Contacts of the helix formed by residues 271 - 292 (chain B) in PDB entry 4TVJ
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 271 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LYS 3.6 13.7 - - - +
270B LEU* 1.3 75.9 - - - +
272B VAL* 1.3 65.3 + - - +
273B ALA* 3.5 9.2 + - - +
274B GLN* 3.0 44.5 + - - +
275B ILE* 3.1 28.3 + - - +
341B GLU* 4.7 2.9 - - - -
345B LYS* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ILE* 6.6 0.2 - - + -
448A PRO* 6.5 0.9 - - + -
271B THR* 1.3 73.4 - - - +
273B ALA* 1.3 59.4 + - - +
275B ILE* 3.1 12.5 + - + +
276B LYS* 2.9 31.7 + - + +
338B GLY* 6.5 0.7 - - - -
341B GLU* 3.8 31.0 - - + +
447B HIS* 5.8 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ILE* 5.6 4.3 - - + -
563A ASN* 3.8 16.3 + - - +
564A PRO* 3.9 31.0 - - + -
271B THR* 3.2 9.3 + - - +
272B VAL* 1.3 80.5 - - - +
274B GLN* 1.3 58.8 + - + +
276B LYS* 3.3 11.6 + - - +
277B ALA* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ALA* 6.3 0.8 - - - +
563A ASN* 5.6 0.2 - - - +
269B LYS 3.6 7.5 + - - +
270B LEU* 3.4 20.6 - - + +
271B THR* 3.0 43.4 + - - +
273B ALA* 1.3 75.6 - - + +
275B ILE* 1.3 64.8 + - - +
277B ALA* 3.4 8.1 + - - +
278B GLY* 3.0 18.5 + - - -
308B ARG* 5.0 9.8 - - - +
309B ILE* 3.9 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 4.1 21.8 - - + -
271B THR 3.1 16.7 + - - +
272B VAL* 3.6 11.4 - - + +
274B GLN* 1.3 75.3 - - - +
276B LYS* 1.3 58.1 + - - +
278B GLY* 2.9 5.0 + - - -
279B TYR* 2.9 47.1 + - + +
309B ILE* 4.4 6.7 - - + -
334B LEU* 3.8 26.4 - - + +
337B LEU* 3.7 15.7 - - + +
338B GLY* 3.6 31.2 - - - +
341B GLU* 4.5 9.2 - - + -
447B HIS* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ILE* 4.6 17.4 - - - +
459A LYS 5.0 0.2 + - - -
506A GLU* 2.9 31.4 + - - -
562A TYR* 2.9 29.0 + - - +
563A ASN* 5.6 5.8 - - - +
272B VAL* 2.9 18.1 + - + +
273B ALA* 3.5 13.6 - - - +
274B GLN 3.2 0.2 - - - -
275B ILE* 1.3 77.4 - - - +
277B ALA* 1.3 61.7 + - - +
279B TYR* 2.9 26.0 + - - +
280B GLN* 3.0 32.9 + - - +
447B HIS* 4.0 30.5 - - + +
449B GLU* 4.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A ASN* 4.2 13.2 - - - +
565A ASN* 5.6 4.3 - - - +
273B ALA 2.9 13.1 + - - +
274B GLN* 3.6 11.2 - - - +
275B ILE 3.3 0.2 - - - -
276B LYS* 1.3 76.2 - - - +
278B GLY* 1.3 63.8 + - - +
280B GLN* 3.3 14.9 + - - +
281B SER* 3.0 19.4 + - - -
308B ARG* 3.2 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B GLN 3.0 10.6 + - - -
275B ILE 2.9 9.8 + - - -
277B ALA* 1.3 75.4 - - - +
279B TYR* 1.3 61.7 + - - +
281B SER* 3.2 3.3 + - - -
282B LEU* 3.0 19.2 + - - +
305B PHE* 3.6 13.1 - - - -
308B ARG* 4.7 3.5 - - - +
309B ILE* 3.9 23.8 - - - -
334B LEU* 3.5 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ILE* 2.9 37.4 + - + -
276B LYS* 2.9 9.8 + - - +
278B GLY* 1.3 71.2 - - - +
280B GLN* 1.3 57.5 + - - +
282B LEU* 3.1 8.0 + - + +
283B LYS* 2.9 27.9 + - - +
331B ILE* 4.6 12.6 - - + -
334B LEU* 3.3 26.5 + - + +
335B GLU* 3.3 34.1 + - + +
447B HIS* 3.5 41.6 + + + +
449B GLU* 3.7 22.7 - - + +
450B ALA* 3.7 29.6 - - + -
451B PRO* 4.2 4.9 - - + +
455B TYR* 5.1 0.2 - - - -
601B 09L 5.6 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A GLU* 4.7 3.4 + - - +
509A LEU* 5.9 4.2 - - - +
562A TYR* 6.2 0.2 - - - +
563A ASN* 5.3 4.0 + - - -
276B LYS* 3.0 32.6 + - - +
277B ALA* 3.5 19.4 + - - +
278B GLY 3.2 0.2 - - - -
279B TYR* 1.3 75.7 - - - +
281B SER* 1.3 60.9 + - - +
283B LYS* 3.1 18.0 + - - +
284B LYS* 3.2 22.4 + - + +
308B ARG* 4.5 7.6 + - - +
449B GLU* 3.5 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA 3.0 6.3 + - - -
