Contacts of the helix formed by residues 232 - 250 (chain A) in PDB entry 1ZXN
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 232 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 6.2 0.2 - - - +
76A THR* 4.8 7.0 - - - +
228A MET* 4.0 13.6 - - - +
230A SER* 2.8 19.2 + - - +
231A LEU* 1.3 76.3 - - - +
233A LYS* 1.3 67.0 + - - +
234A ASP* 3.6 8.2 + - - +
235A ILE* 3.2 24.4 + - - +
236A VAL* 2.9 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 5.5 4.9 - - - +
73A ARG* 5.7 1.1 - - - +
232A ASP* 1.3 76.9 - - + +
234A ASP* 1.3 56.9 + - - +
236A VAL* 3.0 7.9 + - - +
237A ALA* 2.6 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 2.5 33.6 + - - -
74A GLU 4.5 0.2 - - - +
75A VAL* 3.3 20.4 - - + +
76A THR* 2.9 38.6 + - - +
232A ASP* 3.4 7.6 + - - +
233A LYS* 1.3 74.5 - - - +
235A ILE* 1.3 66.3 + - - +
237A ALA* 2.9 7.7 + - - +
238A LEU* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 4.3 21.5 - - + +
78A VAL 4.6 2.5 - - - +
81A LEU* 4.0 14.4 - - + -
82A TYR* 4.0 35.7 - - + +
228A MET* 4.4 11.0 - - + -
231A LEU* 3.9 14.6 - - + -
232A ASP* 3.2 34.3 + - - +
234A ASP* 1.3 77.6 - - - +
236A VAL* 1.3 67.2 + - + +
238A LEU* 3.1 9.3 + - + +
239A MET* 3.0 49.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 5.4 6.5 - - - +
109A ILE* 4.5 18.4 - - + -
111A PRO* 4.2 13.7 - - + -
231A LEU* 3.4 27.4 - - + +
232A ASP 2.9 19.7 - - - +
233A LYS* 3.0 10.5 + - - +
235A ILE* 1.3 81.6 - - + +
237A ALA* 1.3 65.2 + - - +
239A MET* 3.9 7.3 - - - +
240A VAL* 3.0 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 3.7 22.0 - - + -
64A TYR 3.3 27.6 + - - +
65A ASP* 3.8 20.9 - - - +
73A ARG* 4.2 1.6 - - - +
233A LYS 2.6 17.4 + - - +
234A ASP* 2.9 12.5 + - - +
236A VAL* 1.3 76.1 - - - +
238A LEU* 1.3 61.5 + - - +
240A VAL* 4.7 0.4 - - - -
241A ARG* 3.1 17.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
61A MET* 3.7 26.0 - - - -
63A VAL* 3.6 16.8 - - + -
75A VAL* 3.6 26.9 - - + -
77A PHE* 4.7 14.4 - - + -
82A TYR* 4.1 27.8 - - + -
234A ASP 2.9 22.2 + - - +
235A ILE* 3.3 11.4 - - + +
237A ALA* 1.3 74.2 - - - +
239A MET* 1.3 66.4 + - - +
241A ARG* 3.1 28.3 + - - +
242A ARG* 3.1 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.5 14.8 - - + +
82A TYR* 5.2 3.4 - - + -
85A PHE* 3.4 50.7 - - + -
109A ILE* 3.7 22.0 - - + -
116A ILE* 3.9 28.3 - - + -
231A LEU* 4.7 11.4 - - + -
235A ILE* 3.0 44.3 + - + +
236A VAL* 3.9 3.6 - - - +
238A LEU* 1.3 77.1 - - + +
240A VAL* 1.3 58.6 + - - +
242A ARG* 2.8 22.7 + - - +
243A ALA* 3.1 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 3.7 34.5 - - + +
66A GLU* 5.1 10.3 - - - +
109A ILE* 4.2 11.4 - - + +
236A VAL* 3.0 34.9 + - + +
237A ALA* 3.9 4.0 - - - +
239A MET* 1.3 73.0 - - - +
241A ARG* 1.3 64.0 + - - +
243A ALA* 3.0 16.4 + - - +
244A TYR* 3.2 23.3 + - + -
257A LEU* 3.8 30.5 - - + -
258A ASN* 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A MET* 5.1 3.6 - - - +
62A TRP* 2.5 55.3 + - - +
63A VAL* 4.0 9.2 - - - +
64A TYR* 3.7 24.6 - - + +
70A ILE* 4.9 6.3 - - + -
82A TYR* 4.5 5.7 + - - -
237A ALA 3.1 6.5 + - - +
238A LEU* 3.1 26.4 + - - +
240A VAL* 1.3 77.3 - - - +
242A ARG* 1.3 70.4 + - - +
244A TYR* 3.2 9.0 + - + +
245A ASP* 2.7 67.5 + - - +
270A TYR* 5.9 0.9 - - + -
274A TYR* 4.0 12.8 + - + +
318A ALA* 4.4 9.1 - - - +
