Contacts of the helix formed by residues 312 - 338 (chain E) in PDB entry 5X8X
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 312 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E ARG 3.8 1.2 + - - -
311E LYS* 1.3 75.3 - - - +
313E MET* 1.3 66.2 + - - +
314E TRP* 4.1 12.1 - - - -
315E GLU* 2.8 36.3 + - - +
316E MET* 3.0 12.3 + - - +
390E ALA* 4.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 313 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E LYS 3.7 1.8 + - - -
312E SER* 1.3 70.5 - - - +
314E TRP* 1.3 64.3 + - - +
316E MET* 3.4 1.6 + - - +
317E TRP* 3.1 41.3 + - + +
390E ALA* 3.5 26.1 + - - +
391E LEU 3.2 20.9 - - - +
392E GLY* 4.8 5.4 - - - -
393E CYS* 5.2 6.7 - - - -
479E HIS* 6.2 0.2 - - + -
482E ARG* 5.0 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 314 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E SER* 3.1 9.7 + - - +
313E MET* 1.3 80.3 - - - +
315E GLU* 1.3 85.9 + - + +
317E TRP* 3.4 4.1 + - + +
318E GLU* 2.8 47.0 + - + +
483E LEU* 5.0 14.3 - - + +
487E GLN* 6.0 1.6 - - - +
490E HIS* 3.2 52.7 - + + +
491E PRO* 3.4 51.1 - - + -
492E ILE 4.7 4.0 - - - -
493E VAL* 4.0 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 315 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E LYS* 3.0 50.7 + - + +
312E SER* 2.8 23.2 + - - +
314E TRP* 1.3 96.6 - - + +
316E MET* 1.3 61.0 + - - +
318E GLU* 3.2 7.4 + - + +
319E ARG* 3.0 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 316 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E TYR* 3.9 23.8 - - + +
311E LYS* 4.3 13.8 - - + +
312E SER 3.0 13.8 + - - +
313E MET 3.8 2.7 - - - +
315E GLU* 1.3 76.3 - - - +
317E TRP* 1.3 56.1 + - - +
319E ARG* 3.2 10.3 + - - +
320E CYS* 2.8 35.2 + - - -
378E PHE* 3.8 30.1 - - + -
387E LEU* 3.7 22.7 - - + +
388E PHE* 3.8 16.8 - - + -
390E ALA* 3.8 24.0 - - + +
391E LEU* 3.5 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 317 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313E MET* 3.1 39.8 + - + +
314E TRP* 3.9 4.3 - - + +
316E MET* 1.3 72.6 - - - +
318E GLU* 1.3 66.7 + - - +
320E CYS* 4.3 13.0 - - + -
321E ALA* 2.9 31.9 + - + +
324E LEU* 4.8 13.5 - - + -
391E LEU* 3.0 53.5 + - + +
393E CYS* 4.2 10.2 - - + -
396E LEU* 4.4 8.1 - - + -
397E ILE* 5.0 0.9 - - + -
476E CYS* 6.4 0.4 - - - -
479E HIS* 3.5 50.7 - + + -
482E ARG* 3.7 19.7 - - - +
483E LEU* 3.3 20.3 - - + +
9000E 82O 4.7 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314E TRP* 2.8 45.0 + - + +
315E GLU* 3.4 10.1 - - + +
316E MET 3.2 0.4 - - - -
317E TRP* 1.3 74.5 - - - +
319E ARG* 1.3 61.5 + - + +
321E ALA* 4.0 1.2 - - - +
322E HIS* 3.1 31.7 + - - +
483E LEU* 3.7 13.3 - - - +
493E VAL* 3.2 41.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 319 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E TYR* 4.5 2.1 - - - -
311E LYS* 3.3 27.1 - - - +
315E GLU* 3.0 45.0 + - + +
316E MET* 3.6 13.0 - - - +
318E GLU* 1.3 77.5 - - + +
320E CYS* 1.3 67.0 + - - +
322E HIS* 3.1 7.1 + - - +
323E HIS* 3.0 31.9 + - + -
378E PHE* 4.9 4.5 - - + -
379E GLU* 2.9 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 320 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E MET* 2.8 23.2 + - - +
317E TRP* 4.1 19.1 - - + +
319E ARG* 1.3 76.6 - - - +
321E ALA* 1.3 57.1 + - - +
323E HIS* 2.9 6.8 + - - +
324E LEU* 2.8 33.2 + - + +
378E PHE* 4.2 17.9 - - - -
