Contacts of the helix formed by residues 270 - 286 (chain B) in PDB entry 5J1T
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 270 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLN* 1.3 75.3 + - - +
271B SER* 1.3 65.6 + - - +
272B PHE* 3.7 30.9 - - - -
273B LEU* 3.0 27.5 + - - +
274B TRP* 3.8 5.2 + - - -
407B ALA 4.2 15.7 + - - -
409B VAL* 4.5 1.7 + - - +
456B PRO* 3.6 23.4 + - - +
458B GLN* 5.6 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLN 3.4 4.3 + - - -
270B SER* 1.3 71.7 - - - +
272B PHE* 1.3 65.0 + - - +
273B LEU 3.3 0.3 + - - -
274B TRP* 3.3 11.6 + - - +
275B GLN* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B SER* 3.1 17.3 - - - -
271B SER* 1.3 79.0 + - - +
273B LEU* 1.3 62.5 + - - +
275B GLN* 3.8 12.1 - - - +
276B ARG* 2.9 52.9 + - + +
409B VAL 3.6 16.8 - - - -
410B GLY* 3.8 2.7 - - - -
411B PRO* 3.6 49.8 - - + -
454B VAL 4.5 1.6 - - - -
455B LEU* 3.7 15.7 - - + -
456B PRO* 3.4 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B PHE* 4.5 3.0 - - + -
269B GLN* 4.4 11.7 - - + +
270B SER* 3.0 19.9 + - - +
272B PHE* 1.3 82.0 - - + +
274B TRP* 1.3 94.3 + - + +
277B GLY* 2.9 27.7 + - - -
298B PHE* 4.0 33.9 - - + -
311B LEU* 4.1 15.5 - - + -
315B VAL* 6.1 0.2 - - + -
455B LEU* 3.9 19.0 - - + +
456B PRO* 3.3 25.4 - - + +
457B VAL* 4.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B PHE* 3.5 35.6 - + + -
262B LEU* 3.8 31.4 - - + -
263B GLU* 3.3 49.9 - - + +
266B PHE* 3.6 31.6 + - + -
269B GLN* 3.7 24.2 + - + +
270B SER 3.9 12.6 - - - -
271B SER* 3.3 10.1 + - - +
273B LEU* 1.3 92.1 - - + +
275B GLN* 1.3 64.5 + - - +
278B ARG* 3.0 28.1 + - - +
311B LEU* 4.0 18.2 - - + -
315B VAL* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B SER 3.1 17.2 + - - +
272B PHE* 4.2 8.7 - - - +
274B TRP* 1.3 79.4 - - - +
276B ARG* 1.3 67.9 + - + +
278B ARG* 3.8 22.2 + - - +
279B LYS* 3.1 54.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LYS* 5.6 8.9 - - - +
327A TYR* 3.7 53.7 - - + +
328A TYR* 5.5 4.8 + - - -
272B PHE* 2.9 39.4 + - + +
275B GLN* 1.3 77.8 + - + +
277B GLY* 1.3 60.8 + - - +
279B LYS 3.3 0.5 + - - -
280B PHE* 2.9 33.4 + - - +
411B PRO* 3.4 38.6 - - - +
453B LEU* 3.8 25.4 - - + +
455B LEU* 4.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B PHE* 4.0 12.1 - - - -
273B LEU 2.9 20.1 + - - -
276B ARG* 1.3 78.0 - - - +
278B ARG* 1.3 61.2 + - - +
281B LEU* 3.0 31.0 + - - +
296B ILE* 4.9 6.1 - - - -
298B PHE* 6.3 0.9 - - - -
453B LEU* 4.0 13.8 - - - +
455B LEU* 4.5 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PHE* 4.2 6.3 - - + -
256B LEU* 3.8 28.5 - - + -
259B PHE* 3.6 24.0 - - + -
274B TRP 3.0 19.6 + - - +
275B GLN* 3.8 28.7 - - - +
277B GLY* 1.3 76.4 - - - +
279B LYS* 1.3 82.4 + - - +
282B GLN* 2.9 46.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ASP* 3.6 28.8 + - + +
