Contacts of the helix formed by residues 323 - 339 (chain B) in PDB entry 2DW1
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 ILE 323 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ARG* 4.1 0.7 - - - -
321B SER* 2.8 12.8 + - - +
322B GLU* 1.3 76.2 - - + +
324B ASN* 1.3 70.0 + - - +
325B LEU* 4.1 16.2 - - + +
326B VAL* 2.8 38.7 + - + +
327B VAL* 3.5 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ARG* 2.7 47.4 - - - +
227B GLU* 2.8 43.6 - - + +
228B ILE* 4.2 13.9 - - + +
231B THR* 5.8 2.9 - - - +
322B GLU 3.2 8.5 + - - -
323B ILE* 1.3 71.2 - - - +
325B LEU* 1.3 65.5 + - - +
327B VAL* 2.9 5.9 + - - +
328B ALA* 2.8 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B THR* 4.3 17.0 - - + -
235B ILE* 4.8 0.7 - - + -
323B ILE* 3.1 12.1 + - + +
324B ASN* 1.3 77.7 - - - +
326B VAL* 1.3 57.7 + - + +
328B ALA* 3.1 6.9 + - + +
329B VAL* 2.9 36.0 + - + +
365B PRO* 3.7 35.7 - - + +
366B SER* 4.7 0.4 - - - +
367B THR* 3.5 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B TYR* 4.0 15.7 - - + -
321B SER* 3.9 24.9 - - - +
323B ILE* 2.8 35.1 + - + +
325B LEU* 1.3 78.9 - - + +
327B VAL* 1.3 58.7 + - - +
329B VAL* 3.5 5.2 + - - +
330B ILE* 3.0 30.1 + - + +
361B ILE* 3.4 24.2 - - + -
365B PRO* 4.0 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ARG* 3.2 31.9 - - - +
228B ILE* 3.5 26.2 - - + -
290B LEU* 4.8 16.2 - - + -
317B ILE* 4.5 15.7 - - + -
318B GLN 5.0 3.6 - - - +
319B ASP* 4.1 10.5 - - - +
320B TYR* 5.9 0.4 - - + -
321B SER 3.6 17.0 - - - +
323B ILE 3.5 3.3 + - - +
324B ASN 2.9 7.4 + - - +
326B VAL* 1.3 74.6 - - + +
328B ALA* 1.3 66.2 + - - +
330B ILE* 3.4 8.6 + - - +
331B MET* 3.1 22.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
228B ILE* 4.0 18.3 - - + +
231B THR* 3.7 35.2 - - + -
232B VAL* 3.9 6.7 - - + +
235B ILE* 4.5 5.4 - - + -
324B ASN 2.8 11.7 + - - +
325B LEU 3.1 9.8 + - - +
327B VAL* 1.3 78.0 - - - +
329B VAL* 1.3 53.7 + - - +
331B MET* 3.1 3.7 + - - +
332B ALA* 2.7 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GM6 5.3 3.1 - - + -
235B ILE* 4.9 4.3 - - + -
325B LEU* 2.9 25.9 + - + +
326B VAL 3.8 5.6 - - - +
327B VAL 3.3 0.2 - - - -
328B ALA* 1.3 76.0 - - - +
330B ILE* 1.3 54.1 + - - +
332B ALA* 3.7 6.1 - - - +
333B HIS* 2.6 38.8 + - + +
356B ILE* 4.0 31.5 - - + +
361B ILE* 4.5 20.2 - - + -
365B PRO* 4.3 16.2 - - + -
366B SER 3.6 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GM6 3.4 12.3 - - + -
299B ILE* 3.2 50.7 - - + +
300B GLY* 4.3 1.8 - - - -
317B ILE* 3.4 27.6 - - + -
318B GLN 4.8 5.4 - - - +
320B TYR* 5.1 3.4 - - + -
326B VAL* 3.0 23.3 - - + +
327B VAL* 3.6 8.7 - - - +
328B ALA 3.3 0.4 - - - -
329B VAL* 1.3 75.5 - - - +
331B MET* 1.3 54.0 + - - +
333B HIS* 3.1 7.6 + - - +
334B GLU* 2.8 52.2 + - + +
361B ILE* 3.6 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU* 4.2 21.5 - - - -
204B LEU* 3.9 29.4 - - + -
225B MET* 5.2 0.9 - - + -
228B ILE* 3.5 23.3 - - + -
229B VAL* 4.4 4.7 - - - -
232B VAL* 3.7 22.2 - - + -
288B GLN* 4.5 10.5 - - + -
290B LEU* 4.1 10.3 - - + -
317B ILE* 3.4 29.3 - - + +
327B VAL* 3.1 9.8 + - + +
328B ALA 3.5 6.5 - - - +
330B ILE* 1.3 76.7 - - - +
332B ALA* 1.3 61.4 + - - +
334B GLU* 3.0 2.4 + - - +