388E PHE* 4.2 7.0 - - - -
391E LEU* 3.8 24.7 - - + -
9000E 82O 3.9 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E TRP* 2.9 25.6 + - + +
318E GLU 4.1 1.6 - - - +
320E CYS* 1.3 69.2 - - - +
322E HIS* 1.3 65.6 + - - +
324E LEU* 3.7 11.7 - - + +
325E THR* 2.9 30.0 + - - +
480E VAL* 4.6 22.8 - - + +
483E LEU* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 322 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318E GLU* 3.1 27.3 + - - +
319E ARG* 3.1 6.9 + - - +
321E ALA* 1.3 76.9 - - - +
323E HIS* 1.3 72.1 + + - +
325E THR* 3.6 7.9 - - + +
326E GLU* 2.9 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 323 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E ARG* 3.0 25.6 + - + -
320E CYS 2.9 6.2 + - - +
322E HIS* 1.3 87.3 - + - +
324E LEU* 1.4 64.3 + - - +
326E GLU* 3.2 24.7 + - - +
327E ALA* 2.9 24.6 + - - +
378E PHE* 4.0 10.9 - - - -
379E GLU* 3.3 42.7 - - + +
9000E 82O 3.6 36.7 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 324 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E TRP* 4.8 16.4 - - + -
320E CYS 2.8 23.4 + - - +
321E ALA* 3.7 9.6 - - - +
323E HIS* 1.4 72.7 - - - +
325E THR* 1.3 63.5 + - - +
327E ALA* 3.2 4.0 + - - +
328E ILE* 3.0 27.5 + - - +
358E MET* 4.2 21.8 - - + -
361E VAL* 4.5 5.1 - - + +
362E LEU* 5.7 1.3 - - + -
365E MET* 5.0 3.6 - - + -
476E CYS* 4.5 23.3 - - + +
480E VAL* 3.9 26.7 - - + -
9000E 82O 3.9 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 325 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321E ALA* 2.9 17.4 + - - +
322E HIS* 3.6 9.9 - - - +
324E LEU* 1.3 73.8 - - - +
326E GLU* 1.3 65.9 + - - +
328E ILE* 3.1 10.3 + - - +
329E GLN* 3.1 43.7 + - - +
480E VAL* 4.0 9.3 - - - +
2353F ILE* 3.7 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 326 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286E GLN* 3.1 32.0 + - - +
322E HIS* 2.9 32.9 + - + +
323E HIS* 3.2 28.4 + - - +
325E THR* 1.3 75.6 - - - +
327E ALA* 1.3 62.7 + - - +
329E GLN* 3.3 19.7 + - - +
330E TYR* 3.2 35.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286E GLN* 5.2 5.1 - - - +
323E HIS 2.9 5.9 + - - -
324E LEU 3.5 4.5 - - - +
326E GLU* 1.3 73.6 - - - +
328E ILE* 1.3 68.5 + - - +
330E TYR* 3.0 11.4 + - - +
331E VAL* 3.0 23.2 + - - +
361E VAL* 3.8 16.2 - - + -
364E ARG* 5.2 1.1 + - - -
9000E 82O 3.4 41.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 328 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E LEU 3.0 21.6 + - - +
325E THR* 3.1 9.4 + - - +
327E ALA* 1.3 77.2 - - - +
329E GLN* 1.3 63.6 + - - +
331E VAL* 3.0 6.1 + - - +
332E VAL* 2.9 23.0 + - + +
357E ALA* 3.8 11.2 - - + -
358E MET* 3.6 53.4 - - + +
361E VAL* 3.6 14.3 - - + +
2350F LEU* 4.5 12.3 - - + -
2353F ILE* 4.4 13.9 - - + -
2354F ILE* 4.2 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 329 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325E THR* 3.1 39.3 + - - +
326E GLU* 3.6 19.6 - - - +
327E ALA 3.2 0.2 - - - -
328E ILE* 1.3 75.9 - - - +
330E TYR* 1.3 64.3 + - + +
332E VAL* 3.1 11.4 + - - +
333E GLU* 3.1 25.7 + - + +
2353F ILE* 4.3 11.1 + - + +
2357F ALA* 4.3 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 330 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E GLU 5.5 1.6 - - - -
284E THR* 3.2 36.3 - - - +
285E CYS 4.4 2.9 - - - -
286E GLN* 3.5 57.4 + - + +
326E GLU* 3.2 32.2 + - + -
