Contacts of the helix formed by residues 324 - 336 (chain A) in PDB entry 4ZZH
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 324 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A VAL 2.7 28.6 + - - -
267A SER* 3.3 25.1 - - - -
268A CYS* 3.7 5.1 - - - -
323A PRO* 1.3 76.7 - - - +
325A LEU* 1.3 65.3 + - - +
326A CYS* 3.1 19.4 + - - +
327A HIS* 3.0 13.7 + - - -
328A LYS* 3.1 24.0 + - - +
483A ASP* 3.7 5.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A SER* 1.3 73.7 - - - +
326A CYS* 1.3 51.5 + - - +
328A LYS* 3.3 14.3 + - + +
329A PHE* 2.8 31.2 + - - +
483A ASP* 3.7 24.9 + - + +
486A ILE* 3.9 12.6 - - + -
487A ASN* 3.4 46.2 - - + +
490A CYS* 4.8 3.1 - - - -
500A LEU* 3.4 44.6 - - + +
501A CYS* 5.0 0.2 - - - -
502A CYS* 4.9 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLY 5.3 0.2 - - - -
264A VAL* 3.6 27.4 - - + -
324A SER* 3.1 8.2 + - - +
325A LEU* 1.3 73.4 - - - +
327A HIS* 1.3 65.6 + - - +
329A PHE* 3.2 8.4 + - - +
330A ILE* 3.0 29.7 + - + +
439A ILE* 4.7 4.9 - - + +
482A CYS* 3.6 22.2 - - - -
483A ASP* 3.2 20.9 - - - -
486A ILE* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A VAL* 3.3 27.6 - - + +
265A SER* 3.3 24.0 + - - -
268A CYS* 4.0 1.6 - - - -
323A PRO* 3.7 17.5 - - + +
324A SER* 3.0 29.8 + - - +
326A CYS* 1.3 80.2 - - - +
328A LYS* 1.3 64.5 + - - +
330A ILE* 3.2 8.0 + - + +
331A ALA* 2.9 22.7 + - - +
342A ASN* 6.0 0.2 - - - -
346A ASN* 4.7 0.2 + - - -
350A LEU* 3.7 31.5 - - + +
351A GLU* 3.4 32.1 + - + -
354A ALA* 3.7 11.0 - - + -
356A ILE* 3.7 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLN* 4.8 10.4 + - - +
323A PRO* 2.7 39.0 + - + +
324A SER 3.1 9.6 + - - +
325A LEU* 3.3 19.7 - - + +
327A HIS* 1.3 77.5 - - - +
329A PHE* 1.3 62.1 + - - +
331A ALA* 3.3 8.8 + - - +
332A LEU* 3.0 24.4 + - - +
354A ALA* 5.1 4.3 - - + -
500A LEU* 4.1 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 4.2 30.7 - - + -
325A LEU 2.8 18.1 + - - +
326A CYS 3.2 8.9 + - - +
328A LYS* 1.3 72.9 - - - +
330A ILE* 1.3 70.2 + - + +
332A LEU* 3.3 16.9 + - - +
437A ILE* 5.3 8.3 - - + -
439A ILE* 4.9 7.6 - - + -
464A ILE* 6.2 0.4 - - + -
486A ILE* 3.5 35.2 - - + -
489A LEU* 5.4 5.4 - - + -
490A CYS* 3.6 23.6 - - - -
493A LEU* 3.7 15.7 - - + -
497A TYR* 3.6 30.3 - + - -
500A LEU* 4.1 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 4.0 17.5 - - + -
260A THR* 3.5 31.6 - - + -
264A VAL* 5.3 3.8 - - + -
326A CYS 3.0 17.1 + - - +
327A HIS* 3.6 8.7 - - + +
329A PHE* 1.3 85.2 - - + +
331A ALA* 1.3 63.4 + - - +
332A LEU 3.4 0.2 + - - -
334A ASP* 3.2 20.8 + - - +
339A LEU* 3.9 30.0 - - + +
342A ASN* 3.6 27.8 - - + +
356A ILE* 3.9 9.6 - - + -
439A ILE* 4.8 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A HIS 2.9 13.5 + - - +
328A LYS* 3.4 12.3 - - - +
330A ILE* 1.3 76.7 - - - +
332A LEU* 1.3 57.1 + - - +
334A ASP* 3.2 7.3 + - - +
335A LYS* 3.0 24.9 + - - +
354A ALA 3.5 24.7 - - - +
355A GLY 4.6 7.1 - - - +
356A ILE* 3.7 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LYS 3.0 15.4 + - - +
329A PHE* 3.3 12.9 + - - +
331A ALA* 1.3 81.0 - - - +
334A ASP 3.1 13.2 - - - -
335A LYS* 3.0 22.7 + - + +
336A GLU* 2.9 58.8 + - + +
496A GLU* 3.5 42.2 - - + +
497A TYR* 3.6 40.8 - - + +
500A LEU* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ILE 3.2 12.9 + - - +
331A ALA* 3.6 10.5 - - - +
332A LEU 3.1 22.2 + - - -
335A LYS* 1.3 68.5 + - - +
336A GLU* 3.2 3.3 - - - +
337A GLY* 3.3 12.2 + - - +
338A LYS* 4.8 3.0 - - - +
339A LEU* 3.6 47.2 + - + +
356A ILE* 4.0 2.2 - - + +
357A GLN* 3.2 20.7 + - - +
358A ARG* 2.8 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ALA 3.0 11.5 + - - +
332A LEU* 3.0 28.1 + - + +
334A ASP* 1.3 79.3 - - - +
336A GLU* 1.3 60.8 + - + +
337A GLY* 3.1 1.3 + - - -
357A GLN* 6.1 0.9 - - - -
496A GLU* 6.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 2.9 33.5 + - + +
334A ASP 3.2 0.6 - - - +
335A LYS* 1.3 78.6 - - + +
337A GLY* 1.3 60.4 + - - +
338A LYS* 3.3 27.7 + - + +
496A GLU* 4.2 13.3 - - - +
497A TYR* 2.9 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LYS* 3.4 12.7 - - - +
334A ASP* 3.3 10.9 + - - -
335A LYS 3.1 6.4 + - - -
336A GLU* 1.3 78.1 - - - +
338A LYS* 1.3 60.9 + - - +
339A LEU 3.6 5.6 - - - +
358A ARG* 6.5 0.2 - - - -
----------------------------------------------------------
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