Contacts of the helix formed by residues 317 - 343 (chain B) in PDB entry 2XZ0
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 317 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ASP* 2.9 30.0 + - - -
315B GLY 4.1 1.2 + - - -
316B LEU* 1.3 75.6 - - - +
318B ALA* 1.3 57.3 + - - +
319B GLU* 2.9 21.3 - - - -
320B GLY* 2.8 20.5 + - - -
321B GLN* 2.9 13.6 + - - +
1367B EDO 3.6 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B SER* 1.3 73.8 - - - +
319B GLU* 1.3 66.9 + - + +
321B GLN* 3.9 11.9 + - - +
322B LYS* 3.6 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ASP* 4.8 1.2 - - - +
253B LEU* 4.3 17.5 - - + +
260B ARG* 5.7 0.5 + - - -
317B SER* 2.9 27.2 - - - -
318B ALA* 1.3 78.7 + - + +
320B GLY* 1.3 52.8 + - - +
321B GLN 3.4 0.2 - - - -
322B LYS* 3.4 10.1 + - - +
323B ALA* 2.7 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ASP* 3.8 20.5 + - - -
252B VAL* 3.3 10.7 - - - +
253B LEU* 4.6 1.3 - - - +
316B LEU* 4.2 9.1 - - - +
317B SER* 2.8 13.7 + - - +
319B GLU* 1.3 79.5 + - - +
321B GLN* 1.3 53.9 + - - -
323B ALA* 3.2 6.5 + - - -
324B GLN* 2.7 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 3.8 35.0 + - + +
317B SER 2.9 12.3 + - - +
318B ALA* 4.2 11.3 - - - +
320B GLY* 1.3 72.1 - - - +
322B LYS* 1.3 60.0 + - - +
324B GLN* 3.4 12.3 + - - +
325B ASP* 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ARG* 4.5 20.9 - - - +
318B ALA 3.6 12.0 + - - +
319B GLU* 3.4 11.8 + - - +
320B GLY 3.3 0.2 - - - -
321B GLN* 1.3 76.7 - - - +
323B ALA* 1.3 62.8 + - - +
325B ASP* 4.3 3.0 - - - +
326B TYR* 3.2 28.1 + - + +
17D LEU 5.5 2.8 + - - -
18D ALA* 5.4 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B VAL* 3.5 19.3 - - + +
253B LEU* 4.3 10.5 - - + -
256B ALA* 3.6 23.5 - - + +
260B ARG* 4.6 9.0 - - - +
319B GLU 2.7 21.9 + - - +
320B GLY* 3.2 8.5 + - - +
322B LYS* 1.3 72.0 - - - +
324B GLN* 1.3 59.8 + - - +
326B TYR* 4.4 0.8 - - - +
327B VAL* 3.2 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B VAL* 3.7 8.3 - - + +
310B VAL* 2.8 41.8 + - + +
311B ASP 4.0 7.5 + - - -
313B LEU* 3.9 18.2 + - - +
316B LEU* 3.8 25.8 - - + +
320B GLY 2.7 19.4 + - - +
321B GLN* 3.6 10.7 - - - +
322B LYS 3.2 0.2 - - - -
323B ALA* 1.3 71.7 - - - +
325B ASP* 1.3 69.5 + - - +
327B VAL* 3.0 8.3 + - - +
328B CYS* 2.9 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B GLN 3.0 14.4 + - - +
322B LYS* 4.3 4.5 - - - +
324B GLN* 1.3 80.5 + - - +
326B TYR* 1.3 67.2 + - - +
328B CYS* 3.1 7.5 + - - +
329B ARG* 2.9 70.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ALA* 4.4 4.7 - - + -
259B MET* 3.9 19.8 + - + -
260B ARG* 3.9 44.2 - - + +
322B LYS* 3.2 21.0 + - + +
323B ALA* 4.4 3.4 - - - +
325B ASP* 1.3 81.1 + - - +
327B VAL* 1.3 71.9 + - + +
329B ARG* 3.5 3.1 + - - +
330B LEU* 3.1 58.6 + - + +
333B ARG* 3.8 33.1 + - - -
16D LYS* 5.8 0.4 - - - -
