Contacts of the helix formed by residues 232 - 250 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 5.6 3.3 - - - +
76B THR 4.5 5.8 - - - +
77B PHE* 5.9 0.3 - - - -
228B MET* 3.4 20.6 - - - +
230B SER* 2.9 15.6 + - - +
231B LEU* 1.3 78.3 - - - +
233B LYS* 1.3 65.4 + - + +
234B ASP* 3.3 11.1 + - - +
235B ILE* 3.0 26.3 + - - +
236B VAL* 3.1 20.3 + - - +
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Residues in contact with LYS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP* 3.8 26.7 + - - +
66B GLU 5.9 1.8 - - - +
73B ARG* 4.3 10.2 - - - +
232B ASP* 1.3 77.4 - - + +
234B ASP* 1.3 63.2 + - - +
236B VAL* 3.4 4.7 + - - +
237B ALA* 2.9 30.9 + - + +
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Residues in contact with ASP 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 5.1 0.2 - - - +
73B ARG* 2.6 35.3 + - - +
74B GLU 4.4 0.2 - - - +
75B VAL* 3.5 15.7 - - + +
76B THR* 2.8 46.7 + - - +
232B ASP* 3.3 7.4 + - - +
233B LYS* 1.3 81.8 - - - +
235B ILE* 1.3 64.5 + - - +
237B ALA* 3.1 16.1 + - - +
238B LEU* 3.1 13.0 + - - +
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Residues in contact with ILE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B THR 4.7 0.2 + - - -
77B PHE* 4.0 23.1 - - + -
78B VAL 5.0 1.3 - - - +
81B LEU* 3.7 27.4 - - + -
82B TYR* 4.4 22.2 - - + -
228B MET* 4.9 5.6 - - + -
231B LEU* 4.0 28.9 - - + -
232B ASP* 3.0 22.1 + - - +
234B ASP* 1.3 77.2 - - - +
236B VAL* 1.3 62.3 + - + +
238B LEU* 3.4 10.1 + - + +
239B MET* 3.0 41.5 + - + +
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 4.3 12.3 - - + -
111B PRO* 4.2 16.6 - - + -
231B LEU* 3.7 26.9 - - + +
232B ASP 3.1 20.2 + - - +
233B LYS* 3.8 4.5 - - - +
234B ASP 3.2 0.8 - - - -
235B ILE* 1.3 76.8 - - - +
237B ALA* 1.3 61.5 + - - +
239B MET* 3.7 15.1 - - + +
240B VAL* 2.8 49.0 + - + +
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Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 3.7 19.5 - - + -
64B TYR 3.0 36.3 + - - +
65B ASP* 3.6 24.0 - - - +
73B ARG* 4.5 0.7 - - - +
233B LYS* 2.9 17.7 + - + +
234B ASP* 3.1 8.0 + - - +
236B VAL* 1.3 77.1 - - - +
238B LEU* 1.3 57.1 + - - +
240B VAL* 3.6 0.8 + - - -
241B ARG* 3.1 14.7 + - - +
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B MET* 3.8 28.5 - - + -
62B TRP 4.3 2.9 - - - +
63B VAL* 4.2 8.0 - - + +
75B VAL* 5.5 1.8 - - + -
77B PHE* 3.9 34.3 - - + -
82B TYR* 3.4 36.8 - - + -
234B ASP 3.1 10.3 + - - +
235B ILE* 3.6 10.8 - - + +
236B VAL 3.1 0.2 - - - -
237B ALA* 1.3 77.5 - - - +
239B MET* 1.3 64.9 + - - +
240B VAL 3.1 0.2 - - - -
241B ARG* 3.2 25.4 + - - +
242B ARG* 3.1 23.7 + - - +
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Residues in contact with MET 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 5.5 4.5 - - - -
82B TYR* 5.6 2.7 - - + -
85B PHE* 3.6 55.4 - - + -
109B ILE* 3.3 40.4 - - + +
116B ILE* 3.8 14.4 - - + -
231B LEU* 4.2 8.1 - - + -
235B ILE* 3.0 34.3 + - + +
236B VAL* 3.3 18.1 + - + +
238B LEU* 1.3 76.9 - - - +
240B VAL* 1.3 63.5 + - - +
242B ARG* 3.3 12.7 + - - +
243B ALA* 3.3 10.2 + - - +
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.9 22.7 - - + +
109B ILE* 3.8 20.4 - - + -
236B VAL* 2.8 36.0 + - + +
237B ALA* 3.9 4.9 - - - +
239B MET* 1.3 76.3 - - - +
241B ARG* 1.3 63.9 + - - +
243B ALA* 3.2 13.3 + - - +
244B TYR* 3.2 28.8 + - + -
257B LEU* 3.6 28.7 - - + -
258B ASN* 6.3 0.4 - - - +
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B MET* 5.1 3.8 - - - +
62B TRP* 2.7 48.0 + - - +
63B VAL* 3.9 9.0 - - - -
64B TYR* 3.7 11.2 - - + +
70B ILE* 3.8 19.5 - - + -
82B TYR* 4.9 1.2 + - - -
237B ALA 3.1 17.7 + - - +
238B LEU* 3.2 21.8 + - - +
240B VAL* 1.3 74.9 - - - +
242B ARG* 1.3 75.7 + - - +
244B TYR* 3.1 6.6 + - + +
245B ASP* 2.8 64.0 + - - +
270B TYR* 5.3 0.2 - - - -
274B TYR* 3.9 17.7 + - - -
313B PHE* 5.4 0.8 - - - -
318B ALA* 4.0 13.7 - - - +
320B SER* 5.1 8.1 + - - -
