Contacts of the helix formed by residues 319 - 337 (chain B) in PDB entry 3N2Z
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 319 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ARG* 3.3 4.5 - - - +
318B VAL* 1.3 76.2 - - - +
320B ASP* 1.3 52.2 + - - +
321B SER* 3.4 10.5 + - - -
322B LEU* 3.1 26.8 + - - +
323B LEU* 2.7 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ARG* 3.1 28.8 + - - +
243B ALA* 3.7 22.2 - - + +
246B ARG* 2.9 41.7 + - - +
247B LEU* 5.3 7.9 - - + -
319B SER* 1.3 72.0 - - - +
321B SER* 1.3 61.8 + - - +
323B LEU* 3.3 5.8 + - - +
324B LEU* 3.1 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU* 5.5 2.8 - - - +
256B TRP* 3.2 48.4 + - - -
319B SER* 3.2 8.9 + - - -
320B ASP* 1.3 79.0 - - - +
322B LEU* 1.3 59.8 + - - +
325B GLN* 3.4 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ASN* 5.7 1.8 - - - +
317B ASN 5.6 0.2 - - - +
318B VAL* 3.6 26.7 - - + -
319B SER* 3.1 23.3 + - - +
321B SER* 1.3 73.4 + - - +
323B LEU* 1.4 64.8 + - - +
325B GLN* 3.0 35.2 + - + +
326B ASN* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B SER* 3.7 36.6 - - - +
239B ARG* 3.6 31.6 - - + +
240B SER* 3.8 35.0 - - - +
243B ALA* 4.4 11.2 - - + -
313B LEU* 5.2 1.8 - - + -
318B VAL* 3.7 18.8 - - + +
319B SER 2.7 21.2 + - - +
320B ASP* 3.5 4.7 - - - +
322B LEU* 1.4 72.1 - - - +
324B LEU* 1.3 58.0 + - + +
326B ASN* 3.3 13.2 + - - +
327B ILE* 3.0 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B SER* 3.9 24.2 - - - +
243B ALA* 4.2 9.9 - - + +
244B ILE* 3.8 30.3 - - + -
247B LEU* 3.6 30.1 - - + -
256B TRP* 4.2 15.3 - - + -
257B LEU* 3.7 22.9 - - + -
260B ALA* 4.8 2.7 - - + +
261B LEU* 3.8 14.3 - - + +
320B ASP 3.1 14.6 + - - +
321B SER 3.6 0.6 + - - +
322B LEU 3.3 0.4 - - - -
323B LEU* 1.3 74.9 - - + +
325B GLN* 1.3 59.8 + - - +
326B ASN 3.3 0.2 - - - -
327B ILE* 3.7 10.1 - - + +
328B PHE* 3.1 24.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
256B TRP* 4.2 19.5 - - + +
260B ALA* 4.7 12.3 - - + +
321B SER* 3.4 15.9 + - - +
322B LEU* 3.0 37.0 + - + +
324B LEU* 1.3 74.9 - - - +
326B ASN* 1.4 62.3 + - - +
328B PHE* 3.3 10.5 + - - +
329B GLN* 3.1 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B SER* 5.9 0.6 + - - -
312B TYR* 3.2 31.8 + - - +
313B LEU* 3.7 20.2 + - + +
315B ASN* 5.0 5.3 + - - +
318B VAL* 4.1 22.2 - - - +
322B LEU* 3.1 24.3 + - - +
323B LEU* 3.4 13.8 - - - +
325B GLN* 1.4 75.1 - - - +
327B ILE* 1.4 63.8 + - - +
329B GLN* 3.2 11.6 + - - +
330B ALA* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B SER 4.6 2.5 - - - +
237B ILE* 4.0 24.2 - - + -
240B SER* 3.9 32.1 - - - +
244B ILE* 5.5 2.0 - - + -
261B LEU* 4.8 6.3 - - + -
279B ILE* 4.7 12.1 - - + -
283B TRP* 4.2 15.7 - - + -
313B LEU* 3.9 20.4 - - + -
323B LEU* 3.0 22.5 + - + +
324B LEU* 3.8 13.7 - - + +
325B GLN 3.4 0.2 - - - -
326B ASN* 1.4 73.7 - - - +
328B PHE* 1.3 63.7 + - - +
330B ALA* 3.2 7.3 + - - +
331B LEU* 3.0 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A NAG 3.3 34.1 - - + -
260B ALA 3.4 18.8 - - - +
261B LEU* 3.5 31.2 - - + +
262B HIS* 3.4 27.4 - + - -
324B LEU 3.1 13.0 + - - +
