Contacts of the helix formed by residues 266 - 281 (chain A) in PDB entry 1ZU4
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 266 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ASN 3.9 0.4 + - - -
265A ALA* 1.3 72.1 - - - +
267A PRO* 1.4 62.3 - - - +
268A ALA* 3.0 11.4 + - - +
269A SER* 2.7 40.2 + - - +
270A VAL* 3.8 2.4 + - - +
303A GLU* 2.6 34.9 - - - +
306A LYS* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA* 3.4 29.4 - - + +
234A THR* 3.8 17.9 - - + +
265A ALA 3.2 8.3 - - - +
266A ASP* 1.4 90.7 - - - +
268A ALA* 1.3 61.4 + - - +
270A VAL* 3.2 15.5 + - + +
271A VAL* 3.3 9.2 + - - +
291A ALA* 6.3 2.9 - - + -
299A ASN* 5.9 0.7 - - - +
303A GLU* 3.5 22.4 - - + +
307A MET* 3.4 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ASP* 3.0 14.7 + - - +
267A PRO* 1.3 78.1 - - - +
269A SER* 1.3 56.5 + - - +
271A VAL* 3.3 7.2 + - - -
272A PHE* 2.8 24.9 + - - +
303A GLU* 3.4 3.4 + - - +
306A LYS* 3.8 34.5 - - + -
307A MET* 4.2 8.0 - - + +
310A ILE* 3.5 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ALA* 4.3 8.8 - - - +
266A ASP* 2.7 33.7 + - - +
268A ALA* 1.3 78.9 - - - +
270A VAL* 1.3 58.9 + - - +
272A PHE* 3.3 9.5 + - - +
273A ASP* 3.0 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ALA* 4.3 6.1 - - + -
231A ALA 3.8 20.2 - - - +
232A ALA* 4.2 3.8 - - - +
234A THR* 3.9 19.3 - - + -
258A VAL* 3.7 26.8 - - + +
259A LYS* 4.1 7.6 - - - -
260A ALA* 3.9 32.3 - - + +
266A ASP 4.3 4.9 - - - +
267A PRO 3.2 9.6 + - - +
269A SER* 1.3 80.1 + - - +
271A VAL* 1.3 57.9 + - - +
273A ASP* 3.2 7.9 + - - +
274A ALA* 2.8 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ALA* 4.5 4.0 - - + -
232A ALA* 4.0 4.9 - - + -
267A PRO 3.3 8.5 + - - +
268A ALA 3.3 7.7 + - - +
270A VAL* 1.3 74.6 - - - +
272A PHE* 1.3 63.9 + - - +
274A ALA* 3.2 5.9 + - - +
275A ILE* 2.9 25.2 + - + +
286A LEU* 5.6 0.7 - - + -
288A ILE* 3.9 31.9 - - + -
307A MET* 3.7 35.9 - - + +
310A ILE* 4.1 10.5 - - + -
311A ILE* 3.7 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ALA 2.8 17.1 + - - +
269A SER* 3.4 13.2 - - - +
270A VAL 3.3 0.2 - - - -
271A VAL* 1.3 74.7 - - - +
273A ASP* 1.3 78.5 + - - +
275A ILE* 3.6 2.9 + - - +
276A LYS* 3.5 32.4 + - + +
310A ILE* 4.1 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 3.8 18.8 - - + +
259A LYS 5.0 5.9 - - - +
261A ASN* 5.3 6.4 + - - -
269A SER* 3.0 18.1 + - - +
270A VAL* 3.2 8.5 + - - +
272A PHE* 1.3 94.4 - - - +
274A ALA* 1.3 63.1 + - - +
276A LYS* 3.5 9.8 - - - +
277A LYS* 3.3 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 3.4 13.3 - - + +
230A ALA* 3.7 25.4 - - + -
258A VAL* 3.9 13.8 - - + +
270A VAL 2.8 19.7 + - - +
271A VAL* 3.8 3.4 - - - +
273A ASP* 1.3 71.8 - - - +
275A ILE* 1.3 58.9 + - - +
277A LYS 3.3 0.9 + - - -
278A ALA* 2.8 33.3 + - - +
286A LEU* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 4.1 10.8 - - + -
198A ILE* 3.7 27.1 - - + -
271A VAL 2.9 16.4 + - - +
272A PHE 4.2 3.4 - - - +
274A ALA* 1.3 75.3 - - - +
276A LYS* 1.3 60.2 + - + +
278A ALA* 3.8 1.5 - - - +
279A LYS* 3.0 31.7 + - + +
286A LEU* 3.9 12.1 - - + -
310A ILE* 4.3 14.6 - - + +
311A ILE* 3.6 28.7 - - + -
314A VAL* 3.7 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A PHE* 3.5 26.3 + - + +
273A ASP* 3.5 15.0 - - - +
275A ILE* 1.3 78.8 - - + +
277A LYS* 1.3 65.5 + - - +
279A LYS* 3.6 3.4 + - - +
280A GLU* 3.0 66.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 4.0 14.4 - - + -
256A ASP* 4.5 7.0 + - - -
257A LEU 5.5 2.2 - - - -
258A VAL* 3.7 21.5 - - + -
273A ASP 3.3 10.0 + - - +
274A ALA* 3.7 7.2 - - - +
276A LYS* 1.3 79.2 - - - +
278A ALA* 1.3 58.9 + - - +
280A GLU* 4.7 5.4 - - - -
281A GLN* 2.8 72.3 + - - +
283A TYR* 3.3 25.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 3.8 30.6 - - + +
228A LEU* 3.8 12.3 - - + -
274A ALA 2.8 21.7 + - - +
275A ILE* 3.8 3.8 - - - +
277A LYS* 1.3 72.8 - - - +
279A LYS* 1.3 62.5 + - - +
282A ASN* 3.5 3.5 + - - -
283A TYR* 3.1 42.4 + - + +
286A LEU* 4.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 4.2 6.8 - - + +
275A ILE* 3.0 18.1 + - + +
276A LYS* 3.9 4.0 - - - +
278A ALA* 1.3 78.1 - - - +
280A GLU* 1.3 64.9 + - + +
281A GLN 3.7 0.2 + - - -
282A ASN* 3.9 5.7 + - - -
313A GLN 6.0 0.2 - - - -
314A VAL* 3.5 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LYS* 3.0 62.8 + - - +
277A LYS* 3.3 4.2 + - - +
279A LYS* 1.3 83.9 - - + +
281A GLN* 1.3 67.9 + - + +
282A ASN* 3.4 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LYS* 2.8 34.8 + - - +
277A LYS* 2.8 51.5 + - - +
278A ALA 4.1 0.4 - - - -
280A GLU* 1.3 87.3 + - + +
282A ASN* 1.3 69.4 + - - +
283A TYR* 3.2 15.5 + - + -
----------------------------------------------------------
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