Contacts of the helix formed by residues 333 - 346 (chain A) in PDB entry 1ZD4
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 333 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLY* 3.6 5.4 - - - -
265A PHE 2.9 25.3 + - - +
332A HIS* 1.3 93.9 - - + +
334A TRP* 1.3 74.3 + - - +
336A GLY 3.1 6.1 + - - -
337A MET 3.2 4.9 + - - -
356A LEU 3.6 4.6 + - - -
358A THR* 2.4 32.7 + - - +
498A LEU* 4.2 6.9 - - - +
523A HIS* 3.2 17.3 - - + -
700A NC6 2.6 48.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A HIS 5.0 0.4 - - - +
264A GLY* 4.0 6.5 - - - -
265A PHE* 3.6 18.2 - - + +
308A MET* 4.7 3.6 - - - -
333A ASP* 1.3 102.2 - - - +
335A GLY* 1.3 63.3 + - - +
337A MET* 2.9 30.9 + - + +
338A LEU* 2.8 20.8 + - - +
382A GLN* 5.7 0.4 - - - -
464A TRP* 3.1 66.3 - + + +
465A TYR* 3.2 48.4 - + - -
468A MET* 4.9 13.5 - - + -
471A ASN* 4.6 15.3 - - - -
700A NC6 3.6 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A CYS* 3.4 23.8 - - - -
263A HIS 3.5 9.8 + - - -
291A MET* 5.1 2.0 - - - -
331A GLY* 3.6 3.6 - - - -
332A HIS 2.7 20.7 + - - -
334A TRP* 1.3 72.7 - - - +
336A GLY* 1.3 62.4 - - - -
338A LEU* 2.8 18.6 + - - +
339A VAL* 2.9 15.6 + - - +
464A TRP* 5.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLY 3.6 4.9 - - - -
332A HIS 2.8 19.5 - - - +
333A ASP 3.1 6.6 + - - -
335A GLY* 1.3 74.1 - - - +
337A MET* 1.3 61.3 + - - +
339A VAL* 2.8 26.1 - - - +
340A TRP* 3.1 17.9 + - - -
355A SER* 3.5 19.7 - - - -
358A THR* 4.1 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A MET* 4.1 13.2 - - + -
333A ASP 3.2 7.9 + - - +
334A TRP* 2.9 39.2 + - + +
336A GLY* 1.3 75.9 - - - +
338A LEU* 1.3 60.0 + - - +
340A TRP* 3.2 12.4 + - - +
341A TYR* 3.2 48.2 - - + -
358A THR* 3.7 13.8 - - + +
359A PRO 5.3 5.8 - - - +
360A PHE* 6.3 0.9 - - - -
361A ILE 6.2 1.1 - - - +
471A ASN* 6.0 0.2 - - - +
700A NC6 3.6 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A CYS* 4.3 13.9 - - - -
291A MET* 4.0 16.4 - - + -
308A MET* 3.2 33.1 - - + -
311A LEU* 4.2 12.8 - - + +
312A CYS* 3.3 27.4 - - - +
315A MET* 4.4 10.3 - - + -
329A PHE* 4.6 2.0 - - + -
334A TRP 2.8 10.6 + - - +
335A GLY* 2.8 15.7 + - - +
337A MET* 1.3 77.7 - - - +
339A VAL* 1.3 66.8 + - + +
341A TYR* 3.3 3.6 + - - -
342A MET* 3.0 46.0 + - + +
464A TRP* 4.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A CYS* 4.3 5.8 - - - -
329A PHE* 3.5 26.2 - - + +
330A ILE 3.9 2.5 - - - +
331A GLY* 3.7 16.8 - - - +
335A GLY 2.9 14.0 + - - +
336A GLY* 2.8 33.0 - - - +
338A LEU* 1.3 80.3 - - + +
340A TRP* 1.3 65.9 + - + +
342A MET* 3.0 8.9 + - - +
343A ALA 3.0 18.7 + - - -
350A VAL* 5.3 0.2 - - - +
353A VAL* 3.5 30.7 - - + +
354A ALA 3.9 13.9 - - - +
