Contacts of the helix formed by residues 300 - 320 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248E HIS* 3.8 4.8 - - - -
249E SER* 3.0 23.0 + - - -
250E GLU* 3.6 13.7 - - - +
298E LYS 3.9 2.5 + - - +
299E GLY* 1.3 71.4 - - - -
301E VAL* 1.3 65.4 + - - +
302E GLU* 3.1 11.2 + - + +
303E HIS* 3.4 18.3 + - + +
304E THR* 4.2 0.7 + - - -
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Residues in contact with VAL 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E MET* 3.8 27.6 - - - -
66E VAL* 3.7 22.4 - - + -
67E LEU* 4.4 2.2 - - + -
245E LEU* 3.9 18.6 - - + -
248E HIS* 3.3 33.4 - - + +
250E GLU* 2.9 33.4 + - + +
299E GLY 3.6 1.2 + - - -
300E ASP* 1.3 70.5 - - - +
302E GLU* 1.3 67.5 + - - +
304E THR* 2.9 13.5 + - - -
305E ILE* 3.0 17.0 + - + +
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Residues in contact with GLU 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E VAL* 4.2 16.1 - - + +
69E LYS* 6.6 0.4 - - - -
70E PHE* 3.4 24.9 - - + -
250E GLU* 4.8 0.8 + - - +
300E ASP* 3.1 9.8 - - + +
301E VAL* 1.3 80.6 - - - +
303E HIS* 1.3 63.4 + - - +
305E ILE* 3.4 3.0 + - - +
306E ARG* 3.1 55.0 + - - +
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Residues in contact with HIS 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LYS* 5.7 7.1 + - - -
298E LYS 6.2 0.2 - - - +
300E ASP* 3.4 13.4 + - + +
301E VAL 3.1 0.4 - - - -
302E GLU* 1.3 81.2 - - - +
304E THR* 1.3 61.0 + - - +
306E ARG* 3.5 12.0 + - + +
307E ASP* 3.0 33.3 + - + +
272G GLU* 4.6 19.1 + - - -
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Residues in contact with THR 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E MET* 3.6 26.2 - - + +
245E LEU* 4.4 5.2 - - + -
248E HIS* 2.6 30.1 + - + +
298E LYS* 4.9 4.2 - - + +
300E ASP 4.8 0.5 + - - -
301E VAL* 2.9 8.0 + - - -
303E HIS* 1.3 79.6 + - - +
305E ILE* 1.3 60.6 + - - +
307E ASP* 3.1 10.0 + - + +
308E ILE* 2.9 50.1 + - + +
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Residues in contact with ILE 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E ILE* 6.3 0.4 - - + -
66E VAL* 5.1 0.2 - - + -
67E LEU* 3.9 25.6 - - + -
70E PHE* 3.7 35.4 - - + -
72E LEU* 4.3 20.4 - - + -
245E LEU* 3.8 28.9 - - + -
301E VAL* 3.0 20.1 + - + +
302E GLU* 3.7 8.5 - - - +
304E THR* 1.3 76.0 - - - +
306E ARG* 1.3 54.0 + - - +
308E ILE* 3.1 11.0 + - + +
309E LEU* 2.8 48.6 + - + +
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Residues in contact with ARG 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E PHE* 3.9 26.1 - - + -
302E GLU* 3.1 46.3 + - - +
303E HIS* 3.7 9.6 - - + +
305E ILE* 1.3 81.6 - - - +
307E ASP* 1.3 56.8 + - - +
309E LEU* 4.3 4.7 - - - +
310E GLY* 3.0 27.0 + - - -
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Residues in contact with ASP 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E PRO* 3.7 22.9 - - - +
303E HIS* 3.0 23.4 + - + +
304E THR* 3.1 13.0 + - + +
306E ARG* 1.3 77.0 - - - +
308E ILE* 1.3 62.0 - - - +
310E GLY* 3.9 0.8 - - - -
