Contacts of the helix formed by residues 320 - 339 (chain B) in PDB entry 5Y7G
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 320 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B PRO* 3.2 4.0 + - - +
319B GLU* 1.3 81.8 - - - +
321B ASP* 1.3 62.0 + - - +
322B ALA* 2.6 24.1 + - - +
323B GLU* 2.8 14.1 + - - +
324B ARG* 3.1 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B SER* 1.3 73.8 - - - +
322B ALA* 1.3 59.0 + - - +
324B ARG* 3.3 28.0 + - - +
325B GLN* 2.9 28.4 + - - +
493B ARG* 5.3 6.6 + - - -
536B ARG* 3.9 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 3.9 9.2 - - + +
320B SER* 2.6 15.3 + - - +
321B ASP* 1.3 72.6 - - - +
323B GLU* 1.3 58.3 + - - +
325B GLN* 3.2 6.5 + - - +
326B GLY 3.0 21.8 + - - -
532B ASP* 5.1 3.3 - - + +
536B ARG* 3.2 34.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLY* 4.9 1.6 - - - -
291B ARG* 2.9 59.2 + - - +
292B LEU* 3.5 34.8 + - + +
314B ALA* 3.9 3.9 - - - +
318B PRO* 3.8 3.7 - - + +
319B GLU* 3.0 34.4 + - + +
320B SER* 2.8 20.9 + - - +
322B ALA* 1.3 70.2 - - - +
324B ARG* 1.3 59.4 + - - +
325B GLN 3.1 0.2 - - - -
326B GLY 3.4 0.5 + - - -
327B LEU* 2.9 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B PRO* 3.9 37.2 - - + +
320B SER 3.1 15.7 + - - +
321B ASP* 3.3 31.6 + - - +
323B GLU* 1.3 76.7 - - - +
325B GLN* 1.3 58.2 + - - +
327B LEU* 4.1 8.0 - - + +
328B ALA* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ASP 2.9 14.3 + - - +
322B ALA* 3.6 6.4 - - - +
323B GLU 3.1 0.8 - - - -
324B ARG* 1.3 78.3 - - - +
326B GLY* 1.3 61.4 + - - +
328B ALA* 4.0 8.4 + - - +
329B ARG* 3.5 22.0 + - - +
345B ARG* 5.5 2.3 + - - +
532B ASP* 2.9 62.9 + - - +
535B LEU* 3.7 22.0 - - - +
536B ARG* 3.3 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 4.4 17.3 - - - -
322B ALA 3.0 13.9 + - - -
323B GLU 3.4 1.5 + - - -
324B ARG 3.3 0.2 - - - -
325B GLN* 1.3 74.6 - - - +
327B LEU* 1.3 58.8 + - - +
328B ALA 3.2 1.6 - - - -
329B ARG* 2.9 28.8 + - - +
330B LEU* 2.9 27.8 + - - +
532B ASP* 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 4.1 6.8 - - + +
295B ILE* 3.9 10.1 - - + -
311B ALA* 3.6 33.7 - - + +
314B ALA* 3.4 41.5 - - + +
315B SER* 3.8 9.0 - - - +
318B PRO* 5.0 2.2 - - + -
323B GLU* 2.9 32.0 + - + +
324B ARG* 4.1 7.2 - - + +
326B GLY* 1.3 71.7 - - - +
328B ALA* 1.3 58.6 + - - +
329B ARG 3.0 0.2 - - - -
330B LEU* 4.0 10.8 - - + +
331B LEU* 2.9 41.8 + - + +
343B GLN* 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ARG 3.0 18.7 + - - +
325B GLN* 4.1 8.1 - - - +
326B GLY 3.2 0.6 - - - -
327B LEU* 1.3 76.8 - - - +
329B ARG* 1.3 56.7 + - - +
332B PRO* 3.6 17.9 - - - +
343B GLN* 5.1 6.5 - - - +
345B ARG* 3.9 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLN* 3.5 18.1 + - - +
326B GLY* 3.0 21.0 - - - +
328B ALA* 1.3 77.0 - - + +
330B LEU* 1.3 61.1 + - + +
331B LEU 3.5 0.7 - - - -
332B PRO* 3.3 9.1 - - - +
333B ARG* 3.2 39.8 + - - +
345B ARG* 5.6 6.3 - - - +
532B ASP* 2.7 44.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 3.9 33.4 - - + +
