Contacts of the helix formed by residues 345 - 366 (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 CYS 345 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343E GLU 3.8 1.0 + - - -
344E LEU* 1.3 76.9 - - - +
346E GLN* 1.3 66.7 + - - +
347E ASN* 3.7 13.9 - - - +
348E ASP* 3.1 36.4 + - - -
349E GLN* 3.1 19.9 + - - +
434E GLN* 3.9 16.8 - - - +
435E GLU* 3.3 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 346 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A TYR* 5.5 4.6 + - - -
344E LEU 3.8 0.4 + - - -
345E CYS* 1.3 74.1 - - - +
347E ASN* 1.3 63.6 + - - +
349E GLN* 3.3 14.0 + - - +
350E ILE* 3.1 46.9 + - + +
2355F ARG* 4.2 15.3 + - - +
2358F LEU* 5.2 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 347 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345E CYS* 3.2 10.8 - - - -
346E GLN* 1.3 79.9 + - - +
348E ASP* 1.3 60.8 + - - +
350E ILE* 3.4 7.3 + - - +
351E VAL* 2.9 40.1 + - - +
432E GLY 3.0 27.3 + - - +
434E GLN* 3.3 34.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 348 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344E LEU* 4.2 16.7 - - + +
345E CYS* 3.1 16.6 + - - +
347E ASN* 1.3 77.7 + - - +
349E GLN* 1.3 67.0 + - - +
350E ILE 3.1 0.3 + - - -
351E VAL* 3.1 1.8 + - - +
352E LEU* 3.0 30.4 + - + +
433E LEU* 3.4 23.0 - - + -
434E GLN* 2.7 27.4 + - - -
435E GLU* 3.1 41.7 + - - +
439E VAL* 4.7 3.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 349 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341E PHE* 3.5 46.0 + - + +
342E MET* 3.0 27.3 + - - +
344E LEU* 2.9 23.3 + - + +
345E CYS 3.1 16.8 + - - +
346E GLN* 3.6 14.1 - - - +
348E ASP* 1.3 75.2 - - - +
350E ILE* 1.4 60.5 + - - +
352E LEU* 4.0 0.9 - - - +
353E LEU* 3.2 30.2 + - - +
2358F LEU* 3.5 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 350 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346E GLN* 3.1 34.6 + - + +
347E ASN* 3.8 5.6 - - - +
348E ASP 3.1 0.8 - - - -
349E GLN* 1.4 73.7 - - - +
351E VAL* 1.3 61.6 + - + +
353E LEU* 3.4 5.1 + - - +
354E LYS* 2.8 38.0 + - + +
2351F GLU* 4.0 29.8 - - + +
2354F ILE* 4.7 9.6 - - + +
2355F ARG* 3.7 42.8 - - + +
2358F LEU* 3.4 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 351 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347E ASN* 2.9 32.4 + - - +
348E ASP* 3.1 4.5 + - - +
350E ILE* 1.3 76.4 - - + +
352E LEU* 1.3 62.8 + - - +
354E LYS* 3.4 8.3 + - - +
355E ALA* 3.1 23.3 + - + +
430E ARG* 4.0 10.1 - - + -
431E PRO 3.4 23.6 - - - +
432E GLY* 3.9 21.8 - - - +
433E LEU* 3.8 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341E PHE* 4.3 15.5 - - + -
344E LEU* 4.0 26.9 - - + -
348E ASP 3.0 18.5 + - - +
349E GLN 4.0 2.9 - - - +
351E VAL* 1.3 75.5 - - - +
353E LEU* 1.3 58.6 + - - +
355E ALA* 3.2 2.6 + - - +
356E GLY* 2.8 28.8 + - - -
425E LEU* 3.6 29.8 - - + +
426E ILE* 4.3 9.9 - - + -
427E ASN 3.2 28.3 - - - +
430E ARG* 3.8 11.1 + - + -
433E LEU* 3.7 21.1 - - + -