311E GLY* 3.0 20.1 + - - -
191G LYS* 3.2 32.4 + - - +
287G ALA* 6.0 1.8 - - - +
288G SER 5.5 1.4 + - - -
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Residues in contact with ILE 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E ILE* 4.2 15.5 - - + -
72E LEU* 6.5 0.2 - - + -
225E PRO* 3.9 12.5 - - + +
228E VAL* 4.5 14.1 - - + -
241E LEU* 4.1 17.9 - - + -
244E MET* 3.8 27.8 - - + -
245E LEU* 4.6 2.9 - - + -
304E THR* 2.9 38.3 + - + +
305E ILE* 3.6 17.0 - - + +
307E ASP* 1.3 75.9 - - + +
309E LEU* 1.3 66.0 + - + +
311E GLY* 3.2 2.8 + - - -
312E ILE* 3.1 42.3 + - + +
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Residues in contact with LEU 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU* 3.6 14.6 - - + +
48E VAL* 4.0 18.8 - - + -
50E ILE* 3.9 27.1 - - + -
70E PHE* 4.2 19.7 - - + +
72E LEU* 4.2 14.4 - - + -
305E ILE* 2.8 40.7 + - + +
306E ARG* 4.3 4.0 - - - +
308E ILE* 1.3 73.6 - - + +
310E GLY* 1.3 58.4 + - - +
312E ILE* 3.4 2.0 + - + -
313E ARG* 3.0 57.4 + - - +
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Residues in contact with GLY 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ARG* 3.3 26.4 + - - -
306E ARG 3.0 17.9 + - - -
307E ASP 3.9 1.1 - - - -
309E LEU* 1.3 75.4 - - - +
311E GLY* 1.3 65.6 + - - +
313E ARG* 3.5 5.6 + - - +
314E SER* 3.1 25.5 + - - -
287G ALA* 4.4 10.5 - - - -
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Residues in contact with GLY 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E PRO* 4.3 2.0 - - - -
307E ASP 3.0 14.6 + - - -
308E ILE 3.2 3.1 + - - -
310E GLY* 1.3 77.2 - - - +
312E ILE* 1.3 55.8 + - - +
314E SER* 3.1 9.4 + - - -
315E THR* 2.9 26.6 + - - -
191G LYS* 3.2 32.1 - - - -
192G THR* 3.7 4.1 - - - +
287G ALA* 5.8 0.4 - - - -
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Residues in contact with ILE 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU* 3.8 22.2 - - + -
50E ILE* 4.0 12.3 - - + -
225E PRO 4.1 15.5 - - - +
228E VAL* 3.5 29.2 - - + -
229E ALA* 4.1 13.2 - - + +
232E PHE* 4.2 9.0 - - + -
308E ILE* 3.1 29.3 + - + +
309E LEU* 4.0 5.2 - - + +
311E GLY* 1.3 71.9 - - - +
313E ARG* 1.3 61.5 + - - +
315E THR* 3.1 8.6 + - - -
316E CYS* 2.9 29.8 + - - -
324E LEU* 4.3 16.2 - - + -
327E LEU* 4.9 2.7 - - + -
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Residues in contact with ARG 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ARG* 3.5 40.3 - - + +
28E SER* 4.3 11.5 + - - +
30E VAL* 3.5 31.7 + - + +
32E LEU* 3.6 30.7 - - + +
309E LEU* 3.0 46.2 + - - +
310E GLY* 3.8 7.2 - - - +
312E ILE* 1.3 75.7 - - - +
314E SER* 1.3 57.6 + - - +
316E CYS* 3.4 4.0 + - - +
317E THR* 2.9 29.5 + - - -
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Residues in contact with SER 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ARG* 2.7 33.2 + - - +
310E GLY 3.1 6.8 + - - -
311E GLY* 3.1 11.3 + - - -
313E ARG* 1.3 74.5 - - - +
315E THR* 1.3 65.4 + - - +
317E THR* 3.3 4.8 + - - -
318E TYR* 2.9 34.4 + - - -
192G THR* 3.8 8.1 - - - -