327E ALA* 3.0 11.0 + - - +
329E GLN* 1.3 76.3 - - + +
331E VAL* 1.3 64.9 + - - +
333E GLU* 3.1 13.7 + - + +
334E PHE* 2.9 21.1 + - - +
364E ARG* 3.9 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 331 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E ALA 3.0 13.7 + - - +
328E ILE* 3.0 8.9 + - - +
330E TYR* 1.3 75.0 - - - +
332E VAL* 1.3 62.7 + - - +
334E PHE* 3.1 11.8 - - + +
335E ALA* 3.1 19.6 + - - +
353E LEU* 4.7 1.8 - - + -
357E ALA* 3.9 20.6 - - + +
360E VAL* 3.6 37.5 - - + -
361E VAL* 3.6 22.4 - - + -
364E ARG* 4.2 14.4 - - - +
425E LEU* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 332 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328E ILE* 2.9 28.7 + - + +
329E GLN 3.1 6.7 + - - +
331E VAL* 1.3 76.1 - - - +
333E GLU* 1.3 64.5 + - - +
335E ALA* 3.1 5.4 + - - +
336E LYS* 3.0 25.7 + - - +
353E LEU* 4.0 26.0 - - + -
357E ALA* 5.4 0.4 - - + -
2354F ILE* 4.5 11.4 - - + -
2357F ALA* 4.1 31.2 - - + +
2358F LEU* 3.9 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 333 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284E THR* 3.8 16.2 - - + -
329E GLN* 3.1 16.1 + - + +
330E TYR* 3.1 17.4 + - + +
332E VAL* 1.3 76.0 - - - +
334E PHE* 1.3 63.2 + - - +
336E LYS* 3.0 45.4 + - - +
337E ARG* 2.8 46.8 + - - +
2357F ALA* 4.2 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 334 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E VAL* 3.9 3.4 - - + -
280E SER* 3.8 12.8 - - - -
281E TYR* 3.7 33.4 - + + -
284E THR* 3.5 26.3 - - - +
330E TYR 2.9 7.5 + - - +
331E VAL* 3.1 10.3 - - - +
333E GLU* 1.3 76.3 - - - +
335E ALA* 1.3 61.3 + - - +
337E ARG* 3.2 10.7 + - - +
338E LEU* 3.3 30.6 + - + +
360E VAL* 4.9 7.6 - - + -
364E ARG* 3.6 14.6 - - - +
418E ALA 3.6 20.9 - - - -
421E THR* 3.4 22.4 - - - -
422E ALA* 3.9 15.9 - - + -
425E LEU* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 335 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331E VAL 3.1 5.1 + - - +
332E VAL 3.1 7.8 + - - +
334E PHE* 1.3 79.2 - - - +
336E LYS* 1.3 63.5 + - - +
338E LEU* 3.0 21.3 + - + +
341E PHE* 3.3 52.8 - - + +
353E LEU* 4.0 16.2 - - + -
425E LEU* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 336 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332E VAL* 3.0 22.0 + - + +
333E GLU* 3.0 37.7 + - - +
335E ALA* 1.3 76.6 - - - +
337E ARG* 1.3 66.9 + - - +
338E LEU 3.4 4.5 + - - +
341E PHE* 4.3 1.5 - - + -
342E MET* 3.4 52.4 - - + +
2357F ALA 3.2 19.3 + - - -
2358F LEU* 3.0 40.7 + - + +
2359F MET 3.3 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 337 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276E SER* 4.9 7.6 + - - -
280E SER* 3.6 26.2 + - - -
283E GLU* 3.8 25.1 + - - +
284E THR* 3.7 22.9 - - - +
333E GLU* 2.8 47.7 + - - +
334E PHE 3.2 4.0 + - - +
335E ALA 3.2 0.4 - - - -
336E LYS* 1.3 81.4 - - + +
338E LEU* 1.3 64.2 + - - +
339E SER* 3.8 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E VAL* 4.4 20.0 - - + -
280E SER* 4.2 7.6 - - - +
334E PHE* 3.3 45.0 + - + +
335E ALA* 3.0 20.8 + - + +
336E LYS 3.6 7.8 - - - +
337E ARG* 1.3 80.7 - - - +
339E SER* 1.3 69.8 + - - +
340E GLY 3.5 0.8 + - - +
341E PHE* 3.6 12.7 + - + +
342E MET* 4.7 1.7 + - - +
422E ALA* 4.4 16.6 - - + +
425E LEU* 4.9 4.9 - - + -
426E ILE* 4.1 31.2 - - + -
446E LEU* 5.2 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