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Residues in contact with ARG 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 3.2 31.0 + - + -
85B PHE* 4.0 7.4 - - + -
86B ASP* 2.8 27.3 + - - +
89B LEU* 3.6 16.5 - - + +
90B VAL* 3.9 10.5 - - - +
238B LEU 3.1 17.5 + - - +
239B MET 3.5 9.0 - - - +
241B ARG* 1.3 84.3 - - - +
243B ALA* 1.3 64.7 + - - +
245B ASP* 2.9 46.2 + - - +
246B ILE* 2.8 37.5 + - - +
313B PHE* 4.2 2.2 - - - -
316B SER 2.7 29.7 + - - -
318B ALA* 3.8 18.8 - - - +
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Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 5.9 0.2 - - + -
89B LEU* 4.2 5.3 - - + +
107B VAL* 4.8 13.7 - - + -
239B MET 3.3 6.6 + - - +
240B VAL* 3.2 16.5 + - - +
242B ARG* 1.3 80.8 - - - +
244B TYR* 1.3 62.4 + - + +
246B ILE* 3.3 9.5 + - - +
247B ALA 3.2 15.6 + - - -
255B VAL* 3.6 17.2 - - + +
257B LEU* 4.8 15.9 - - + -
262B LEU* 3.6 15.8 - - + +
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Residues in contact with TYR 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.1 49.4 + + + -
70B ILE* 5.8 0.7 - - + -
240B VAL* 3.2 32.4 + - + -
241B ARG* 3.1 11.0 + - + +
243B ALA* 1.3 78.0 - - + +
245B ASP* 1.3 65.2 + - - +
247B ALA* 3.0 6.0 + - - +
248B GLY 2.9 18.5 + - - -
257B LEU* 4.8 1.4 - - + +
262B LEU* 3.4 42.7 - - + +
263B PRO* 4.3 15.6 - - + +
264B VAL* 3.8 13.3 - - + +
270B TYR* 3.6 18.4 - - + -
273B MET* 3.5 33.9 - - + -
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Residues in contact with ASP 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B ARG* 2.8 57.5 + - - +
242B ARG* 2.9 37.5 + - - +
244B TYR* 1.3 77.0 - - - +
246B ILE* 1.3 51.9 + - - +
248B GLY* 3.1 3.1 + - - -
249B SER* 2.8 38.4 + - - -
270B TYR* 2.5 37.5 + - - -
313B PHE* 3.7 16.3 - - + -
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Residues in contact with ILE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 3.3 40.4 - - + +
90B VAL* 5.1 0.9 - - - +
93B ALA* 4.5 11.4 - - + -
105B ILE* 4.6 12.6 - - + -
242B ARG* 2.8 39.4 + - - +
243B ALA* 3.6 7.9 - - - +
245B ASP* 1.3 75.8 - - - +
247B ALA* 1.3 58.4 + - - +
249B SER* 3.7 3.8 - - - -
250B THR* 2.7 51.6 + - + +
255B VAL* 4.1 14.4 - - + -
316B SER* 4.2 20.2 - - - +
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B ALA 3.2 9.8 + - - +
244B TYR* 3.0 12.7 + - - +
246B ILE* 1.3 80.0 - - - +
248B GLY* 1.3 61.3 + - - +
250B THR* 3.9 10.9 + - - +
253B VAL 4.5 7.0 - - - +
255B VAL* 3.7 24.4 - - + +
262B LEU* 4.5 6.7 - - + +
264B VAL* 3.7 30.5 - - + +
266B GLY 3.9 14.9 + - - -
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Residues in contact with GLY 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B TYR 2.9 11.5 + - - -
245B ASP 3.5 2.7 - - - -
247B ALA* 1.3 79.6 - - - +
249B SER* 1.3 57.7 + - - +
250B THR 4.6 1.2 - - - +
264B VAL* 3.8 4.6 - - - +
266B GLY* 3.5 3.6 - - - -
267B PHE* 3.0 36.7 + - - +
270B TYR* 3.6 29.2 - - - -
365B ASN* 4.4 0.9 + - - -
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Residues in contact with SER 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ASP 2.8 28.8 + - - -
246B ILE* 3.7 3.3 - - - -
248B GLY* 1.3 74.0 - - - +
250B THR* 1.3 62.7 + - - +
251B LYS 4.0 0.3 + - - -
313B PHE* 4.2 18.5 - - - -
316B SER* 3.0 29.6 + - - -
365B ASN* 3.0 42.3 + - - +
367B LEU* 5.9 2.9 - - - +
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Residues in contact with THR 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ALA* 3.8 25.6 - - + +
96B LYS* 5.3 5.8 - - + -
102B MET* 5.6 0.9 - - + -
246B ILE* 2.7 31.0 + - + +
247B ALA 3.9 9.5 - - - +
248B GLY 4.6 1.7 - - - +
249B SER* 1.3 78.6 - - - +
251B LYS* 1.3 62.4 + - - +
252B ASP 3.8 1.6 + - - -
253B VAL* 3.2 38.0 + - + +
266B GLY* 5.1 6.1 + - - -
316B SER* 3.5 19.3 - - - +
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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) + - + + + + + -
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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