439E VAL* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 353 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331E VAL 4.5 2.7 - - - +
332E VAL* 4.0 26.7 - - + -
335E ALA* 4.0 20.9 - - + -
341E PHE* 3.8 16.2 - - + -
349E GLN 3.2 17.6 + - - +
350E ILE 3.8 1.1 - - - +
352E LEU* 1.3 74.0 - - - +
354E LYS* 1.3 61.0 + - - +
357E ALA* 2.8 41.0 + - + +
425E LEU* 4.4 14.3 - - + +
2350F LEU* 4.8 0.3 - - - +
2354F ILE* 3.7 35.8 - - + +
2358F LEU* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 354 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350E ILE* 2.8 29.6 + - + +
351E VAL* 3.7 7.2 - - - +
353E LEU* 1.3 74.0 - - - +
355E ALA* 1.3 63.3 + - + +
357E ALA 4.6 0.7 + - - -
358E MET* 5.4 1.0 + - - +
2346F THR* 3.7 27.3 + - - +
2347F ASN* 3.5 41.0 + - - +
2348F MET* 4.4 3.0 - - - +
2350F LEU* 3.7 10.0 - - + +
2351F GLU* 3.5 43.4 + - + +
2354F ILE* 3.8 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351E VAL* 3.1 14.3 + - + +
352E LEU 3.9 1.1 - - - +
354E LYS* 1.3 80.2 - - + +
356E GLY* 1.3 59.3 + - - +
358E MET 5.7 0.2 - - - -
359E GLU* 5.1 7.1 + - - +
430E ARG* 3.4 48.1 + - + +
431E PRO* 6.4 0.2 - - + -
2346F THR* 5.3 6.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 356 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352E LEU 2.8 14.0 + - - -
355E ALA* 1.3 80.2 - - - +
357E ALA* 1.3 63.8 + - - +
358E MET 3.4 2.7 - - - -
359E GLU* 3.2 8.7 + - - +
360E VAL* 3.0 23.4 + - - +
424E VAL* 3.9 7.5 - - - +
425E LEU* 3.6 11.7 - - - -
430E ARG* 4.0 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 357 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328E ILE* 3.8 26.5 - - + +
331E VAL* 3.9 23.5 - - + +
332E VAL* 5.4 0.2 - - + -
353E LEU* 2.8 36.1 + - + +
355E ALA 4.0 0.4 - - - -
356E GLY* 1.3 69.5 - - - +
358E MET* 1.3 58.1 + - - +
360E VAL* 3.2 6.1 + - - +
361E VAL* 3.0 28.6 + - - +
425E LEU* 3.7 4.1 - - - +
2350F LEU* 5.5 0.4 - - + -
2354F ILE* 4.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 358 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E LEU* 4.2 17.9 - - + -
328E ILE* 3.6 29.7 - - + +
353E LEU 4.8 0.2 + - - -
354E LYS 5.4 0.8 + - - +
355E ALA 5.7 0.2 - - - -
356E GLY 3.4 0.4 - - - -
357E ALA* 1.3 77.4 - - - +
359E GLU* 1.3 63.1 + - - +
361E VAL* 3.0 22.5 + - - +
362E LEU* 3.0 16.6 + - + +
473E ALA* 3.2 34.8 - - + +
476E CYS* 3.9 20.6 - - + -
477E SER* 3.5 23.1 - - - +
480E VAL* 4.2 21.5 - - + -
2350F LEU* 4.3 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 359 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355E ALA 5.1 5.8 + - - +
356E GLY* 3.2 12.9 + - - +
358E MET* 1.3 75.9 - - - +
360E VAL* 1.3 62.8 + - - +
362E LEU* 3.2 6.3 + - - +
363E VAL* 3.1 25.2 + - + +
420E TYR* 4.3 14.0 + - - -
424E VAL* 4.0 22.8 - - + +
430E ARG* 5.3 5.2 + - - -
469E ALA* 3.6 35.7 + - + +
470E GLY* 4.0 13.7 + - - -
473E ALA* 3.7 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 360 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331E VAL* 3.6 27.4 - - + -
334E PHE* 4.9 4.5 - - + -
356E GLY 3.0 13.9 + - - +
357E ALA 3.2 8.3 + - - +