335B MET* 2.8 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B VAL* 4.4 7.1 - - + +
235B ILE* 4.3 20.9 - - + -
236B TYR* 2.8 31.2 + - + -
328B ALA 2.7 21.2 + - - +
329B VAL* 3.7 6.5 - - - +
331B MET* 1.3 72.2 - - - +
333B HIS* 1.3 57.0 + - - +
335B MET* 4.6 0.9 - - - -
336B GLY* 2.8 26.2 + - - -
356B ILE* 4.2 13.0 - - + -
369B PHE* 4.0 3.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GM6 3.2 28.3 + - + +
329B VAL* 2.6 23.2 + - + +
330B ILE* 3.2 9.2 - - - +
332B ALA* 1.3 72.3 - - - +
334B GLU* 1.3 71.0 + - - +
336B GLY* 3.2 2.8 + - - -
337B HIS* 2.9 23.5 + + - -
343B HIS* 3.4 10.8 - + - -
356B ILE* 2.6 26.4 + - - +
357B MET* 3.6 19.6 - - + +
358B ARG 3.2 24.0 - - - -
700B ZN 2.1 37.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GM6 3.3 27.6 + - - +
288B GLN* 3.8 15.7 - - - +
300B GLY* 3.5 8.9 - - - -
301B LEU* 2.8 38.2 + - - +
302B ALA* 3.1 15.5 + - + +
316B ILE 3.6 16.2 - - - +
317B ILE* 4.1 5.8 - - + -
330B ILE* 2.8 29.5 + - + +
331B MET 3.7 3.4 - - - +
333B HIS* 1.3 79.9 - - - +
335B MET* 1.3 67.4 + - - +
337B HIS* 3.1 8.0 + - - +
338B ASN* 3.1 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B VAL* 3.3 43.1 - - + -
202B LEU* 4.1 15.5 - - + -
232B VAL* 4.4 13.5 - - - -
236B TYR* 3.4 15.5 - - + +
243B VAL* 4.1 27.1 - - + -
286B ASN* 3.6 20.0 - - + +
288B GLN* 3.7 10.1 + - + +
307B MET* 5.7 1.8 - - - -
331B MET* 2.8 24.8 + - + +
332B ALA 3.9 0.2 - - - +
334B GLU* 1.3 72.4 - - - +
336B GLY* 1.3 51.7 + - - +
338B ASN* 2.9 13.0 + - - +
339B LEU* 2.7 41.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
236B TYR* 2.8 19.5 + - - -
332B ALA 2.8 9.9 + - - -
333B HIS 3.2 3.1 + - - -
334B GLU 3.1 0.6 - - - -
335B MET* 1.3 75.2 - - - +
337B HIS* 1.3 54.1 + - - +
339B LEU* 2.7 25.8 + - - +
341B ILE* 3.0 38.5 + - - +
357B MET* 4.6 3.8 - - - -
369B PHE* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GM6 2.9 10.3 + - - -
302B ALA* 4.1 10.1 - - + +
303B TYR 3.2 13.5 - - - +
304B VAL* 3.0 19.2 - - + +
305B GLY 2.7 31.7 + - - -
333B HIS* 2.9 25.6 + + - -
334B GLU* 3.1 13.9 + - - +
336B GLY* 1.3 72.4 - - - +
338B ASN* 1.3 51.6 + - - +
340B GLY* 2.8 7.6 + - - -
341B ILE 2.9 23.7 + - - -
342B ASN* 4.4 2.0 - - - -
343B HIS* 3.4 25.6 - + - -
357B MET* 3.6 8.4 - - + +
700B ZN 2.0 37.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ASN* 3.1 22.8 + - - +
288B GLN* 3.0 25.6 - - - +
302B ALA* 3.8 2.2 - - - +
303B TYR 2.9 22.2 + - - +
305B GLY* 3.5 0.9 - - - +
306B SER* 3.0 33.6 + - - +
307B MET* 3.1 20.7 + - - +
312B ARG 3.8 0.4 + - - -
313B SER 4.7 0.2 - - - -
314B THR 2.9 25.8 + - - +
334B GLU 3.1 9.6 + - - +
335B MET* 2.9 13.2 + - - +
337B HIS* 1.3 70.0 - - - +
339B LEU* 1.3 56.9 + - - +
340B GLY 2.9 10.0 + - - -
380B PHE* 3.8 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B VAL* 5.0 7.6 - - + -
236B TYR* 3.3 41.7 - - + +
241B ILE* 3.5 30.5 - - + -
307B MET* 4.4 26.2 - - + -
335B MET* 2.7 12.3 + - + +
336B GLY* 2.7 18.5 + - - +
338B ASN* 1.3 69.8 - - - +
340B GLY* 1.3 60.0 + - - +
341B ILE* 3.4 7.2 + - + +
377B CYS* 3.8 17.8 - - - +
380B PHE* 3.6 23.3 - - + +
381B ILE* 5.0 6.1 - - + -
389B ILE* 4.5 13.9 - - + -
----------------------------------------------------------
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