Contacts of the helix formed by residues 415 - 428 (chain B) in PDB entry 2ZXI
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 415 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU* 3.2 20.9 - - - -
410B LEU* 3.7 16.5 - - - +
411B ARG 3.5 2.6 + - - -
412B ARG 3.6 2.6 - - - +
414B GLU* 1.3 79.8 - - - +
416B TYR* 1.3 59.7 + - - +
417B ILE* 3.5 1.4 + - - -
418B GLY* 3.0 22.3 + - - -
419B VAL* 3.1 25.5 + - - +
446B ILE* 3.6 8.4 - - - +
454B ARG* 3.6 2.7 - - - +
455B LEU* 4.0 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA* 3.9 17.6 - - + +
59B ILE* 4.5 19.1 - - + -
60B VAL* 4.0 12.1 - - + -
63B GLU* 2.9 17.5 + - - +
415B SER* 1.3 70.9 - - - +
417B ILE* 1.3 65.0 + - - +
419B VAL* 3.2 11.4 + - + -
420B MET* 3.0 21.1 + - - +
435B LEU* 3.2 36.5 + - + +
436B PHE* 4.9 1.6 + - - -
438B SER* 2.6 45.3 + - - -
440B SER* 4.5 20.1 + - - -
443B ARG* 6.4 0.9 - - + -
446B ILE* 3.6 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 4.0 17.3 - - + -
63B GLU* 3.0 29.6 + - + +
64B ILE* 4.0 19.1 - - + +
67B LEU* 4.5 17.7 - - + -
389B GLY* 3.6 38.1 - - - +
392B ILE* 4.6 0.9 - - + -
393B VAL* 4.0 1.1 - - + -
410B LEU* 3.7 20.4 - - + -
415B SER* 3.2 1.1 - - - +
416B TYR* 1.3 76.6 - - - +
418B GLY* 1.3 64.3 + - - +
420B MET* 3.2 12.2 + - + +
421B ILE* 3.0 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 3.3 29.8 - - - +
411B ARG 4.2 1.8 - - - -
412B ARG* 3.9 7.7 - - - +
415B SER* 3.0 18.8 + - - -
417B ILE* 1.3 79.6 - - - +
419B VAL* 1.3 61.1 + - - +
421B ILE* 4.0 4.5 - - - +
422B ASP* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ARG* 3.4 55.8 - - + +
415B SER 3.1 9.8 + - - +
416B TYR* 3.2 17.9 + - + +
418B GLY* 1.3 75.6 - - - +
420B MET* 1.3 57.3 + - - +
422B ASP* 3.5 1.2 - - - +
423B ASP* 2.9 32.5 + - - +
438B SER* 3.6 32.1 - - - +
439B ARG 4.8 3.6 - - - +
440B SER* 4.2 18.4 - - - +
446B ILE* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 5.2 1.6 - - + -
381B THR* 4.3 1.6 - - - -
386B GLU* 3.2 52.0 - - - +
389B GLY* 4.2 9.0 - - - -
390B GLN* 3.8 24.5 - - + +
416B TYR 3.0 11.4 + - - +
417B ILE* 3.2 18.8 + - + +
419B VAL* 1.3 78.1 - - - +
421B ILE* 1.3 58.5 + - + +
423B ASP* 3.3 2.6 + - - +
424B LEU* 2.9 45.3 + - + +
433B TYR* 3.6 25.2 - - + -
435B LEU* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B PRO* 3.2 37.0 - - + +
364B LEU* 4.0 27.8 - - + -
390B GLN* 4.5 14.6 - - + -
393B VAL* 3.7 38.4 - - + -
410B LEU* 5.5 5.8 - - + +
417B ILE* 3.0 28.8 + - + +
418B GLY* 4.0 5.8 - - - +
420B MET* 1.3 75.6 - - + +
422B ASP* 1.3 60.5 + - - +
424B LEU* 3.7 6.2 - - - +
425B THR* 3.0 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B PRO* 5.3 5.8 - - - +
410B LEU 5.8 0.4 - - - +
412B ARG* 2.7 34.6 + - + +
418B GLY 2.9 19.7 + - - +
419B VAL 3.5 3.6 - - - +
421B ILE* 1.3 77.8 - - - +
423B ASP* 1.3 57.3 + - - +
425B THR* 4.1 4.3 - - - -
426B THR* 2.8 43.1 + - - -
427B LYS* 6.1 0.7 - - - +
594B GLN* 3.9 7.4 - - - +
597B ARG* 2.6 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ARG* 2.9 27.8 + - - -
419B VAL* 2.9 19.3 + - - +
420B MET 3.7 3.4 - - - +
422B ASP* 1.3 77.2 - - - +
424B LEU* 1.3 59.2 + - - +
426B THR* 4.9 0.7 - - - -
427B LYS* 2.8 51.5 + - + +
428B GLY 3.3 3.2 + - - +
429B VAL* 6.1 0.2 - - - -
433B TYR* 3.7 18.4 + - + -
438B SER* 3.5 29.5 - - - -
439B ARG 4.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B PRO* 3.2 33.3 - - + +
358B THR 4.0 0.2 + - - -
364B LEU* 5.6 0.9 - - + -
379B ASN* 3.9 12.6 - - - +
380B GLY 4.7 0.4 - - - -
381B THR* 3.5 35.0 - - + -
390B GLN* 3.8 19.1 - - + +
420B MET* 2.9 32.9 + - + +
421B ILE* 3.7 8.5 - - + +
423B ASP* 1.3 77.8 - - - +
425B THR* 1.3 60.4 + - + +
428B GLY* 3.2 22.6 + - - +
429B VAL* 3.9 15.9 - - + -
433B TYR* 3.7 20.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
357B PRO* 3.6 16.8 - - + +
358B THR* 4.2 8.7 - - - +
360B LEU* 3.4 29.9 - - + +
361B TYR 3.7 16.4 - - - +
362B PRO* 3.8 20.4 - - + +
364B LEU* 4.8 5.8 - - + -
367B LYS* 5.0 2.4 + - - -
379B ASN* 5.8 0.2 - - - +
421B ILE* 3.0 23.0 + - + +
422B ASP* 3.6 3.5 + - - -
424B LEU* 1.3 80.4 - - + +
426B THR* 1.3 61.8 + - - +
587B PHE* 3.6 17.7 - - - +
594B GLN* 4.2 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ASP* 2.8 24.3 + - - -
425B THR* 1.3 81.0 + - - +
427B LYS* 1.3 63.9 + - + +
428B GLY 3.6 0.2 - - - -
587B PHE* 3.1 25.2 - - + -
594B GLN* 3.2 49.0 + - + +
597B ARG* 3.7 29.2 - - + +
598B ILE* 3.9 14.7 - - + +
599B ASP 4.9 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B THR* 4.6 2.6 - - - +
422B ASP* 6.1 0.2 - - - +
423B ASP* 2.8 34.0 + - + +
426B THR* 1.3 82.3 - - + +
428B GLY* 1.3 69.1 + - - +
587B PHE* 5.1 2.7 - - - -
597B ARG* 3.1 34.4 + - + +
599B ASP* 4.3 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B PRO* 4.9 3.4 - - - -
358B THR* 3.6 18.3 - - - +
423B ASP 3.3 2.9 + - - +
424B LEU 3.2 21.4 + - - -
426B THR 3.6 1.0 - - - -
427B LYS* 1.3 88.7 - - - +
429B VAL* 1.3 71.1 + - - +
----------------------------------------------------------
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