B PRO* 3.6 6.2 - - - +
313B GLU* 3.7 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 4.6 7.4 - - + -
254A GLN 2.8 21.8 + - - +
255A VAL* 3.4 11.0 - - - +
257A TYR* 1.3 74.0 - - - +
259A MET* 1.3 57.3 + - - +
261A ARG* 3.2 11.2 + - - +
262A ILE* 3.0 34.8 + - - +
330A THR* 6.1 0.4 - - + -
331A THR* 3.6 35.8 + - + +
334A SER* 5.1 4.7 - - - +
335A LEU* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 3.5 46.6 - - + +
211A LEU* 3.8 20.2 - - + +
212A GLN* 3.2 46.9 - - + +
215A HIS* 4.8 6.5 - - - -
255A VAL 3.1 16.4 + - - +
256A LYS* 3.6 8.7 - - - +
258A ALA* 1.3 71.7 - - - +
260A THR* 1.3 65.5 + - - +
262A ILE* 3.4 2.6 + - - +
263A LYS* 3.0 45.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
256A LYS* 3.1 19.4 + - - +
257A TYR* 3.2 15.3 + - + -
259A MET* 1.3 76.5 - - - +
261A ARG* 1.3 56.9 + - - +
263A LYS* 3.4 8.9 + - + +
264A ALA* 2.9 29.9 + - + +
268B ARG* 3.7 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A GLN* 4.6 2.4 + - - +
257A TYR* 2.8 46.6 + - - +
258A ALA* 3.6 8.7 - - - +
259A MET 3.2 0.2 - - - -
260A THR* 1.3 74.4 - - - +
262A ILE* 1.3 64.8 + - - +
264A ALA* 3.4 7.4 + - - +
265A ALA* 3.2 22.5 + - - +
327A ALA* 3.6 16.8 - - + +
330A THR* 3.6 22.6 - - - +
334A SER* 4.7 1.6 + - - -
268B ARG* 3.6 26.0 - - - +
313B GLU* 4.8 2.4 + - - -
319B ASP* 3.5 26.5 + - - +
320B ALA* 3.3 29.1 - - - +
323B GLU* 2.6 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 3.8 29.2 - - + -
207A LEU* 3.5 26.7 - - + -
208A LEU* 4.0 9.6 - - + -
211A LEU* 3.4 34.5 - - + -
258A ALA 3.0 18.3 + - - +
259A MET 3.8 3.6 - - - +
261A ARG* 1.3 76.3 - - - +
263A LYS* 1.3 61.2 + - - +
265A ALA* 3.0 13.9 + - - +
266A MET* 3.3 12.6 + - - +
324A LEU* 4.3 9.5 - - + +
327A ALA* 4.0 18.4 - - + +
328A MET* 4.8 3.4 - - + -
331A THR* 3.7 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A HIS* 5.9 6.1 - - + -
208A LEU* 4.1 25.6 - - + -
212A GLN* 5.7 1.0 + - - -
259A MET* 3.0 40.4 + - - +
260A THR* 3.7 7.2 - - + +
262A ILE* 1.3 77.4 - - - +
264A ALA* 1.3 59.6 + - - +
265A ALA 3.1 1.2 + - - -
266A MET* 3.1 22.4 + - + +
267A PRO* 3.4 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A THR* 2.9 20.3 + - + +
261A ARG* 3.7 9.0 - - - +
262A ILE 3.3 0.2 - - - -
263A LYS* 1.3 75.6 - - - +
265A ALA* 1.3 55.8 + - - +
266A MET 3.4 0.4 - - - -
267A PRO* 3.4 14.5 - - - +
268A ARG* 3.4 13.9 + - - -
323A GLU* 3.5 1.9 - - - +
264B ALA* 4.9 22.8 - - + +
268B ARG* 5.2 5.6 - - - +
323B GLU* 5.6 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ARG 3.2 11.2 + - - +
262A ILE 3.0 10.8 + - - +
263A LYS 3.0 1.4 - - - -
264A ALA* 1.3 75.0 - - - +
266A MET* 1.3 59.3 + - - +
267A PRO* 3.6 2.2 - - - -
268A ARG 4.9 1.0 + - - -
269A ILE* 3.6 17.3 + - - +
320A ALA* 4.6 0.7 - - - +
323A GLU* 3.4 39.6 - - + +
324A LEU* 4.0 22.6 + - + +
327A ALA* 4.0 6.5 - - + -
----------------------------------------------------------
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