Contacts of the helix formed by residues 300 - 320 (chain A) in PDB entry 2BZN
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 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A HIS* 3.7 4.7 - - - -
249A SER* 2.9 23.4 + - - -
250A GLU* 3.7 13.8 - - - +
298A LYS 3.9 2.1 + - - +
299A GLY* 1.3 73.1 - - - -
301A VAL* 1.3 64.1 + - - +
302A GLU* 3.3 7.6 + - + +
303A HIS* 3.4 38.6 + - + +
304A THR* 4.2 1.2 + - - -
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A MET* 3.8 28.7 - - - -
66A VAL* 3.6 26.9 - - + -
67A LEU* 4.2 3.6 - - + -
245A LEU* 3.9 18.2 - - + -
248A HIS* 3.4 32.6 - - + +
250A GLU* 2.8 28.0 + - - +
300A ASP* 1.3 70.8 - - - +
302A GLU* 1.3 67.7 + - - +
304A THR* 2.9 13.1 + - - -
305A ILE* 3.0 17.5 + - + +
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Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 4.1 20.2 - - + +
69A LYS* 6.0 2.1 - - - +
70A PHE* 3.7 18.8 - - + -
250A GLU* 4.9 0.6 + - - +
300A ASP* 3.2 7.1 - - + +
301A VAL* 1.3 82.0 - - - +
303A HIS* 1.3 73.8 + - + +
305A ILE* 3.4 3.3 + - - +
306A ARG* 2.6 62.9 + - - +
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Residues in contact with HIS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LYS 5.7 2.0 - - - -
299A GLY* 6.0 0.2 - - - -
300A ASP* 3.4 37.3 + - + +
301A VAL 3.2 1.0 - - - -
302A GLU* 1.3 88.1 - - + +
304A THR* 1.3 62.1 + - - +
306A ARG* 3.6 10.9 + - - +
307A ASP* 3.1 22.7 + - - +
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Residues in contact with THR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A MET* 3.8 22.4 - - + +
245A LEU* 4.4 5.2 - - + -
248A HIS* 2.6 27.9 + - + +
298A LYS* 5.1 2.4 + - - +
300A ASP 4.2 0.7 + - - -
301A VAL 2.9 10.3 + - - -
303A HIS* 1.3 78.2 - - - +
305A ILE* 1.3 58.8 + - - +
307A ASP* 3.3 7.2 + - - +
308A ILE* 3.0 46.5 + - + +
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Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 6.1 0.4 - - + -
67A LEU* 3.8 27.4 - - + -
70A PHE* 3.7 39.7 - - + -
72A LEU* 3.9 21.8 - - + -
245A LEU* 3.8 28.9 - - + -
301A VAL* 3.0 15.8 + - + +
302A GLU* 3.7 8.3 - - - +
304A THR* 1.3 74.6 - - - +
306A ARG* 1.3 57.2 + - - +
308A ILE* 3.1 12.5 + - + +
309A LEU* 2.9 46.1 + - + +
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Residues in contact with ARG 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE* 3.8 25.1 - - + -
302A GLU* 2.6 49.1 + - - +
303A HIS* 3.8 11.2 + - - +
305A ILE* 1.3 76.7 - - - +
307A ASP* 1.3 56.9 + - - +
309A LEU* 4.2 4.8 - - - +
310A GLY* 2.9 27.9 + - - -
313A ARG* 5.4 0.7 + - - -
287C ALA* 5.7 1.4 - - - +
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Residues in contact with ASP 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A PRO* 3.5 24.9 - - - +
303A HIS 3.1 14.9 + - - +
304A THR* 3.5 10.3 - - + +
305A ILE 3.3 0.2 - - - -
306A ARG* 1.3 72.3 - - - +
308A ILE* 1.3 68.2 + - - +
310A GLY* 3.9 0.6 - - - -
311A GLY* 3.0 20.3 + - - -
191C LYS* 2.4 38.1 + - - +
287C ALA* 5.8 3.6 - - - +
288C SER* 5.1 3.6 + - - -
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Residues in contact with ILE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 4.0 17.0 - - + -
72A LEU* 6.3 0.4 - - + -
225A PRO* 4.0 13.7 - - + +
228A VAL* 4.5 13.0 - - + -
241A LEU* 3.9 23.8 - - + -
244A MET* 3.8 22.0 - - + -
245A LEU* 4.5 2.9 - - + -
304A THR* 3.0 37.8 + - + +
305A ILE* 3.1 18.8 + - + +
307A ASP* 1.3 77.7 - - - +
309A LEU* 1.3 63.0 + - + +
311A GLY* 3.3 2.4 + - - -
312A ILE* 3.0 41.8 + - + +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.6 15.3 - - + +
48A VAL* 3.8 28.5 - - + -
50A ILE* 4.0 17.7 - - + -
70A PHE* 4.1 25.1 - - + +
72A LEU* 4.3 6.7 - - + -
305A ILE* 2.9 36.5 + - + +
306A ARG* 4.2 3.4 - - - +
308A ILE* 1.3 77.4 - - + +
310A GLY* 1.3 58.2 + - - +
312A ILE* 3.3 3.7 + - + -
313A ARG* 2.8 61.1 + - - +
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Residues in contact with GLY 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ARG* 2.7 32.9 + - - -
306A ARG 2.9 17.9 + - - -
307A ASP 3.9 1.1 - - - -
309A LEU* 1.3 77.8 - - - +
311A GLY* 1.3 60.3 + - - +
313A ARG* 3.4 7.8 + - - +
314A SER* 3.1 13.9 + - - -
287C ALA* 4.5 12.1 - - - -
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Residues in contact with GLY 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A PRO* 4.4 1.3 - - - -
