Contacts of the helix formed by residues 414 - 443 (chain B) in PDB entry 1ZDT
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 ASP 414 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B SER* 3.1 1.4 - - - -
413B GLY* 1.3 78.7 - - - +
415B LYS* 1.3 64.8 + - - +
416B PHE* 3.2 3.6 - - - -
417B GLN* 3.1 23.5 + - - +
418B GLN* 3.0 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU* 2.9 38.9 + - + +
362B GLN* 2.9 19.6 + - - -
363B LEU* 4.1 0.6 - - - +
367B GLU* 2.9 33.0 + - - -
405B THR* 4.0 13.9 - - + -
409B TYR* 3.5 33.2 - - + -
412B SER* 3.3 30.0 + - - +
413B GLY 3.6 0.6 - - - -
414B ASP* 1.3 78.1 - - - +
416B PHE* 1.3 63.1 + - - +
418B GLN* 3.3 7.0 + - - +
419B LEU* 2.9 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ASN* 3.5 52.9 - - - -
401B LEU* 3.6 30.3 - - + -
402B LEU* 3.6 40.2 - - + -
405B THR* 3.7 18.6 + - - +
413B GLY 5.5 1.1 + - - +
414B ASP* 3.2 1.1 - - - -
415B LYS* 1.3 80.1 - - - +
417B GLN* 1.3 96.6 + - - +
419B LEU* 3.3 5.5 + - - +
420B LEU* 3.1 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ASP* 3.1 23.7 + - - +
416B PHE* 1.3 117.4 - - - +
418B GLN* 1.3 60.5 + - - +
420B LEU* 3.3 15.2 + - + +
421B LEU* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU* 3.8 32.3 - - + +
414B ASP* 3.0 45.6 + - + +
415B LYS* 3.7 5.6 - - - +
417B GLN* 1.3 79.0 - - - +
419B LEU* 1.3 60.9 + - - +
421B LEU* 3.4 25.5 + - - +
422B CYS* 3.2 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B LEU* 4.0 25.8 - - + -
361B LEU* 4.2 17.5 - - + -
363B LEU* 4.0 15.7 - - + -
367B GLU* 3.9 31.4 - - + +
371B LEU* 4.2 17.1 - - + +
401B LEU* 4.4 9.4 - - + -
405B THR* 4.1 8.7 - - + -
415B LYS* 2.9 37.3 + - + +
416B PHE 3.6 4.7 - - - +
418B GLN* 1.3 76.4 - - - +
420B LEU* 1.3 63.5 + - - +
422B CYS* 3.2 15.2 + - - +
423B LEU* 3.3 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 4.5 0.4 - - + -
374B ILE* 4.7 12.1 - - + -
398B ASN* 4.3 10.1 - - - +
401B LEU* 4.5 16.2 - - + -
416B PHE* 3.1 46.9 + - + +
417B GLN* 3.6 19.1 - - + +
419B LEU* 1.3 76.3 - - - +
421B LEU* 1.3 62.5 + - - +
423B LEU* 3.1 39.4 + - + +
424B VAL* 3.3 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B GLN* 5.8 4.9 - - - +
417B GLN 3.0 16.3 + - - +
418B GLN* 3.6 28.9 - - - +
419B LEU 3.2 0.2 - - - -
420B LEU* 1.3 72.3 - - - +
422B CYS* 1.3 65.0 + - - +
424B VAL* 3.0 35.0 + - + +
425B GLU* 3.2 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 6.1 1.3 - - + -
354B LEU* 4.0 16.9 - - + +
357B GLN* 3.7 23.1 - - - -
358B LEU* 3.7 24.5 - - + -
361B LEU* 3.7 22.4 - - - -
418B GLN 3.2 19.8 + - - -
419B LEU* 3.2 10.5 + - - +
421B LEU* 1.3 76.3 - - - +
423B LEU* 1.3 61.6 + - + +
425B GLU* 3.2 7.1 + - - +
426B VAL* 3.0 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU* 5.8 0.2 - - - +
308B PHE* 4.4 13.9 - - + -
371B LEU* 3.4 41.3 - - + +
374B ILE* 3.8 26.2 - - + -
375B ILE* 4.1 31.0 - - + -
419B LEU 3.3 5.3 + - - +
420B LEU* 3.1 25.5 + - + +
422B CYS* 1.3 78.5 - - + +
424B VAL* 1.3 62.9 + - - +