37D ASP* 5.2 7.3 + - - -
39D LEU* 5.8 3.1 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
252B VAL* 5.1 0.7 - - + +
255B PHE* 3.5 40.4 - - + +
256B ALA* 3.6 29.6 - - + +
259B MET* 4.6 8.5 - - + -
301B LEU* 4.4 4.0 - - + +
305B VAL* 3.9 12.6 - - + +
310B VAL* 4.8 7.2 - - + -
323B ALA 3.2 16.3 + - - +
324B GLN* 3.0 10.8 + - - +
326B TYR* 1.3 86.6 - - + +
328B CYS* 1.3 62.6 + - - +
330B LEU* 3.3 8.4 + - - +
331B PRO* 3.3 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B VAL* 3.7 30.2 - - + +
310B VAL* 4.0 12.8 - - - -
311B ASP* 3.9 24.9 - - - -
324B GLN* 2.9 23.3 + - - +
325B ASP* 3.7 7.0 - - - +
327B VAL* 1.3 77.6 - - - +
329B ARG* 1.3 60.5 + - + +
331B PRO* 3.3 15.2 - - - +
332B PRO* 4.1 5.0 - - - +
----------------------------------------------------------
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 ASP* 2.9 50.3 + - - +
326B TYR* 3.9 3.4 - - - +
328B CYS* 1.3 77.9 - - + +
330B LEU* 1.3 62.6 + - - +
331B PRO* 3.5 0.9 - - - -
332B PRO* 3.4 7.4 - - - +
333B ARG* 3.3 8.7 - - - +
329C ARG* 2.3 55.4 + - - +
332C PRO* 6.1 5.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
259B MET* 3.9 23.6 - - + +
301B LEU* 3.8 18.4 - - + -
326B TYR* 3.1 53.7 + - + +
327B VAL* 3.4 9.4 - - - +
329B ARG* 1.3 78.4 - - - +
331B PRO* 1.4 56.7 - - + +
333B ARG* 3.2 22.2 + - - +
334B ILE* 2.7 59.9 + - + +
39D LEU* 5.6 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ALA* 3.8 18.2 - - + +
301B LEU* 4.1 12.6 - - + -
302B GLU* 3.7 48.9 - - + +
305B VAL* 4.7 5.2 - - + -
327B VAL 3.3 14.6 - - - +
328B CYS 3.3 13.2 - - - +
330B LEU* 1.4 90.5 - - + +
332B PRO* 1.4 66.7 - - + +
334B ILE* 3.5 1.1 + - + -
335B ARG* 3.1 28.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
302B GLU* 5.4 8.1 - - + +
328B CYS 4.1 5.2 - - - +
329B ARG* 3.4 14.6 - - - +
331B PRO* 1.4 98.0 - - + +
333B ARG* 1.3 58.1 + - - +
335B ARG* 3.8 12.3 - - + +
336B ARG* 3.2 31.4 + - - +
321C GLN* 5.6 3.6 - - + +
324C GLN* 6.0 2.9 - - - +
325C ASP* 3.0 31.0 - - + +
329C ARG* 4.6 1.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
326B TYR* 3.8 34.6 + - - +
329B ARG* 3.3 18.0 + - - +
330B LEU* 3.2 23.6 - - + +
332B PRO* 1.3 77.5 - - - +
334B ILE* 1.3 60.9 + - + +
336B ARG* 3.2 5.8 + - - +
337B LEU* 2.8 28.8 + - - +
329C ARG* 3.5 23.7 - - - +
16D LYS* 3.0 25.3 - - - +
37D ASP* 4.7 6.9 + - - -
39D LEU* 5.0 7.4 - - - +
40D ASP* 3.0 30.3 + - - +
43D GLU* 2.7 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ALA* 4.5 11.2 - - + +
297B TYR* 3.9 31.9 - - + -
298B ALA* 3.9 18.8 - - + -
301B LEU* 4.6 8.3 - - + -
330B LEU* 2.7 53.7 + - + +
331B PRO 4.1 2.9 - - - +
333B ARG* 1.3 73.5 - - + +
335B ARG* 1.3 58.4 - - - +
337B LEU* 3.2 13.8 + - + +
338B GLU* 2.9 31.5 + - + +
39D LEU* 5.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LYS* 4.7 22.8 + - + +
