Contacts of the helix formed by residues 300 - 320 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B HIS* 3.8 4.6 - - - -
249B SER* 3.0 20.4 + - - -
250B GLU* 3.7 14.1 - - - +
298B LYS 3.9 2.5 + - - +
299B GLY* 1.3 73.9 - - - -
301B VAL* 1.3 65.2 + - - +
302B GLU* 3.3 8.5 + - + +
303B HIS* 3.4 42.0 + - + +
304B THR* 4.1 1.6 + - - -
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B MET* 3.9 28.9 - - - -
66B VAL* 3.7 25.6 - - + -
67B LEU* 4.1 4.7 - - + -
245B LEU* 4.0 15.7 - - + -
248B HIS* 3.4 36.8 - - + +
250B GLU* 2.9 27.9 + - + +
299B GLY 3.6 0.6 + - - -
300B ASP* 1.3 70.6 - - - +
302B GLU* 1.3 68.5 + - - +
304B THR* 2.8 13.4 + - - -
305B ILE* 2.9 16.7 + - + +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 4.1 20.4 - - + +
70B PHE* 3.9 18.1 - - + -
250B GLU* 4.9 0.8 + - - +
300B ASP* 3.2 6.3 - - + +
301B VAL* 1.3 80.8 - - - +
303B HIS* 1.3 84.3 + - + +
305B ILE* 3.2 5.6 + - - +
306B ARG* 3.0 55.5 + - - +
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Residues in contact with HIS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B LYS 5.8 1.6 - - - -
300B ASP* 3.4 35.8 + - + +
301B VAL 3.1 0.6 - - - -
302B GLU* 1.3 97.0 - - + +
304B THR* 1.3 62.7 + - - +
306B ARG* 3.6 10.7 + - - +
307B ASP* 3.1 32.3 + - - +
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Residues in contact with THR 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B MET* 3.8 21.1 - - + +
245B LEU* 4.5 6.1 - - + -
248B HIS* 2.6 28.9 + - + +
298B LYS* 5.1 2.1 + - - +
300B ASP 4.1 1.3 + - - -
301B VAL* 2.8 11.3 + - - -
303B HIS* 1.3 76.6 - - - +
305B ILE* 1.3 56.8 + - - +
307B ASP* 3.1 10.9 + - + +
308B ILE* 2.8 48.9 + - + +
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Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 5.2 0.2 - - + -
67B LEU* 3.9 27.4 - - + -
70B PHE* 3.6 39.3 - - + -
72B LEU* 4.2 21.3 - - + -
245B LEU* 3.9 28.7 - - + -
301B VAL* 2.9 21.9 + - + +
302B GLU* 3.2 9.2 + - - +
304B THR* 1.3 74.7 - - - +
306B ARG* 1.3 57.7 + - - +
308B ILE* 3.2 10.1 + - + +
309B LEU* 2.9 46.5 + - + +
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Residues in contact with ARG 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 3.7 27.6 - - + -
302B GLU* 3.0 44.8 + - - +
303B HIS* 3.8 12.5 + - - +
304B THR 3.3 0.2 - - - -
305B ILE* 1.3 74.9 - - - +
307B ASP* 1.3 62.7 + - - +
309B LEU* 4.1 5.1 - - - +
310B GLY* 2.8 28.6 + - - -
313B ARG* 5.3 0.6 + - - +
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Residues in contact with ASP 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LYS* 4.8 20.1 + - - +
272A GLU* 5.7 0.7 - - - +
287A ALA* 5.9 4.9 - - - +
225B PRO* 4.0 11.0 - - + +
303B HIS* 3.1 22.9 + - - +
304B THR* 3.1 12.0 + - + +
306B ARG* 1.3 77.4 - - - +
308B ILE* 1.3 63.5 + - + +
310B GLY* 3.9 0.6 - - - -
311B GLY* 3.0 20.1 + - - -
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Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 3.9 17.5 - - + -
225B PRO* 3.9 13.8 - - + +
228B VAL* 4.7 11.4 - - + -
241B LEU* 4.0 16.2 - - + -
244B MET* 3.5 32.3 - - + -
245B LEU* 4.5 7.9 - - + -
304B THR* 2.8 39.8 + - + +
305B ILE* 3.2 12.1 + - + +
307B ASP* 1.3 72.9 - - + +
309B LEU* 1.3 64.8 + - + +
311B GLY* 3.2 3.8 + - - -
312B ILE* 3.1 40.2 + - + +
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.6 19.8 - - + +
48B VAL* 4.1 15.3 - - + -
50B ILE* 4.1 25.6 - - + -
70B PHE* 4.1 19.3 - - + +
72B LEU* 4.3 13.2 - - + -
305B ILE* 2.9 42.8 + - + +
306B ARG* 4.1 4.3 - - - +
308B ILE* 1.3 72.7 - - + +
310B GLY* 1.3 57.6 + - - +
312B ILE* 3.2 4.3 + - + +
313B ARG* 2.9 58.6 + - - +
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Residues in contact with GLY 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ALA* 4.7 21.6 - - - +
306B ARG 2.8 18.5 + - - -
307B ASP* 3.9 1.1 - - - -
309B LEU* 1.3 73.6 - - - +
311B GLY* 1.3 62.7 + - - +
313B ARG* 3.7 13.7 + - - +
314B SER* 3.2 23.0 + - - -
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Residues in contact with GLY 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LYS* 3.1 29.8 - - - -
192A THR* 3.6 6.6 - - - +
225B PRO* 4.3 2.2 - - - -
307B ASP 3.0 15.7 + - - -
308B ILE 3.2 4.2 + - - -
310B GLY* 1.3 75.2 - - - +
312B ILE* 1.3 57.0 + - - +
314B SER* 3.2 6.7 + - - -