327A TYR* 3.6 36.8 + - + -
328A TYR 6.1 0.2 - - - -
330A ASP* 4.8 11.6 + - - -
275B GLN* 3.1 38.3 + - + +
276B ARG 3.3 2.7 + - - +
278B ARG* 1.3 105.9 - - - +
280B PHE* 1.3 62.4 + - - +
282B GLN* 3.9 14.6 + - - +
283B LYS* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A THR* 3.7 35.0 - - + -
326A ASP* 5.8 5.2 - - - -
327A TYR* 4.6 5.6 - + + +
276B ARG 2.9 18.8 + - - +
277B GLY 3.9 1.6 - - - +
279B LYS* 1.3 80.8 - - - +
281B LEU* 1.3 66.8 + - + +
283B LYS* 3.4 11.0 + - + +
284B HIS* 3.4 12.3 + - - +
293B PRO 5.2 1.1 - - - -
294B ALA* 3.8 14.5 - - + +
295B THR 3.4 41.1 - - - -
296B ILE* 3.6 26.7 - - + -
452B HIS* 4.0 14.8 - + + -
453B LEU* 3.6 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PHE* 3.6 31.9 - - + -
259B PHE* 4.8 2.0 - - + -
277B GLY 3.0 17.6 + - - +
280B PHE* 1.3 73.1 - - + +
282B GLN* 1.3 60.5 + - - +
284B HIS* 3.2 4.9 + - - +
285B LEU* 2.9 33.4 + - + +
294B ALA* 3.8 25.8 - - + +
296B ILE* 3.8 31.9 - - + -
315B VAL* 3.8 23.3 - - + +
319B TYR* 4.2 21.7 - - + -
393B ALA* 4.5 6.1 - - + -
395B VAL* 6.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 3.9 26.1 - - + +
255B PHE* 4.2 3.2 - - + -
256B LEU* 3.5 31.7 - - + +
278B ARG* 2.9 33.4 + - - +
279B LYS* 3.9 18.7 + - - +
281B LEU* 1.3 75.6 - - - +
283B LYS* 1.3 59.9 + - - +
285B LEU* 3.2 2.0 + - - +
286B ASN* 2.9 33.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
288A ARG* 3.4 21.2 - - - +
290A TYR* 4.6 3.3 + - - -
326A ASP* 2.8 43.5 + - + +
279B LYS 3.1 18.6 + - - +
280B PHE* 3.7 6.7 - - + +
281B LEU 3.2 0.2 - - - -
282B GLN* 1.3 78.1 - - - +
284B HIS* 1.3 62.0 + - - +
286B ASN* 3.4 5.3 + - - +
287B ALA* 3.3 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B PHE 3.4 8.8 + - - +
281B LEU* 3.2 8.6 + - - +
283B LYS* 1.3 77.8 - - - +
285B LEU* 1.3 64.5 + - - +
287B ALA* 3.2 21.1 + - + +
290B PRO* 3.6 12.2 - - + +
292B GLU 3.0 17.9 + - - -
293B PRO* 3.7 1.6 - - - +
294B ALA* 3.9 20.8 - - + +
319B TYR* 2.3 34.8 + - + +
390B LYS 2.9 25.3 + - - -
391B ASP* 3.8 15.6 - - - +
392B VAL 3.3 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ASN* 3.0 18.6 + - - +
251B ALA* 4.5 17.8 - - + +
252B LEU* 4.0 17.9 - - + +
255B PHE* 3.5 46.2 - - + -
281B LEU 2.9 20.1 + - - +
282B GLN 3.2 3.3 + - - +
284B HIS* 1.3 76.3 - - - +
286B ASN* 1.3 60.3 + - - +
287B ALA 3.3 3.3 + - - +
319B TYR* 3.5 52.0 - - + +
391B ASP* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ASN* 3.6 18.9 + - - +
252B LEU* 3.6 19.2 - - + +
282B GLN* 2.9 20.2 + - + +
283B LYS* 3.9 6.3 - - + +
284B HIS 3.1 0.2 - - - -
285B LEU* 1.3 76.5 - - - +
287B ALA* 1.3 62.6 + - - +
288B SER* 3.4 3.8 + - - -
----------------------------------------------------------
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