426B VAL* 3.2 7.3 + - + +
427B ARG* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LEU 3.3 11.6 + - - +
421B LEU* 3.0 26.5 + - + +
423B LEU* 1.3 76.4 - - - +
425B GLU* 1.3 62.8 + - - +
427B ARG* 3.2 12.0 + - + +
428B ALA* 3.1 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ARG* 2.8 51.7 + - - +
354B LEU* 4.0 28.9 - - + -
357B GLN* 4.7 10.1 - - - +
421B LEU 3.2 7.0 + - - +
422B CYS* 3.2 11.3 + - - +
423B LEU 3.2 0.6 - - - -
424B VAL* 1.3 78.8 - - - +
426B VAL* 1.3 59.1 + - - +
428B ALA* 3.4 5.5 + - - +
429B LEU* 3.0 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU* 3.6 37.7 - - + +
307B VAL* 4.0 11.9 - - + -
308B PHE* 4.0 29.4 - - + -
311B ILE* 5.1 0.2 - - + -
354B LEU* 3.7 17.9 - - + -
358B LEU* 6.0 0.4 - - + -
375B ILE* 4.7 4.5 - - + -
422B CYS* 3.0 20.8 + - + +
423B LEU* 3.2 11.9 + - + +
425B GLU* 1.3 77.6 - - - +
427B ARG* 1.3 53.0 + - - +
429B LEU* 3.6 7.2 - - - +
430B SER* 2.7 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ASN* 5.8 1.6 + - - -
304B GLU* 3.5 28.6 + - + +
423B LEU 3.1 11.8 + - - +
424B VAL* 3.2 13.2 + - - +
426B VAL* 1.3 77.8 - - - +
428B ALA* 1.3 61.5 + - - +
430B SER* 3.3 3.5 + - - -
431B MET* 3.1 66.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ARG* 3.9 23.3 - - - +
424B VAL* 3.1 12.7 + - + +
425B GLU* 3.6 14.6 - - - +
426B VAL 3.4 0.2 - - - -
427B ARG* 1.3 72.3 - - - +
429B LEU* 1.3 64.5 + - - +
431B MET* 3.3 9.2 + - - +
432B GLN* 3.2 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B VAL* 4.0 22.3 - - + +
311B ILE* 4.3 0.4 - - + -
347B LEU* 3.5 27.8 - - + +
350B ARG* 3.8 39.4 - - + +
351B ALA* 3.9 24.5 - - + +
354B LEU* 3.7 31.2 - - + -
425B GLU* 3.0 19.3 + - - +
426B VAL* 3.6 4.9 - - - +
428B ALA* 1.3 75.6 - - - +
430B SER* 1.3 57.5 + - - +
432B GLN* 3.3 2.9 + - - +
433B ALA* 3.0 28.0 + - - +
1002B PEF 4.7 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B SER* 3.3 23.1 + - - -
304B GLU* 3.2 33.8 + - - -
307B VAL* 3.5 11.5 - - - +
426B VAL 2.7 21.8 + - - -
427B ARG 3.4 7.0 - - - -
429B LEU* 1.3 74.5 - - - +
431B MET* 1.3 61.6 + - - +
433B ALA* 3.6 3.8 - - - +
434B LYS* 3.0 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ASN 5.7 0.2 - - - +
304B GLU* 3.3 26.5 - - - +
427B ARG* 3.1 51.2 + - - +
428B ALA* 3.8 9.0 - - - +
429B LEU 3.2 0.4 - - - -
430B SER* 1.3 80.3 - - - +
432B GLN* 1.3 65.1 + - - +
434B LYS* 3.2 38.0 + - - +
435B GLU* 3.0 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU* 5.2 1.5 + - - +
346B SER* 3.6 22.4 + - - -
347B LEU* 3.4 33.2 - - + +
350B ARG* 3.1 44.8 + - - +
428B ALA 3.2 9.4 + - - +
429B LEU* 3.6 3.4 - - - +
431B MET* 1.3 77.2 - - - +
433B ALA* 1.3 58.0 + - - +
435B GLU* 3.3 16.2 + - - +
436B TYR* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B VAL* 4.7 4.5 - - + -
347B LEU* 3.6 20.8 - - + +
429B LEU 3.0 16.9 + - - +
430B SER* 3.6 9.6 - - - +
431B MET 3.2 0.2 - - - -
432B GLN* 1.3 74.8 - - - +
434B LYS* 1.3 64.0 + - - +
436B TYR* 3.1 5.9 + - - +
437B LEU* 3.0 27.5 + - - +
