Contacts of the helix formed by residues 417 - 448 (chain B) in PDB entry 3TKL
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 417 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B SER* 3.1 24.3 - - - -
416B THR* 1.3 74.4 - - + +
418B PRO* 1.3 61.1 - - + +
419B LYS* 2.5 24.1 + - + +
420B GLU* 2.9 33.6 + - - +
421B ASN* 3.3 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B THR 3.1 11.2 - - - +
417B ASP* 1.3 80.0 - - + +
419B LYS* 1.3 59.2 + - + +
421B ASN* 4.3 9.2 - - + +
422B GLU* 3.0 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B ASP* 2.5 16.7 + - + +
418B PRO* 1.3 75.5 - - + +
420B GLU* 1.3 62.9 + - + +
421B ASN 3.2 1.3 - - - -
422B GLU* 3.4 22.8 + - - +
423B GLU* 3.0 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LEU* 3.5 34.4 - - + +
415B SER* 2.8 28.8 + - - -
417B ASP* 2.9 29.7 + - - +
419B LYS* 1.3 76.7 - - + +
421B ASN* 1.3 59.5 + - - +
423B GLU* 3.3 15.0 - - - +
424B ALA 2.9 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LEU 2.7 23.0 - - - +
413B ILE* 3.8 15.2 + - + +
415B SER* 2.4 32.9 + - - +
416B THR* 3.1 25.5 + - - +
417B ASP 3.5 8.5 + - - +
418B PRO* 4.1 5.6 - - + +
419B LYS 3.2 0.4 - - - -
420B GLU* 1.3 74.7 - - - +
422B GLU* 1.3 59.3 - - - +
423B GLU 3.1 1.1 - - - -
424B ALA* 3.5 7.5 + - - +
425B THR* 3.0 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B PRO* 3.0 24.5 + - - +
419B LYS* 3.4 21.2 + - - +
421B ASN* 1.3 75.4 - - - +
423B GLU* 1.3 62.9 + - - +
425B THR* 3.5 8.1 + - + -
426B LYS* 3.2 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LEU* 4.2 16.2 - - + +
419B LYS* 3.0 20.6 + - - +
420B GLU* 3.3 20.9 - - - +
422B GLU* 1.3 72.5 - - - +
424B ALA* 1.3 57.6 + - - +
425B THR 3.0 0.9 - - - -
426B LYS* 2.7 29.5 + - + +
427B LEU* 2.8 13.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ILE* 3.8 20.6 - - + +
412B LEU* 3.7 26.7 - - + +
413B ILE* 3.9 18.6 - - + +
420B GLU 2.9 17.4 + - - +
421B ASN 3.5 9.4 - - - +
423B GLU* 1.3 70.8 - - - +
425B THR* 1.3 56.9 + - - +
427B LEU* 3.2 6.2 + - - +
428B LEU* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ILE* 6.0 1.0 - - - +
421B ASN 3.0 18.6 + - - -
422B GLU* 3.5 11.4 - - + +
423B GLU 2.9 1.2 + - - -
424B ALA* 1.3 76.1 - - - +
426B LYS* 1.3 69.2 + - + +
428B LEU* 3.6 6.9 + - - +
429B HIS* 2.7 52.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B GLU* 3.2 37.7 + - - +
423B GLU* 2.7 16.6 + - + +
425B THR* 1.3 83.3 - - + +
427B LEU* 1.3 58.2 + - - +
429B HIS* 3.4 16.3 + - + +
430B LYS* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLN* 3.9 32.3 - - + +
408B THR* 3.6 31.4 - - + -
409B ILE* 3.5 27.6 - - + +
412B LEU* 4.3 7.0 - - + -
423B GLU* 2.8 12.6 + - + +
424B ALA* 3.4 11.4 - - - +
426B LYS* 1.3 76.9 - - - +
428B LEU* 1.3 56.9 + - - +
430B LYS* 3.3 12.2 + - + -
431B HIS* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 3.7 31.0 - - + +
47A ASP* 3.4 28.9 - - - +
48A PHE* 3.9 19.1 - - + +