287G ALA* 4.7 4.0 - - - +
289G GLU* 3.6 23.8 + - - -
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Residues in contact with THR 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LEU* 3.9 25.1 - - + -
229E ALA* 3.4 22.9 - - + +
311E GLY 2.9 9.1 + - - -
312E ILE* 3.4 8.7 - - - -
314E SER* 1.3 75.5 - - - +
316E CYS* 1.3 64.0 + - - +
318E TYR* 3.3 1.6 + - - +
319E VAL* 3.2 23.4 + - - +
327E LEU* 4.3 9.4 - - + -
192G THR* 2.5 38.4 + - - +
194G VAL* 4.1 13.7 - - + -
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Residues in contact with CYS 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E VAL* 3.6 20.2 - - + -
32E LEU* 4.4 3.6 - - - -
312E ILE* 2.9 16.3 + - - -
313E ARG 3.6 8.5 - - - +
315E THR* 1.3 76.1 - - - +
317E THR* 1.3 54.8 + - - +
319E VAL* 3.4 8.1 + - - +
320E GLY 3.0 9.4 + - - -
321E ALA* 2.7 48.6 + - + +
324E LEU* 4.3 19.1 - - - -
327E LEU* 4.2 28.9 - - - -
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Residues in contact with THR 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E SER* 3.5 15.3 + - - +
24E LEU* 3.8 27.7 - - + +
26E SER 5.0 0.2 - - - -
27E ARG* 3.4 32.6 - - + +
30E VAL* 3.6 7.1 - - - +
313E ARG 2.9 14.6 + - - -
314E SER* 3.6 10.1 - - - -
316E CYS* 1.3 74.1 - - - +
318E TYR* 1.3 65.5 + - - +
319E VAL 3.2 0.5 + - - -
320E GLY* 3.3 8.5 + - - -
132G ASN* 3.8 17.7 + - + +
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Residues in contact with TYR 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E PRO* 3.3 10.8 - - + +
20E LYS 2.8 27.9 + - - +
314E SER* 2.9 32.4 + - - +
315E THR 3.7 4.5 - - - +
317E THR* 1.3 73.4 - - - +
319E VAL* 1.3 59.2 + - + +
320E GLY 3.5 0.2 - - - -
131G ALA* 3.8 34.3 + - + +
132G ASN* 3.8 29.5 - - + +
180G ILE* 4.2 16.1 - - + +
188G THR* 3.8 12.7 + - + +
192G THR* 4.1 13.9 - - + -
194G VAL* 3.8 35.2 - - + -
289G GLU* 2.7 37.6 + - - -
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Residues in contact with VAL 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E LEU* 4.1 24.7 - - + -
18E ARG 3.5 22.9 - - - +
20E LYS* 3.6 22.6 - - + +
21E ARG 4.7 0.3 - - - +
315E THR 3.2 20.3 + - - +
316E CYS* 3.6 7.9 - - - +
317E THR 3.1 0.8 - - - -
318E TYR* 1.3 79.4 - - + +
320E GLY* 1.3 58.4 + - - +
321E ALA* 4.1 8.3 - - + -
327E LEU* 3.6 24.2 - - + -
330E ARG* 3.7 35.6 + - + +
331E THR* 5.4 0.4 - - - -
194G VAL* 4.7 1.8 - - + -
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Residues in contact with GLY 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ARG 4.3 4.3 - - - -
22E SER* 3.4 30.5 - - - -
24E LEU* 4.2 8.5 - - - +
316E CYS 3.0 4.1 + - - -
317E THR 3.3 5.6 + - - -
318E TYR 3.5 0.4 - - - -
319E VAL* 1.3 79.3 - - - +
321E ALA* 1.3 59.9 + - - +
322E ALA 3.7 2.8 + - - -
326E GLU* 4.1 0.5 - - - +
330E ARG* 3.4 23.3 + - - -
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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
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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