Contacts of the helix formed by residues 230 - 245 (chain A) in PDB entry 1Z6Z
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 230 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP* 6.1 2.0 - - - -
228A LEU 3.6 4.2 + - - -
229A VAL* 1.3 77.2 - - - +
231A CYS* 1.3 66.2 + - - +
232A LYS* 2.7 40.4 + - - +
233A VAL* 3.1 20.6 + - + +
234A SER* 3.1 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY 4.3 3.4 - - - -
16A PHE* 3.9 22.3 - - + -
19A THR* 3.5 23.8 - - - +
198A LEU* 4.1 20.6 - - - -
199A ASP* 4.9 7.3 - - - +
200A THR* 3.7 29.6 - - - -
229A VAL 3.4 3.4 + - - -
230A ASP* 1.3 74.4 + - - +
232A LYS* 1.3 57.9 + - - +
234A SER* 3.4 1.7 + - - -
235A ALA* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR* 3.6 16.6 - - + +
23A LEU* 4.0 24.0 - - + -
230A ASP* 2.7 19.8 + - - +
231A CYS* 1.3 73.1 - - - +
233A VAL* 1.3 58.2 + - + +
235A ALA* 3.2 3.5 + - - +
236A GLN* 2.8 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 4.9 0.9 - - + -
230A ASP* 3.1 28.7 + - + +
232A LYS* 1.3 75.8 - - + +
234A SER* 1.3 62.4 + - - +
236A GLN* 3.3 12.1 + - - +
237A LYS* 3.1 20.8 + - - +
255A PHE* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.8 5.0 - - - -
193A TYR* 3.1 20.6 + - - -
195A PRO* 2.7 38.3 + - - +
198A LEU* 3.8 13.0 - - - -
229A VAL* 3.9 5.8 - - - -
230A ASP 3.1 13.9 + - - -
231A CYS 3.9 2.0 - - - -
233A VAL* 1.3 75.1 - - - +
235A ALA* 1.3 65.7 + - - +
237A LYS 3.1 2.4 + - - -
238A LEU* 3.0 19.9 + - - +
255A PHE* 3.9 11.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.6 17.6 - - + -
19A THR* 4.7 0.4 - - + -
20A LEU* 3.8 26.0 - - + +
23A LEU* 3.7 19.1 - - + -
231A CYS 2.8 23.2 + - - +
232A LYS 3.6 4.0 - - - +
234A SER* 1.3 71.2 - - - +
236A GLN* 1.3 63.3 + - - +
238A LEU* 3.2 4.8 + - - +
239A LEU* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.3 16.8 - - + -
232A LYS* 2.8 32.7 + - - +
233A VAL* 3.6 9.9 - - - +
234A SER 3.2 0.2 - - - -
235A ALA* 1.3 76.0 - - - +
237A LYS* 1.3 57.1 + - - +
239A LEU* 3.4 10.5 + - + +
240A SER* 2.9 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR* 3.5 18.4 - - + +
233A VAL 3.1 13.7 + - - +
234A SER 3.1 9.1 + - - +
236A GLN* 1.3 76.0 - - - +
238A LEU* 1.3 61.9 + - - +
240A SER* 3.2 13.2 + - - +
241A LEU* 2.9 44.0 + - + +
253A VAL* 5.1 1.2 - - - +
254A ASP 3.9 9.9 + - - -
255A PHE* 3.5 31.7 + - + -
257A ASP* 3.2 26.4 + - - +
258A LYS 5.0 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 4.2 8.5 - - + -
20A LEU* 4.1 28.9 - - + -
95A ILE* 4.8 7.4 - - + -
150A VAL* 4.2 10.1 - - + -
152A ILE* 4.1 20.4 - - + -
191A LEU* 3.7 28.3 - - + -
193A TYR* 3.8 27.9 + - + -
234A SER 3.0 8.2 + - - +
235A ALA* 3.2 8.9 + - - +
237A LYS* 1.3 76.1 - - - +
239A LEU* 1.3 58.5 + - + +
241A LEU* 3.2 12.4 + - - +
242A LEU* 3.0 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 4.9 6.2 - - + +
20A LEU* 4.0 14.6 - - + -
23A LEU* 3.8 32.3 - - + -
24A LEU* 3.8 29.2 - - + -
27A LEU* 4.0 29.9 - - + +
95A ILE* 5.9 0.7 - - + -
235A ALA 3.0 24.1 + - - +
236A GLN* 3.7 9.6 - - + +
238A LEU* 1.3 74.9 - - + +
240A SER* 1.3 58.6 + - - +
242A LEU* 3.1 17.6 + - + +
243A GLU* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLN 2.9 15.6 + - - -
237A LYS* 3.2 18.2 + - - +
239A LEU* 1.3 73.3 - - - +
241A LEU* 1.3 62.9 + - - +
243A GLU* 3.8 6.9 - - - +
244A LYS* 2.9 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LEU* 4.7 13.2 - - + -
193A TYR* 3.7 36.3 - - + -
237A LYS* 2.9 32.0 + - + +
238A LEU* 3.3 8.7 - - - +
240A SER* 1.3 79.7 + - - +
242A LEU* 1.3 56.7 + - - +
244A LYS* 4.0 6.0 - - + +
245A ASP* 3.0 25.6 + - - -
246A GLU 4.4 0.5 + - - -
247A PHE* 3.7 23.6 - - + +
253A VAL* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 4.6 7.0 - - + -
91A ARG* 3.9 25.4 + - - +
93A LEU* 4.1 28.9 - - + -
95A ILE* 4.9 4.0 - - + -
148A THR* 3.8 28.7 - - + -
150A VAL* 4.0 14.6 - - + -
191A LEU* 4.1 13.0 - - + -
238A LEU* 3.0 33.2 + - + +
239A LEU* 3.1 19.5 + - + +
241A LEU* 1.3 76.8 - - - +
243A GLU* 1.3 63.6 + - - +
245A ASP* 3.3 17.7 + - - +
247A PHE* 4.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A HIS* 4.4 31.0 - - + +
1A MET 6.1 0.2 - - - +
2A LEU* 4.7 9.8 - - + +
27A LEU* 6.4 1.1 - - + -
91A ARG* 4.8 4.2 + - - +
239A LEU 2.8 17.0 + - - +
240A SER* 3.8 7.4 - - - +
242A LEU* 1.3 78.8 - - - +
244A LYS* 1.3 62.1 + - + +
245A ASP* 3.4 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A SER* 2.9 28.8 + - - +
241A LEU* 4.1 5.6 - - + +
243A GLU* 1.3 79.1 - - + +
245A ASP* 1.3 67.6 + - - +
246A GLU* 3.2 23.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 5.2 2.3 + - - +
146A ASN* 3.1 27.4 + - - -
148A THR* 4.9 2.1 + - - -
189A ARG* 2.8 46.4 + - - +
241A LEU 3.0 14.8 + - - -
242A LEU 3.6 11.9 - - - +
243A GLU 3.2 3.7 - - - +
244A LYS* 1.3 79.0 - - - +
246A GLU* 1.3 58.3 + - - +
247A PHE* 3.9 10.8 - - - -
----------------------------------------------------------
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