295B ILE* 3.8 33.0 - - + -
296B ARG* 4.6 12.3 - - + +
299B GLU* 3.1 28.7 - - - +
311B ALA* 5.1 0.9 - - + -
326B GLY* 2.9 17.9 + - - +
327B LEU* 3.1 11.2 + - + +
329B ARG* 1.3 73.1 - - + +
331B LEU* 1.3 70.2 + - - +
333B ARG* 3.2 19.2 - - - +
334B LEU* 3.2 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B HIS* 4.1 18.8 - - + -
311B ALA* 3.4 43.1 - - + +
312B ARG* 4.3 7.4 - - - +
315B SER* 4.2 17.5 - - - +
327B LEU* 2.9 29.6 + - + +
330B LEU* 1.3 78.6 - - - +
332B PRO* 1.3 63.9 - - + +
334B LEU* 3.9 1.1 - - + +
335B GLN* 2.9 43.5 + - - +
343B GLN* 3.7 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU 3.9 0.2 - - - +
328B ALA* 3.6 17.3 - - - +
329B ARG* 3.3 19.3 - - - +
331B LEU* 1.3 94.1 - - + +
333B ARG* 1.3 55.3 + - - +
335B GLN* 3.6 12.3 - - - +
336B GLY* 2.9 23.6 + - - -
342B ARG* 3.8 42.5 + - + +
343B GLN* 4.6 8.5 - - - +
345B ARG* 5.5 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ARG* 3.7 13.1 - - - +
299B GLU* 3.3 38.3 + - - -
329B ARG* 3.2 39.4 + - - +
330B LEU* 3.2 20.6 - - - +
332B PRO* 1.3 74.9 - - - +
334B LEU* 1.3 62.5 + - - +
336B GLY* 3.1 2.7 + - - -
337B LYS* 2.9 33.7 + - + +
342B ARG* 5.0 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 4.1 12.3 - - + -
299B GLU* 3.5 36.6 - - + +
304B PHE* 3.7 23.1 - - + +
307B ALA* 3.4 20.9 - - + +
308B HIS* 3.3 38.1 - - + +
311B ALA* 4.2 5.4 - - + -
330B LEU* 3.2 17.1 + - + +
331B LEU* 4.0 1.6 - - - +
333B ARG* 1.3 78.4 - - - +
335B GLN* 1.3 62.5 + - - +
336B GLY 3.1 0.2 - - - -
337B LYS* 3.2 6.9 + - + +
338B LEU* 2.9 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B HIS* 3.9 27.4 + - + +
312B ARG* 5.1 12.9 - - - +
331B LEU* 2.9 31.8 + - + +
332B PRO* 3.6 13.2 - - - +
334B LEU* 1.3 75.5 - - - +
336B GLY* 1.3 56.5 + - - +
338B LEU* 3.3 3.2 + - - +
339B GLY 3.0 7.3 + - - -
340B LEU* 2.7 46.8 + - + +
341B PRO* 2.8 31.0 + - - +
342B ARG 3.8 3.6 - - - -
343B GLN* 3.8 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B PRO 2.9 16.8 + - - -
333B ARG 3.1 4.7 + - - -
334B LEU 3.1 0.2 - - - -
335B GLN* 1.3 76.8 - - - +
337B LYS* 1.3 61.5 + - - +
339B GLY* 2.9 19.4 + - - -
340B LEU 4.4 4.7 + - - -
342B ARG* 4.3 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A CYS* 3.0 23.7 - - - +
304B PHE* 4.7 26.9 - - + -
333B ARG* 2.9 21.1 + - + +
334B LEU* 3.2 8.0 + - - +
336B GLY* 1.3 78.2 + - - +
338B LEU* 1.3 57.8 + - - +
342B ARG* 6.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 4.2 17.7 + - - +
313A GLU* 4.8 16.8 + - + +
316A CYS* 3.4 27.2 - - + -
304B PHE* 3.8 28.9 - - + -
305B ALA* 3.9 21.1 - - + +
308B HIS* 3.8 34.5 - - + +
334B LEU 2.9 17.4 + - - +
335B GLN* 3.3 4.0 + - - +
337B LYS* 1.3 80.4 - - - +
339B GLY* 1.3 58.5 + - - +
340B LEU* 3.4 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 4.3 25.8 + - - +
336B GLY* 2.9 16.2 + - - -
337B LYS 3.4 0.6 - - - -
338B LEU* 1.3 78.5 - - - +
340B LEU* 1.3 64.5 + - - +
341B PRO* 4.8 0.3 - - - +
----------------------------------------------------------
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