320A SER* 4.7 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 3.2 36.5 + - + -
85A PHE* 4.1 4.5 - - + -
86A ASP* 2.6 30.9 + - - +
89A LEU* 3.7 15.5 - - + +
90A VAL* 3.7 12.5 - - - +
238A LEU 3.1 9.5 + - - +
239A MET* 2.8 14.4 + - - +
241A ARG* 1.3 81.2 - - - +
243A ALA* 1.3 65.4 + - - +
245A ASP* 3.0 32.8 + - - +
246A ILE* 2.9 34.8 + - - +
313A PHE* 3.6 4.0 - - - -
316A SER 2.8 24.2 + - - -
318A ALA* 3.1 31.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 5.9 0.2 - - + -
89A LEU* 4.2 10.4 - - + +
107A VAL* 4.5 18.6 - - + -
239A MET 3.1 7.9 + - - +
240A VAL* 3.0 14.4 + - - +
242A ARG* 1.3 76.0 - - - +
244A TYR* 1.3 59.1 + - - +
246A ILE* 3.4 6.4 + - - +
247A ALA* 3.0 27.9 + - - +
255A VAL* 3.7 15.4 - - + +
257A LEU* 5.0 8.5 - - + -
262A LEU* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 3.3 35.5 + + + -
240A VAL* 3.2 40.2 + - + -
241A ARG* 3.2 12.9 + - + +
242A ARG 3.1 0.4 - - - -
243A ALA* 1.3 78.2 - - - +
245A ASP* 1.3 64.8 + - - +
247A ALA* 3.3 4.1 + - - +
248A GLY 3.0 17.7 + - - -
257A LEU* 4.9 0.9 - - + -
262A LEU* 3.4 37.5 - - + +
263A PRO* 3.9 25.6 - - + +
264A VAL* 3.8 9.8 - - + +
270A TYR* 3.4 20.2 - - + -
273A MET* 3.6 38.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
241A ARG* 2.7 53.1 + - - +
242A ARG* 3.0 28.0 + - - +
244A TYR* 1.3 76.8 - - - +
246A ILE* 1.3 52.2 + - - +
248A GLY* 2.9 3.3 + - - -
249A SER* 2.7 38.3 + - - -
270A TYR* 2.8 23.8 + - - -
313A PHE* 3.2 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.4 33.0 - - + +
90A VAL* 4.9 3.4 - - + -
93A ALA* 4.1 9.0 - - + -
105A ILE* 3.9 25.1 - - + -
242A ARG* 2.9 22.6 + - - +
243A ALA 3.6 7.2 - - - +
245A ASP* 1.3 77.5 - - - +
247A ALA* 1.3 63.1 + - - +
248A GLY 2.9 1.6 + - - -
249A SER* 3.0 2.6 + - - +
250A THR* 3.0 41.9 + - + +
255A VAL* 3.9 11.7 - - + -
316A SER* 3.8 36.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ALA 3.0 14.3 + - - +
244A TYR* 3.5 7.4 - - - +
245A ASP 3.3 0.2 - - - -
246A ILE* 1.3 76.3 - - - +
248A GLY* 1.3 58.3 + - - +
250A THR* 4.1 11.2 + - - +
253A VAL 4.6 7.7 - - - +
255A VAL* 3.3 32.3 - - + +
262A LEU* 4.6 4.7 - - + -
264A VAL* 3.4 34.7 - - + +
266A GLY 4.3 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TYR 3.0 6.8 + - - -
245A ASP 2.9 6.8 + - - -
247A ALA* 1.3 79.1 - - - +
249A SER* 1.3 59.8 + - - +
250A THR 3.6 3.6 - - - +
264A VAL* 3.6 15.7 - - - +
266A GLY 3.7 5.9 - - - -
267A PHE* 3.4 34.8 + - - +
270A TYR* 3.8 12.3 - - - -
313A PHE* 6.1 0.2 - - - -
365A ASN* 4.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASP 2.7 20.6 + - - -
246A ILE* 3.5 6.8 + - - +
248A GLY* 1.3 73.0 - - - +
250A THR* 1.3 63.0 + - - +
267A PHE* 4.9 0.2 - - - -
313A PHE* 4.2 16.7 - - - -
316A SER* 3.1 32.4 + - - -
365A ASN* 3.2 39.9 + - - +
367A LEU* 5.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 4.0 13.7 - - + +
96A LYS* 5.4 7.6 - - + -
102A MET* 6.1 0.4 - - + -
105A ILE* 5.4 0.9 - - + -
246A ILE* 3.0 35.0 + - + +
247A ALA* 4.1 10.6 + - - +
248A GLY 4.2 3.6 - - - +
249A SER* 1.3 80.4 - - - +
251A LYS* 1.3 60.8 + - - +
252A ASP 4.3 0.5 + - - -
253A VAL* 3.2 31.8 + - + +
266A GLY* 5.1 6.8 - - - -
316A SER* 3.4 23.1 - - - +
----------------------------------------------------------
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