325B GLN* 3.4 9.9 - - - +
326B ASN 3.2 0.2 - - - -
327B ILE* 1.3 76.7 - - - +
329B GLN* 1.3 77.1 + - - +
331B LEU* 2.9 11.8 + - - +
332B ASN* 2.7 50.2 + - + +
344B LEU* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TYR* 3.3 51.3 + - + -
325B GLN 3.1 14.3 + - - +
326B ASN* 3.2 11.2 + - - +
328B PHE* 1.3 102.9 - - - +
330B ALA* 1.4 59.9 + - - +
332B ASN* 3.3 27.6 + - - +
333B VAL* 3.3 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B TRP* 3.9 19.0 - - + -
286B LEU* 5.5 0.2 - - - +
309B VAL* 3.5 42.1 - - + +
312B TYR* 4.1 3.7 - - + -
313B LEU* 4.2 15.5 - - + -
326B ASN 3.1 12.1 + - - +
327B ILE* 3.3 9.9 - - - +
329B GLN* 1.4 72.5 - - - +
331B LEU* 1.4 64.1 + - - +
333B VAL* 3.2 12.5 + - - -
334B TYR* 3.6 5.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
261B LEU* 4.6 9.6 - - + -
278B TRP* 4.2 20.2 - - + -
279B ILE* 4.2 23.3 - - + -
282B THR* 3.9 24.2 - - + +
283B TRP* 3.5 31.6 - - + -
327B ILE* 3.0 33.7 + - + +
328B PHE* 2.9 12.0 + - - +
330B ALA* 1.4 74.0 - - - +
332B ASN* 1.3 56.8 + - - +
334B TYR* 3.4 2.1 + - - +
335B TYR* 2.9 37.2 + - + +
344B LEU* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A NAG 3.5 16.6 + - - +
312B TYR* 5.5 1.4 + - - -
328B PHE* 2.7 31.6 + - + +
329B GLN* 3.3 26.7 + - - +
330B ALA 3.2 0.2 - - - -
331B LEU* 1.3 74.9 - - - +
333B VAL* 1.4 57.6 + - - +
335B TYR* 5.2 0.9 - - - -
336B ASN* 2.8 72.8 + - - +
344B LEU* 5.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 5.5 0.4 - - + -
301B LEU* 4.0 3.8 - - + +
302B PRO* 4.5 14.8 - - + -
305B PRO* 4.6 7.9 - - + +
308B VAL* 4.3 21.1 - - + -
309B VAL* 3.6 26.0 - - + -
312B TYR* 3.7 22.2 - - + -
329B GLN 3.3 16.4 + - - +
330B ALA 3.2 7.1 + - - +
332B ASN* 1.4 76.0 - - - +
334B TYR* 1.4 63.5 + - - +
337B TYR* 3.1 38.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B THR* 3.9 20.9 - - + -
285B ASN* 3.2 41.7 + - + +
286B LEU* 3.6 34.1 - - + -
289B VAL* 5.9 3.8 - - + +
298B LEU* 4.3 17.6 - - + +
299B GLN* 2.9 48.8 + - + +
301B LEU* 3.7 27.6 - - + +
309B VAL* 5.8 0.2 - - + -
330B ALA 3.6 4.6 + - - +
331B LEU 3.4 5.1 + - - +
333B VAL* 1.4 81.3 - - - +
335B TYR* 1.3 97.7 + + - +
340B GLN* 4.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B TRP* 3.4 52.7 + + - -
281B GLU* 5.2 2.1 - - - +
282B THR* 2.5 35.4 + - + -
285B ASN* 5.2 2.4 + - - -
299B GLN* 3.9 16.0 + - - +
331B LEU* 2.9 31.3 + - + +
334B TYR* 1.3 105.3 - + - +
336B ASN* 1.3 57.3 + - - +
340B GLN* 3.2 19.3 + - - -
341B VAL* 3.4 15.6 - - + +
344B LEU* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A NAG 1.4 62.0 + - - +
332B ASN* 2.8 34.6 + - - +
335B TYR* 1.3 73.9 - - + +
337B TYR* 1.4 58.7 + - - +
338B SER 2.9 9.9 + - - -
339B GLY 3.0 6.9 + - - -
340B GLN* 3.0 14.0 + - - -
341B VAL* 2.7 41.0 + - + -
344B LEU* 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PRO* 3.2 33.0 - - + +
301B LEU 4.2 2.9 - - - -
302B PRO* 3.3 48.7 - - + +
308B VAL* 5.3 4.5 - - + -
332B ASN 3.5 1.5 + - - -
333B VAL* 3.1 31.9 + - + +
336B ASN* 1.4 73.2 - - - +
338B SER* 1.3 59.9 + - - +
339B GLY 3.7 0.4 + - - -
340B GLN* 3.1 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