315B THR* 3.0 28.0 + - - -
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Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.9 19.5 - - + -
50B ILE* 3.8 20.0 - - + -
225B PRO 4.3 15.5 - - - +
228B VAL* 3.6 29.6 - - + -
229B ALA* 4.5 6.5 - - + +
232B PHE* 4.1 9.6 - - + -
308B ILE* 3.1 19.9 + - + +
309B LEU* 3.8 7.9 - - + +
311B GLY* 1.3 72.0 - - - +
313B ARG* 1.3 65.8 + - - +
315B THR* 3.1 9.8 + - - -
316B CYS* 3.0 24.8 + - - -
324B LEU* 4.1 18.6 - - + -
327B LEU* 4.8 6.3 - - + -
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Residues in contact with ARG 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU* 3.6 43.9 + - - -
30B VAL* 3.7 27.8 + - + +
32B LEU* 3.7 30.4 - - + +
306B ARG* 5.3 0.4 + - - +
309B LEU* 2.9 49.5 + - - +
310B GLY* 3.9 11.6 - - - +
311B GLY 3.4 0.2 - - - -
312B ILE* 1.3 75.1 - - - +
314B SER* 1.3 57.9 + - - +
316B CYS* 3.2 5.9 + - - +
317B THR* 2.9 32.1 + - - -
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Residues in contact with SER 314 (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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192A THR* 3.4 5.5 - - - +
287A ALA* 6.4 1.3 - - - -
289A GLU* 2.7 28.1 + - - -
310B GLY 3.2 12.4 + - - -
311B GLY* 3.2 9.4 + - - -
313B ARG* 1.3 79.4 - - - +
315B THR* 1.3 55.6 + - - +
317B THR* 3.3 8.1 + - - -
318B TYR* 2.8 44.9 + - - -
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Residues in contact with THR 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A THR* 2.8 38.3 + - - +
194A VAL* 4.3 7.6 - - + -
17B LEU* 3.8 27.8 - - + -
229B ALA* 3.5 20.0 - - + +
311B GLY 3.0 14.9 + - - -
312B ILE* 3.1 9.6 + - - -
314B SER* 1.3 76.1 + - - +
316B CYS* 1.3 62.3 + - - +
318B TYR* 3.1 5.0 + - - +
319B VAL* 3.0 23.9 + - + +
327B LEU* 4.1 10.5 - - + -
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Residues in contact with CYS 316 (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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30B VAL* 3.6 22.7 - - + -
32B LEU* 4.3 9.2 - - - -
312B ILE* 3.0 21.8 + - - -
313B ARG 3.3 9.0 - - - +
315B THR* 1.3 71.5 - - - +
317B THR* 1.3 66.5 + - - +
319B VAL* 3.3 9.0 + - - +
320B GLY 2.9 4.7 + - - -
321B ALA* 2.8 52.4 + - - +
324B LEU* 4.5 17.9 - - - -
327B LEU* 4.6 8.7 - - - -
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Residues in contact with THR 317 (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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132A ASN* 3.8 21.6 + - + +
135A SER* 6.5 0.2 - - - -
22B SER* 3.9 8.2 + - - +
24B LEU* 3.9 18.1 - - + +
30B VAL* 3.5 14.0 - - - +
313B ARG* 2.9 15.3 + - - +
314B SER* 3.3 11.7 + - - -
316B CYS* 1.3 76.3 - - - +
318B TYR* 1.3 62.8 + - + +
320B GLY* 3.1 13.0 + - - -
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Residues in contact with TYR 318 (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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131A ALA* 3.7 28.1 + - + +
132A ASN* 3.8 40.2 - - + +
180A ILE* 4.3 13.7 - - + +
188A THR* 3.7 19.7 + - + +
192A THR* 4.1 3.1 - - - -
194A VAL* 3.8 35.7 - - + -
289A GLU* 2.7 27.1 + - - -
19B PRO* 3.3 10.9 - - + +
20B LYS 2.8 27.0 + - - +
314B SER* 2.8 44.5 + - - -
315B THR 3.5 7.6 - - - +
317B THR* 1.3 73.1 - - + +
319B VAL* 1.3 58.1 + - - +
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Residues in contact with VAL 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL* 4.8 1.6 - - + -
17B LEU* 4.2 24.7 - - + -
18B ARG 3.4 23.8 - - - +
19B PRO* 4.6 0.4 - - + -
20B LYS* 3.7 22.4 - - + +
21B ARG 4.9 0.2 - - - +
315B THR 3.0 19.1 + - - +
316B CYS* 3.6 7.0 - - - +
318B TYR* 1.3 80.4 - - + +
320B GLY* 1.3 59.0 + - - +
321B ALA* 4.1 5.4 - - + -
327B LEU* 3.7 23.3 - - + -
330B ARG* 3.5 42.1 + - + +
331B THR* 5.4 0.4 - - - -
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Residues in contact with GLY 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG 4.5 2.5 - - - -
22B SER* 3.5 32.5 - - - -
24B LEU* 4.1 8.7 - - - +
316B CYS 2.9 4.6 + - - -
317B THR 3.1 5.9 + - - -
318B TYR 3.5 1.0 + - - -
319B VAL* 1.3 78.9 - - - +
321B ALA* 1.3 60.7 + - - +
322B ALA* 3.7 2.3 + - - +
330B ARG* 3.1 25.4 + - - -
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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