307A ASP 3.0 15.2 + - - -
308A ILE 3.7 3.4 - - - -
309A LEU 3.3 0.2 - - - -
310A GLY* 1.3 75.2 - - - +
312A ILE* 1.3 57.6 + - - +
314A SER* 3.4 1.5 + - - -
315A THR* 3.0 28.7 + - - -
191C LYS* 3.1 33.6 - - - +
192C THR* 3.6 7.7 - - - +
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Residues in contact with ILE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.8 22.2 - - + -
50A ILE* 3.8 12.6 - - + -
225A PRO 4.2 14.4 - - - +
228A VAL* 3.7 26.2 - - + -
229A ALA* 4.3 9.4 - - + +
232A PHE* 4.2 8.3 - - + -
308A ILE* 3.0 31.8 + - + +
309A LEU* 3.8 7.0 - - + +
311A GLY* 1.3 75.1 - - - +
313A ARG* 1.3 63.1 + - - +
315A THR* 3.2 7.8 + - - -
316A CYS* 3.0 23.7 + - - -
324A LEU* 4.2 18.2 - - + -
327A LEU* 4.7 6.1 - - + -
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Residues in contact with ARG 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ARG* 3.9 31.6 - - - +
28A SER* 5.4 3.8 - - - +
30A VAL* 3.8 32.4 + - + +
32A LEU* 3.6 32.7 - - + +
306A ARG 5.4 0.6 + - - -
309A LEU* 2.8 53.1 + - - +
310A GLY* 3.7 10.3 - - - +
311A GLY 3.4 0.2 - - - -
312A ILE* 1.3 72.0 - - - +
314A SER* 1.3 58.1 + - - +
316A CYS* 3.3 4.3 + - - +
317A THR* 2.9 30.8 + - - -
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Residues in contact with SER 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ARG* 2.9 34.3 + - - +
310A GLY 3.1 8.6 + - - -
311A GLY* 3.7 7.2 - - - -
313A ARG* 1.3 72.6 - - - +
315A THR* 1.3 56.5 + - - +
317A THR* 3.1 8.5 + - - -
318A TYR* 2.7 45.1 + - - -
192C THR* 3.8 7.6 - - - -
289C GLU* 3.5 23.3 + - - -
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Residues in contact with THR 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.9 24.2 - - + -
229A ALA* 3.4 22.1 - - + +
311A GLY 3.0 17.2 + - - -
312A ILE* 3.2 8.4 + - - -
314A SER* 1.3 77.6 - - - +
316A CYS* 1.3 62.4 + - - +
318A TYR* 3.2 2.6 + - - +
319A VAL* 3.0 24.8 + - + +
327A LEU* 4.1 9.9 - - + -
192C THR* 2.7 31.4 + - - +
194C VAL* 4.0 14.1 - - + -
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Residues in contact with CYS 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A VAL* 3.7 19.5 - - + -
32A LEU* 4.6 0.9 - - - -
312A ILE* 3.0 18.6 + - - +
313A ARG 3.4 8.5 - - - +
315A THR* 1.3 75.5 - - - +
317A THR* 1.3 58.0 + - - +
319A VAL* 3.3 7.4 + - - +
320A GLY 2.9 10.4 + - - -
321A ALA* 2.9 50.4 + - - +
324A LEU* 4.4 18.4 - - - -
327A LEU* 4.2 26.9 - - - -
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Residues in contact with THR 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER* 3.8 14.4 + - - +
24A LEU* 3.8 16.2 - - + +
26A SER 4.7 3.8 - - - +
27A ARG* 3.1 37.9 - - + +
30A VAL* 3.5 5.9 - - - +
313A ARG 2.9 14.1 + - - -
314A SER* 3.1 11.0 + - - -
316A CYS* 1.3 75.9 - - - +
318A TYR* 1.3 62.2 + - + +
320A GLY* 3.3 8.7 + - - -
132C ASN* 3.8 19.0 + - + +
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Residues in contact with TYR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO* 3.4 10.8 - - + +
20A LYS 2.9 28.6 + - - +
314A SER* 2.7 32.2 + - - +
315A THR 3.6 4.9 - - - +
317A THR* 1.3 74.5 - - + +
319A VAL* 1.3 57.2 + - + +
131C ALA* 3.7 37.7 + - + +
132C ASN* 3.8 29.6 - - + +
180C ILE* 4.3 13.1 - - + +
188C THR* 3.8 20.5 + - + +
192C THR* 4.1 6.1 - - + -
194C VAL* 3.8 33.7 - - + -
289C GLU* 2.7 35.6 + - - -
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Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 4.4 23.8 - - + -
18A ARG 3.5 22.0 - - - +
20A LYS* 3.8 21.3 - - + +
21A ARG 4.8 0.5 - - - +
315A THR* 3.0 20.7 + - + +
316A CYS 3.6 7.0 - - - +
318A TYR* 1.3 80.8 - - + +
320A GLY* 1.3 57.5 + - - +
321A ALA* 3.9 10.8 - - + +
327A LEU* 3.7 22.9 - - + -
330A ARG* 3.6 38.3 + - + +
331A THR* 5.3 0.9 - - - -
194C VAL* 4.8 0.9 - - + -
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Residues in contact with GLY 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG 4.6 2.5 - - - -
22A SER* 3.3 30.4 - - - -
24A LEU* 3.9 12.5 - - - +
316A CYS 2.9 5.4 + - - -
317A THR 3.3 6.8 + - - -
318A TYR 3.4 0.4 - - - -
319A VAL* 1.3 78.7 - - - +
321A ALA* 1.3 61.1 + - - +
322A ALA 3.6 2.5 + - - -
330A ARG* 3.0 24.6 + - - -
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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
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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