298B ALA* 3.8 17.3 + - + +
299B ASP* 2.6 45.3 + - - +
302B GLU* 2.6 33.9 + - - +
331B PRO 3.1 21.0 + - - +
332B PRO* 3.8 13.5 - - + +
333B ARG 3.2 0.2 - - - -
334B ILE* 1.3 76.5 - - - +
336B ARG* 1.3 54.3 + - + +
338B GLU* 3.4 8.5 + - - +
339B GLU* 2.8 40.8 + - + +
321C GLN* 3.4 45.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B PRO 3.2 17.9 + - - +
333B ARG* 3.2 5.5 + - - +
335B ARG* 1.3 76.6 - - + +
337B LEU* 1.3 66.9 - - - +
338B GLU 3.3 0.2 - - - -
339B GLU* 3.2 18.7 - - + +
340B ARG* 3.5 14.2 + - - +
260C ARG* 4.1 6.3 - - - +
321C GLN 5.2 0.4 - - - +
322C LYS* 1.7 95.3 + - + +
325C ASP* 3.6 15.9 - - + +
326C TYR* 2.9 37.7 - - - +
46D MET* 4.7 25.4 - - + +
50D GLU* 5.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ARG 2.8 14.3 + - - +
334B ILE* 3.3 20.6 - - + +
336B ARG* 1.3 79.1 - - - +
338B GLU* 1.3 61.3 + - + +
340B ARG* 3.8 3.0 + - - +
341B ALA* 3.4 20.5 + - + +
39D LEU* 3.6 57.2 - - + +
42D VAL* 3.9 32.0 - - + +
43D GLU* 4.2 19.1 - - + +
46D MET* 6.1 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLN* 3.8 11.1 + - - +
293B THR* 5.5 0.5 - - - -
294B ALA* 3.4 30.9 - - + +
295B LYS* 4.7 19.2 + - - +
334B ILE* 2.9 17.1 + - + +
335B ARG* 3.7 6.9 - - - +
337B LEU* 1.3 76.9 - - + +
339B GLU* 1.3 65.2 + - - +
341B ALA* 3.2 7.9 + - + +
342B GLN* 2.6 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LYS* 6.0 1.0 - - - -
335B ARG* 2.8 23.8 + - + +
336B ARG* 3.2 17.5 - - + +
338B GLU* 1.3 83.2 - - - +
340B ARG* 1.3 59.8 + - + +
342B GLN* 3.3 5.1 + - - +
343B GLY* 3.0 23.6 + - - -
318C ALA* 3.9 36.8 - - + +
319C GLU* 5.8 1.5 - - - +
322C LYS* 4.6 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ARG 3.5 9.8 + - - +
337B LEU 4.1 3.1 - - - +
338B GLU 3.3 0.2 - - - -
339B GLU* 1.3 76.2 - - - +
341B ALA* 1.3 63.7 + - - +
342B GLN 3.3 0.4 - - - -
343B GLY* 3.9 3.5 - - - +
344B ARG* 3.3 45.4 + - + +
322C LYS* 3.5 27.1 - - - +
42D VAL* 4.2 13.2 + - + +
45D VAL* 4.6 3.4 - - - +
46D MET* 3.4 48.5 + - - +
49D GLU* 3.0 51.9 + - - +
50D GLU* 5.2 4.6 + - - -
58D GLU* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LEU 3.4 14.0 + - - +
338B GLU* 3.2 13.4 + - + +
340B ARG* 1.3 78.0 - - - +
342B GLN* 1.3 58.5 + - - +
344B ARG* 3.5 1.6 + - - +
345B ALA* 2.9 30.0 + - - +
42D VAL* 6.0 4.4 - - + +
58D GLU* 4.6 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLN* 4.1 19.2 - - - +
338B GLU* 2.6 45.6 + - - +
339B GLU* 3.4 7.2 - - - +
341B ALA* 1.3 69.8 - - - +
343B GLY* 1.3 56.7 + - - +
344B ARG 3.1 8.3 + - - -
345B ALA* 3.5 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLU* 3.0 15.2 + - - -
340B ARG* 3.8 3.8 + - - -
341B ALA 3.5 0.4 - - - -
342B GLN* 1.3 73.8 - - - +
344B ARG* 1.3 64.1 + - - +
345B ALA 5.2 0.7 - - - -
----------------------------------------------------------
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