Contacts of the helix formed by residues 323 - 334 (chain A) in PDB entry 5HKZ
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 PRO 323 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLN* 5.5 19.3 - - + +
322A LYS* 1.3 93.6 - - + +
324A LEU* 1.3 61.5 + - - +
325A PHE* 3.4 8.7 - - + +
326A GLN* 3.0 18.9 + - + +
327A ALA* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU 5.1 1.3 - - - +
261A LEU* 3.9 21.3 - - + -
293A PHE* 3.9 24.2 - - + -
303A TRP* 3.5 63.3 - - + +
305A ILE* 3.9 24.5 - - + -
319A PRO* 4.7 3.4 - - + -
322A LYS 3.9 1.2 + - - -
323A PRO* 1.3 69.0 - - - +
325A PHE* 1.3 68.9 + - - +
327A ALA* 3.0 6.3 + - + +
328A LEU* 2.9 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLN 5.2 6.3 - - - -
250A PRO* 5.9 2.5 - - + -
256A ARG 5.5 0.4 - - - -
257A ASN* 3.8 28.3 - - + -
260A SER* 3.8 24.0 - - - -
261A LEU* 3.6 33.3 - - + +
323A PRO* 4.6 6.9 - - + +
324A LEU* 1.3 78.3 - - - +
326A GLN* 1.3 56.7 + - - +
328A LEU* 3.4 1.9 + - - +
329A ILE* 3.0 38.4 + - + +
349A LEU* 3.7 53.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LYS* 4.2 9.9 - - + -
323A PRO* 3.0 27.9 + - + +
325A PHE* 1.3 77.8 - - - +
327A ALA* 1.3 62.2 + - - +
329A ILE* 4.0 19.4 - - - +
330A ASP* 2.8 67.5 + - - +
333A ARG* 4.4 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ILE* 4.1 14.6 - - + -
319A PRO* 3.9 29.4 - - + -
322A LYS* 4.0 18.9 - - + +
323A PRO 2.9 12.2 + - - +
324A LEU 3.0 8.3 + - - +
326A GLN* 1.3 75.4 - - - +
328A LEU* 1.3 58.1 + - - +
330A ASP* 4.0 0.7 - - - +
331A GLY* 2.8 26.5 + - - -
337A TYR* 3.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 4.0 9.0 - - + -
265A HIS* 4.2 5.2 - - - +
291A TYR* 3.6 33.4 + - + +
293A PHE* 4.1 22.9 - - + -
305A ILE* 4.3 12.3 - - + -
324A LEU* 2.9 38.2 + - + +
325A PHE 3.8 3.4 - - - +
327A ALA* 1.3 74.5 - - - +
329A ILE* 1.3 65.2 + - - +
331A GLY 3.9 0.5 - - - -
332A PHE* 3.0 24.4 + - - +
337A TYR* 4.2 16.6 - - + +
346A ASN* 5.4 1.0 + - - -
349A LEU* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PHE* 3.0 30.0 + - + +
326A GLN* 3.3 15.9 + - - +
328A LEU* 1.3 75.7 - - - +
330A ASP* 1.3 68.5 + - - +
332A PHE* 3.1 7.3 + - - +
333A ARG* 3.0 65.4 + - - +
349A LEU* 3.8 39.3 - - + +
350A THR* 4.5 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LYS* 2.7 37.6 + - - +
326A GLN* 2.8 51.2 + - - +
327A ALA 4.0 2.0 - - - +
329A ILE* 1.3 74.9 - - - +
331A GLY* 1.3 57.5 + - - +
333A ARG* 3.2 12.2 + - - +
334A GLU* 2.9 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ALA 2.8 15.7 + - - -
328A LEU 3.9 0.2 - - - -
330A ASP* 1.3 73.8 - - - +
332A PHE* 1.3 58.2 + - - +
334A GLU* 3.8 3.8 - - - -
335A GLY 3.2 2.4 + - - -
336A PHE* 2.8 38.1 + - - -
337A TYR* 3.0 32.4 + - - -
59B PRO* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LEU 3.0 16.3 + - - +
329A ILE* 3.6 5.8 - - - +
331A GLY* 1.3 77.7 - - - +
333A ARG* 1.3 73.6 + - + +
335A GLY* 3.1 9.9 + - - -
337A TYR 3.3 20.1 + - - +
338A LEU* 3.7 30.7 - - + +
346A ASN* 3.3 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLN* 4.4 5.5 - - - +
329A ILE* 3.0 42.4 + - - +
330A ASP* 3.2 14.1 + - - +
332A PHE* 1.3 86.9 - - + +
334A GLU* 1.3 61.6 + - + +
335A GLY 3.6 0.3 + - - -
350A THR* 4.3 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LYS* 5.0 3.6 + - - -
330A ASP* 2.9 35.4 + - - +
331A GLY* 5.3 0.4 - - - -
333A ARG* 1.3 78.8 - - + +
335A GLY* 1.3 60.2 + - - +
336A PHE* 3.5 40.4 + - + -
59B PRO 4.3 7.4 - - - +
----------------------------------------------------------
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