Contacts of the helix formed by residues 258 - 268 (chain A) in PDB entry 1Z16
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 ASN 258 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TYR* 3.0 26.9 + - - +
253A ASP 5.1 0.4 - - - +
255A VAL* 2.9 23.2 + - - +
257A ALA* 1.3 80.3 - - - +
259A LYS* 1.3 64.9 + - - +
260A PRO* 3.3 4.7 - - - -
261A ILE* 3.1 20.0 + - + +
262A VAL* 3.1 14.7 + - + +
278A TRP* 3.8 20.9 - - + -
312A VAL* 2.9 49.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ASP 5.6 0.9 - - - -
255A VAL 3.8 2.7 + - - +
256A PRO* 3.0 17.9 + - + +
258A ASN* 1.3 77.6 - - - +
260A PRO* 1.3 83.6 - - + +
262A VAL* 3.1 10.4 + - + +
263A ASP* 2.9 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PRO 4.4 0.9 - - - +
257A ALA 3.5 14.4 - - - +
258A ASN* 3.3 5.8 - - - -
259A LYS* 1.3 110.7 - - + +
261A ILE* 1.3 59.0 + - + +
263A ASP* 3.6 6.1 + - + +
264A ALA* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLN* 4.2 5.4 - - + -
32A ASP* 4.3 6.1 - - - +
257A ALA 5.5 1.1 - - - +
258A ASN* 3.1 18.6 + - - +
260A PRO* 1.3 77.6 - - + +
262A VAL* 1.3 67.6 + - - +
264A ALA* 3.2 6.3 + - - +
265A ILE* 3.0 37.6 + - + +
278A TRP* 3.7 20.0 - - + -
281A TYR* 3.8 36.6 - - + +
312A VAL* 3.4 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ASP* 3.5 30.5 - - + +
258A ASN 3.1 14.9 + - - +
259A LYS* 3.5 10.5 - - + +
261A ILE* 1.3 77.3 - - - +
263A ASP* 1.3 62.5 + - - +
265A ILE* 3.2 1.9 + - - +
266A LYS* 2.9 49.1 + - + +
272A PRO* 4.0 17.4 - - + +
278A TRP* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LYS* 2.9 48.0 + - - +
260A PRO* 3.8 6.2 - - + +
262A VAL* 1.3 80.9 - - - +
264A ALA* 1.3 58.2 + - - +
266A LYS* 3.3 9.5 + - - +
267A ALA* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLN* 3.7 28.0 - - - +
260A PRO 3.1 19.6 + - - +
261A ILE* 3.6 5.8 - - - +
263A ASP* 1.3 76.0 - - - +
265A ILE* 1.3 62.1 + - - +
267A ALA* 3.4 14.9 + - - +
268A LYS* 3.5 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 3.8 15.9 - - + +
25A GLY* 5.4 0.2 - - - -
28A GLN* 4.0 25.4 - - + +
261A ILE* 3.0 34.9 + - + +
262A VAL 3.7 3.1 - - - +
264A ALA* 1.3 74.4 - - - +
266A LYS* 1.3 65.1 + - - +
268A LYS* 3.1 18.6 + - - +
270A GLN* 3.1 48.7 + - + +
272A PRO* 3.7 22.9 - - + -
277A VAL* 3.9 26.2 - - + -
278A TRP* 5.0 0.9 - - + -
281A TYR* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A VAL* 2.9 39.1 + - + +
263A ASP* 3.8 9.9 - - - +
265A ILE* 1.3 75.2 - - - +
267A ALA* 1.3 57.5 + - - +
269A LYS* 2.9 40.4 + - - +
270A GLN 3.9 7.6 - - - +
272A PRO* 3.9 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASP 2.9 17.4 + - - +
264A ALA* 3.5 11.2 - - - +
265A ILE 3.2 0.2 - - - -
266A LYS* 1.3 76.9 - - - +
268A LYS* 1.3 59.4 + - + +
269A LYS* 3.2 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 4.6 11.5 + - - +
28A GLN* 2.9 42.6 + - - +
31A ALA* 5.5 3.8 - - - +
264A ALA 3.7 11.0 - - - +
265A ILE* 3.1 10.4 + - - +
266A LYS 3.1 1.0 - - - -
267A ALA* 1.3 78.2 - - + +
269A LYS* 1.3 70.8 + - - +
270A GLN* 3.2 36.7 + - - +
----------------------------------------------------------
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