278B GLY 3.2 7.1 + - - -
280B GLN* 1.3 75.0 - - - +
282B LEU* 1.3 63.2 + - - +
284B LYS* 3.1 8.8 + - - +
285B ILE* 3.0 25.2 + - - +
301B ALA* 4.6 2.6 - - - +
304B GLU* 2.6 27.7 + - - +
305B PHE* 3.7 28.7 - - - -
308B ARG* 3.0 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B GLY 3.0 12.7 + - - +
279B TYR* 3.4 9.4 - - + +
281B SER* 1.3 76.5 - - - +
283B LYS* 1.3 56.8 + - - +
285B ILE* 3.2 24.5 + - + +
286B GLU* 2.8 27.7 + - - +
305B PHE* 3.8 15.0 - - + -
321B ILE* 4.6 0.4 - - + -
327B LEU* 3.8 16.0 - - + +
330B LYS* 3.5 39.5 - - + -
331B ILE* 3.9 25.6 - - + +
334B LEU* 3.8 22.9 - - + -
451B PRO* 4.0 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR 2.9 13.7 + - - +
280B GLN* 3.1 13.0 + - - +
282B LEU* 1.3 76.8 - - - +
284B LYS* 1.3 58.4 + - + +
286B GLU* 3.1 30.0 + - - +
287B ASP* 2.9 56.9 + - - +
449B GLU* 4.2 15.3 - - - +
450B ALA 5.5 0.7 - - - +
451B PRO* 4.3 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A GLY* 6.1 4.9 - - - -
280B GLN* 3.5 19.7 - - - +
281B SER* 3.1 6.6 + - - +
283B LYS* 1.3 76.2 - - + +
285B ILE* 1.3 65.1 + - - +
287B ASP* 3.3 14.5 + - - +
288B CYS* 3.2 27.6 + - - -
301B ALA* 4.3 12.8 - - + -
304B GLU* 2.8 42.3 + - - +
308B ARG* 5.0 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B SER 3.0 14.2 + - - +
282B LEU* 3.2 18.1 + - + +
284B LYS* 1.3 74.9 - - - +
286B GLU* 1.3 66.7 + - - +
288B CYS* 3.1 4.3 + - - +
289B ILE* 3.0 31.3 + - + +
298B LEU* 4.0 7.2 - - + -
301B ALA* 3.6 23.1 - - + -
302B CYS* 3.8 12.1 - - - +
305B PHE* 3.9 24.2 - - + -
321B ILE* 3.6 52.5 - - + +
327B LEU* 3.9 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU 2.8 14.4 + - - +
283B LYS* 3.3 34.4 - - - +
285B ILE* 1.3 75.9 - - - +
287B ASP* 1.3 58.6 + - - +
289B ILE* 3.2 6.2 + - + +
290B ARG* 2.8 47.8 + - + +
327B LEU* 4.0 16.1 - - + +
451B PRO* 3.5 14.2 - - + +
452B ILE* 3.5 7.1 + - - +
453B THR* 2.4 53.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LYS* 2.9 48.7 + - - +
284B LYS* 3.6 16.2 - - - +
285B ILE 3.2 0.4 - - - -
286B GLU* 1.3 77.1 - - - +
288B CYS* 1.3 59.4 + - - +
290B ARG* 3.5 11.4 - - - +
291B ALA* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LYS* 3.2 17.2 + - - -
285B ILE 3.1 8.3 + - - +
287B ASP* 1.3 79.1 - - - +
289B ILE* 1.3 58.8 + - - +
291B ALA* 3.2 5.1 + - - +
292B GLY 2.9 23.9 + - - -
293B GLN* 3.0 18.1 + - + +
297B ALA* 3.5 43.5 - - + -
298B LEU* 3.6 23.3 - - + +
301B ALA* 4.4 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ILE* 3.0 38.2 + - + +
286B GLU* 3.6 5.2 - - + +
288B CYS* 1.3 74.6 - - - +
290B ARG* 1.3 65.1 + - - +
292B GLY* 3.2 12.7 + - - +
293B GLN 5.3 1.8 - - - -
294B HIS* 6.3 2.7 - - + -
298B LEU* 4.5 5.8 - - + -
321B ILE 3.8 11.4 - - - +
322B ARG* 3.7 35.9 - - + +
323B THR* 4.4 7.9 - - - +
324B GLN 5.7 0.4 - - - +
327B LEU* 4.3 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B GLU* 2.8 29.4 + - + +
287B ASP* 3.5 15.0 - - - +
289B ILE* 1.3 78.8 - - - +
291B ALA* 1.3 60.8 - - - +
292B GLY* 3.3 1.4 + - - -
452B ILE* 5.0 7.2 - - - +
453B THR* 3.5 31.8 - - - +
504B LYS* 4.9 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASP 2.9 17.4 + - - +
288B CYS* 3.9 4.3 - - - +
290B ARG* 1.3 76.0 - - - +
292B GLY* 1.3 60.4 + - - +
293B GLN* 3.7 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B CYS 2.9 5.1 + - - -
289B ILE* 3.2 8.5 + - - -
290B ARG 3.1 5.0 - - - -
291B ALA* 1.3 78.5 - - - +
293B GLN* 1.3 63.3 + - - +
294B HIS* 4.2 8.5 + - - -
----------------------------------------------------------
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