65A TRP* 4.9 4.7 - - + -
409B ILE* 3.8 27.8 - - + +
424B ALA 2.8 15.8 + - - +
425B THR* 3.8 9.2 - - - +
426B LYS 3.3 0.2 - - - -
427B LEU* 1.3 73.7 - - - +
429B HIS* 1.3 62.4 + - + +
431B HIS* 3.3 6.4 + - + +
432B ASN* 2.9 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B THR* 2.7 37.6 + - + -
426B LYS* 3.5 19.6 - - + +
428B LEU* 1.3 78.8 - - + +
430B LYS* 1.3 57.1 + - - +
432B ASN* 3.3 8.6 + - - +
433B GLY* 2.9 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B GLU* 4.3 13.2 + - - -
405B GLN* 3.8 23.3 - - - +
426B LYS 3.0 17.0 + - - +
427B LEU* 3.6 13.9 - - + +
429B HIS* 1.3 73.5 - - - +
431B HIS* 1.3 67.0 + - - +
433B GLY* 3.0 4.0 + - - +
434B LEU* 2.9 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY* 5.3 0.9 - - - -
46A VAL* 4.1 10.9 - - + +
76A ILE* 3.7 8.3 - - + +
80A TYR* 3.3 20.9 + - - -
402B MET* 3.3 40.4 + - + +
405B GLN* 2.9 32.8 + - - +
406B LEU* 3.4 23.6 - - + +
409B ILE* 4.3 4.9 - - + -
427B LEU 2.9 12.8 + - - +
428B LEU* 3.3 12.8 - - + +
430B LYS* 1.3 77.1 - - - +
432B ASN* 1.3 78.4 + - - +
434B LEU* 3.3 7.7 + - - +
435B ASN* 3.1 20.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.1 34.1 - - + +
45A GLY* 3.3 14.1 - - - -
46A VAL 3.2 43.2 + - - +
428B LEU* 2.9 28.0 + - - +
429B HIS* 3.8 7.0 + - - +
431B HIS* 1.3 86.2 - - - +
433B GLY* 1.3 62.4 + - - +
435B ASN* 3.1 10.6 + - - -
436B LEU* 3.3 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B HIS 2.9 14.1 + - - -
430B LYS* 3.0 5.3 + - - -
432B ASN* 1.3 75.4 - - - +
434B LEU* 1.3 63.1 + - - +
436B LEU* 3.2 31.5 + - - +
437B LYS* 3.4 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LEU* 4.0 17.2 - - + +
401B GLU* 3.8 23.6 - - + +
402B MET* 3.7 27.8 - - + +
405B GLN* 3.6 26.5 - - - +
430B LYS* 2.9 29.4 + - + +
431B HIS 3.4 7.6 - - - +
433B GLY* 1.3 76.3 - - - +
435B ASN* 1.3 58.5 + - - +
437B LYS* 3.1 17.5 + - + +
438B LEU* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 2.7 31.7 + - + +
45A GLY* 3.2 15.3 - - - -
72A ARG 5.5 0.2 - - - +
73A PHE* 3.2 21.9 + - - +
75A THR* 3.1 23.0 + - - -
76A ILE* 5.4 2.1 + - - +
80A TYR* 4.7 7.2 + - - -
402B MET* 4.0 11.4 - - - +
431B HIS* 3.1 14.4 + - + +
432B ASN* 3.1 12.7 + - - +
434B LEU* 1.3 77.1 - - - +
436B LEU* 1.3 63.5 + - - +
438B LEU* 4.0 6.6 - - - +
439B ALA* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.9 31.2 - - + +
72A ARG* 4.8 0.3 + - - -
73A PHE* 4.3 15.7 - - + -
432B ASN 3.3 7.8 + - - +
433B GLY* 3.2 24.3 + - - +
435B ASN* 1.3 77.6 - - - +
437B LYS* 1.3 60.6 + - - +
439B ALA* 3.6 2.6 + - - +
440B ASN* 3.2 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU* 6.4 0.9 - - + -
398B LEU* 3.9 22.7 - - + -
433B GLY 3.4 7.0 + - - +
434B LEU* 3.1 18.0 + - + +
436B LEU* 1.3 76.5 - - - +
438B LEU* 1.3 66.1 + - - +
440B ASN* 3.2 10.7 + - - +
441B LEU* 2.9 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A THR* 3.2 37.5 - - + +
76A ILE* 4.3 2.9 - - + -
395B ILE* 3.6 44.0 - - + +