355A SER* 4.6 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLY 3.1 20.0 + - - -
337A MET* 3.2 11.6 + - - +
339A VAL* 1.3 81.8 - - - +
341A TYR* 1.3 61.6 + - + +
343A ALA* 3.3 5.2 + - - +
344A LEU* 3.0 30.8 + - - +
353A VAL* 3.6 32.3 - - + -
355A SER* 3.3 25.4 - - - -
358A THR* 3.2 21.9 + - + -
359A PRO 4.2 2.5 - - - -
360A PHE* 3.6 38.7 - - + +
483A ILE* 4.0 10.0 - - + +
487A ALA* 4.1 13.7 - - + -
488A LEU 4.3 11.2 - - - -
489A MET* 4.2 4.9 - - - -
506A MET* 3.4 26.7 - - + -
510A ILE* 3.9 20.2 - - + -
513A LEU* 4.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A MET* 4.3 9.0 - - + -
312A CYS* 4.2 8.8 - - - -
337A MET* 3.2 43.3 + - + +
338A LEU 3.7 6.3 - - - +
339A VAL 3.2 0.4 - - - -
340A TRP* 1.3 77.8 - - + +
342A MET* 1.3 63.8 + - - +
344A LEU* 3.7 16.2 - - + +
345A PHE* 3.2 46.6 + + - +
360A PHE* 4.0 21.2 - + - -
361A ILE 4.0 17.2 + - - -
362A PRO* 4.8 0.2 - - - +
363A ALA* 4.7 4.5 + - - +
471A ASN 5.5 0.2 - - - -
474A TRP* 4.0 22.4 - + + -
475A ALA* 3.6 33.9 - - + +
478A SER* 4.6 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A CYS* 3.5 34.1 - - - +
315A MET* 4.0 10.3 - - + -
316A VAL* 4.0 22.9 - - + +
319A LEU* 4.9 2.7 - - + -
329A PHE* 3.7 36.1 - - + -
338A LEU* 3.0 37.0 + - + +
339A VAL* 3.0 12.9 + - - +
341A TYR* 1.3 76.6 - - - +
343A ALA* 1.3 59.8 + - - +
346A TYR* 2.8 46.1 + - + +
349A ARG* 5.3 0.9 - - + -
350A VAL* 3.6 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A VAL 3.0 11.5 + - - +
340A TRP* 3.5 5.4 - - - +
342A MET* 1.3 79.5 - - - +
344A LEU* 1.3 56.1 + - - +
347A PRO* 2.9 29.9 - - - +
350A VAL* 3.9 9.8 - - + +
353A VAL* 4.1 17.5 - - + -
483A ILE* 3.5 24.2 - - + +
485A ILE* 3.8 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A TRP 3.0 15.8 + - - +
341A TYR* 4.2 12.8 - - + -
342A MET 3.4 0.2 - - - -
343A ALA* 1.3 77.9 - - - +
345A PHE* 1.3 64.0 + - + +
347A PRO* 4.4 4.5 - - - +
360A PHE* 3.3 41.1 - - + -
478A SER* 3.7 22.7 - - - +
481A ARG* 2.7 59.3 + - + +
482A LYS* 4.6 2.5 - - - +
483A ILE* 3.5 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 3.2 51.9 + + - +
344A LEU* 1.3 82.2 - - + +
346A TYR* 1.3 87.7 + + + +
347A PRO* 3.4 8.2 - - - +
474A TRP* 3.4 64.4 - + - -
477A LYS* 4.7 5.4 - - + -
478A SER* 4.0 13.9 - - - -
481A ARG* 3.0 34.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLU 4.9 0.5 + - - -
312A CYS* 4.1 17.9 - - + -
313A LYS* 3.3 36.2 + - + +
316A VAL* 3.6 38.1 - - + -
341A TYR 4.5 0.7 - - - -
342A MET* 2.8 34.9 + - + +
345A PHE* 1.3 99.7 - + + +
347A PRO* 1.3 55.0 - - - +
348A GLU* 3.1 4.9 - - - -
349A ARG* 2.8 42.2 + - + +
350A VAL* 3.3 5.0 + - - +
474A TRP* 4.9 5.1 - + - -
----------------------------------------------------------
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