359E GLU* 1.3 70.6 - - - +
361E VAL* 1.3 66.7 + - - +
363E VAL* 3.2 5.2 + - - +
364E ARG* 2.8 34.5 + - - +
421E THR* 3.8 38.1 - - + +
424E VAL* 4.0 9.6 - - + +
425E LEU* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 361 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E LEU* 4.5 4.5 - - + +
327E ALA* 3.8 17.3 - - + -
328E ILE* 3.6 20.2 - - + +
331E VAL* 3.6 20.4 - - + -
357E ALA 3.0 18.2 + - - +
358E MET* 3.0 20.8 + - - +
360E VAL* 1.3 76.9 - - - +
362E LEU* 1.3 63.9 + - + +
364E ARG* 3.2 7.7 + - - +
365E MET* 3.0 29.3 + - - +
9000E 82O 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 362 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E LEU* 5.7 1.8 - - + -
358E MET* 3.0 19.1 + - + +
359E GLU* 3.2 8.0 + - - +
361E VAL* 1.3 78.4 - - + +
363E VAL* 1.3 62.0 + - - +
365E MET* 3.3 42.7 + - + +
366E CYS 3.8 2.3 + - - -
400E ILE* 4.5 10.3 - - + -
403E PHE* 3.4 29.0 - - + -
404E SER* 4.5 0.9 + - - -
469E ALA* 4.3 7.4 - - + +
472E LEU* 3.7 37.7 - - + +
473E ALA* 3.8 20.4 - - + +
476E CYS* 4.4 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 363 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359E GLU* 3.1 22.4 + - + +
360E VAL* 3.7 5.8 - - - +
362E LEU* 1.3 75.3 - - - +
364E ARG* 1.3 65.9 + - - +
365E MET 3.1 1.0 + - - -
366E CYS* 3.1 23.7 + - - +
403E PHE* 4.4 13.0 - - + -
407E LEU* 3.9 14.8 - - + -
412E PHE* 5.3 2.5 - - + -
417E ILE* 3.8 22.2 - - + +
420E TYR* 4.0 31.4 - - + -
421E THR* 3.7 23.1 - - + -
424E VAL* 5.3 1.6 - - + -
466E LEU* 6.4 0.2 - - + -
469E ALA* 5.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 364 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281E TYR* 3.7 38.2 + - + +
284E THR* 2.7 51.1 + - - -
285E CYS* 4.0 8.3 - - - +
286E GLN 5.0 0.8 - - - +
327E ALA* 6.5 0.9 - - - -
330E TYR* 3.9 16.4 - - - +
331E VAL* 4.2 14.5 - - - +
334E PHE* 3.6 20.8 - - - +
360E VAL* 2.8 40.4 + - + +
361E VAL* 3.7 6.3 - - - +
363E VAL* 1.3 72.2 - - - +
365E MET* 1.3 56.7 + - + +
367E ARG* 2.5 39.9 - - - +
368E ALA* 4.4 1.2 + - - +
417E ILE* 4.8 3.1 - - - -
421E THR* 4.7 4.0 + - + -
9000E 82O 5.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 365 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E LEU* 5.0 2.0 - - + -
361E VAL* 3.0 23.1 + - - +
362E LEU* 3.4 31.6 - - + +
363E VAL 3.0 0.8 - - - -
364E ARG* 1.3 79.1 - - + +
366E CYS* 1.3 62.6 + - - +
368E ALA 3.0 12.6 + - - -
369E TYR 3.5 1.6 + - - -
400E ILE* 3.7 23.8 - - + -
404E SER* 4.2 2.9 - - - +
9000E 82O 3.3 109.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 366 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362E LEU 3.8 2.2 + - - -
363E VAL 3.1 19.7 + - - +
365E MET* 1.3 77.5 - - - +
367E ARG* 1.3 69.0 + - - +
369E TYR* 3.2 22.2 + - - +
404E SER* 3.9 19.4 + - - +
407E LEU* 3.7 39.9 - - + -
408E SER* 3.6 10.9 + - - +
412E PHE* 5.2 4.3 - - - -
417E ILE* 3.9 21.5 - - - -
----------------------------------------------------------
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