1002B PEF 4.4 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLN 5.5 1.8 + - - -
300B ASN 5.2 7.1 + - - -
302B TRP* 3.9 27.9 - - + +
303B SER* 3.6 18.6 + - - +
430B SER 3.0 18.8 + - - +
431B MET* 3.3 42.2 - - - +
433B ALA* 1.3 76.2 - - - +
435B GLU* 1.3 57.3 + - + +
437B LEU* 3.4 7.5 + - + +
438B TYR* 3.0 27.7 + - - +
456B LEU* 3.6 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU* 5.7 4.8 - - + +
431B MET* 3.0 23.4 + - + +
432B GLN* 3.5 15.6 - - - +
433B ALA 3.2 0.2 - - - -
434B LYS* 1.3 73.4 - - + +
436B TYR* 1.3 64.4 + - - +
438B TYR* 3.5 8.8 + - - +
439B HIS* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PHE* 3.6 11.4 - + - -
343B LEU* 4.3 22.2 - - + +
344B LEU* 3.8 30.5 - - + +
347B LEU* 4.1 12.6 - - + -
432B GLN 3.0 12.3 + - - +
433B ALA 3.3 8.5 - - - +
435B GLU* 1.3 75.4 - - - +
437B LEU* 1.3 65.1 + - + +
439B HIS* 3.3 11.7 + + - +
440B LYS* 3.1 50.2 + - + +
1002B PEF 2.6 84.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B TRP* 3.8 33.0 - - + -
433B ALA 3.0 17.5 + - - +
434B LYS* 3.5 11.2 - - - +
436B TYR* 1.3 80.3 - - + +
438B TYR* 1.3 57.0 + - - +
440B LYS* 3.4 4.3 + - - +
441B HIS* 2.9 29.7 + - - +
446B MET* 3.8 30.7 - - + -
452B LEU* 4.3 19.3 - - + +
453B ILE* 4.0 8.8 - - + +
456B LEU* 4.2 11.7 - - + -
1002B PEF 3.9 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B LYS 3.0 16.6 + - - +
435B GLU* 3.8 9.4 - - - +
436B TYR 3.3 0.2 - - - -
437B LEU* 1.3 73.2 - - - +
439B HIS* 1.3 62.0 + - - +
441B HIS* 3.3 17.9 + + - +
442B LEU* 3.0 68.2 + - + +
456B LEU* 4.0 16.1 - - + +
457B GLN* 6.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU* 4.8 23.3 - - + +
435B GLU 3.1 14.7 + - - +
436B TYR* 3.4 15.3 - + - +
438B TYR* 1.3 78.9 - - - +
440B LYS* 1.3 84.3 + - + +
442B LEU* 3.3 8.1 + - - +
443B GLY* 3.2 19.1 + - - -
445B GLU* 4.6 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PHE* 3.7 29.2 - - + -
436B TYR* 3.1 32.9 + - + +
437B LEU* 3.5 8.3 - - - +
439B HIS* 1.3 94.6 + - + +
441B HIS* 1.3 64.1 + - - +
443B GLY 3.3 5.4 + - - -
445B GLU* 3.1 55.2 + - + +
446B MET* 3.6 18.2 - - + -
1002B PEF 2.7 42.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LEU 2.9 18.0 + - - +
438B TYR* 3.4 21.5 - + - +
439B HIS 3.3 0.2 - - - -
440B LYS* 1.3 77.4 - - - +
442B LEU* 1.3 80.3 + - + +
444B ASN* 3.2 16.6 + - - +
446B MET* 3.8 11.6 - - - +
448B ARG* 6.2 2.0 - - - -
453B ILE* 3.8 27.3 - - + +
456B LEU* 5.3 2.5 - - + -
457B GLN* 3.4 34.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B TYR* 3.0 59.8 + - + +
439B HIS* 3.9 7.4 - - - +
440B LYS 3.3 0.2 - - - -
441B HIS* 1.3 85.0 - - + +
443B GLY* 1.3 58.2 + - - +
444B ASN* 3.1 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLN* 5.1 1.7 + - - -
439B HIS* 3.2 13.5 + - - -
440B LYS 3.3 2.9 + - - -
441B HIS 3.3 0.4 - - - -
442B LEU* 1.3 74.6 - - - +
444B ASN* 1.3 67.2 + - - +
445B GLU* 3.2 21.6 - - - +
----------------------------------------------------------
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