398B LEU* 3.8 23.3 - - + +
399B SER* 4.4 3.8 - - - +
402B MET* 3.1 30.3 - - + -
434B LEU 2.8 20.1 + - - +
435B ASN* 3.8 5.6 - - - +
437B LYS* 1.3 73.1 - - - +
439B ALA* 1.3 63.1 + - - +
441B LEU* 3.1 6.1 + - + +
442B GLN* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 3.3 49.2 - - + +
73A PHE* 3.9 11.0 - - + -
75A THR* 5.1 1.9 + - - -
435B ASN* 3.0 18.6 + - - +
436B LEU 3.8 3.4 - - - +
438B LEU* 1.3 75.9 - - - +
440B ASN* 1.3 57.3 + - - +
442B GLN* 3.1 11.3 + - - +
443B ASP* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 2.8 26.5 + - - -
436B LEU* 3.2 19.9 + - - +
437B LYS* 3.2 10.8 + - + +
439B ALA* 1.3 73.5 - - - +
441B LEU* 1.3 66.9 + - + +
443B ASP* 3.2 18.5 + - - +
444B MET* 3.2 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU* 3.8 33.4 - - + -
395B ILE* 3.8 27.4 - - + +
398B LEU* 3.8 24.7 - - + -
437B LYS* 2.9 22.7 + - + +
438B LEU* 3.3 8.1 - - - +
440B ASN* 1.3 75.9 - - + +
442B GLN* 1.3 63.8 + - - +
443B ASP 3.2 0.2 + - - -
444B MET* 3.0 43.5 + - + +
445B LEU* 3.1 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG 5.8 1.1 - - - +
75A THR* 2.9 34.1 - - + +
306B LYS* 5.1 9.5 + - - +
395B ILE* 3.5 31.0 - - + +
438B LEU* 2.9 20.5 + - + +
439B ALA* 3.1 9.8 + - - +
441B LEU* 1.3 76.0 - - - +
443B ASP* 1.3 63.5 + - - +
445B LEU* 3.5 17.3 + - - +
446B ALA* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 2.7 43.4 + - - +
439B ALA 3.0 11.0 + - - +
440B ASN* 3.3 14.1 - - - +
441B LEU 3.1 0.4 - - - -
442B GLN* 1.3 75.8 - - - +
444B MET* 1.3 64.4 + - - +
446B ALA* 3.3 15.0 + - - +
447B VAL* 3.3 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B MET* 3.7 43.1 - - + +
394B LEU* 6.6 0.2 - - + -
395B ILE* 5.1 2.0 - - + -
440B ASN 3.2 8.8 + - - +
441B LEU* 3.0 50.3 - - + +
443B ASP* 1.3 75.3 - - - +
445B LEU* 1.3 71.5 + - + +
447B VAL* 2.9 19.7 + - + +
448B HIS* 3.1 12.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LYS* 5.3 5.2 - - - +
388B THR* 4.2 23.8 - - + -
391B MET* 4.0 27.6 - - + -
392B GLU* 4.0 21.1 - - + +
395B ILE* 3.9 13.2 - - + -
441B LEU 3.1 14.3 + - - +
442B GLN* 3.5 28.9 - - - +
443B ASP 3.2 0.2 - - - -
444B MET* 1.3 81.7 - - + +
446B ALA* 1.3 59.7 + - - +
448B HIS* 3.0 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B GLN 3.2 10.8 + - - +
443B ASP* 3.5 12.1 - - - +
444B MET 3.2 0.4 - - - -
445B LEU* 1.3 82.1 - - - +
447B VAL* 1.3 59.6 + - + +
448B HIS 3.9 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ASP 3.3 12.3 + - - +
444B MET* 2.9 13.8 + - - +
446B ALA* 1.3 79.0 - - + +
448B HIS* 1.3 64.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B HIS* 3.2 52.9 + + - -
387B ALA* 3.3 24.0 - - + -
388B THR* 2.9 36.4 + - + -
391B MET* 3.7 26.7 - - + +
444B MET* 3.1 9.5 + - + +
445B LEU* 3.0 23.3 + - + +
446B ALA* 3.9 4.3 - - - +
447B VAL* 1.3 83.6 - - + +
----------------------------------------------------------
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