Contacts of the helix formed by residues 300 - 320 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D HIS* 3.9 4.3 - - - -
249D SER* 2.8 29.8 + - - -
250D GLU* 3.8 13.0 - - - +
298D LYS 4.0 1.8 + - - +
299D GLY* 1.3 72.2 - - - -
301D VAL* 1.3 67.1 + - - +
302D GLU* 3.2 11.1 + - + +
303D HIS* 3.5 17.7 + - + +
304D THR* 4.2 1.0 + - - -
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Residues in contact with VAL 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D MET* 3.8 28.9 - - - -
66D VAL* 3.7 23.1 - - + -
67D LEU* 4.3 2.7 - - + -
245D LEU* 4.1 14.8 - - + -
248D HIS* 3.5 35.7 - - + +
250D GLU* 2.9 30.7 + - + +
299D GLY 3.6 1.0 + - - -
300D ASP* 1.3 72.0 - - - +
302D GLU* 1.3 66.8 + - - +
304D THR* 2.9 5.7 + - - -
305D ILE* 2.9 26.8 + - + +
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Residues in contact with GLU 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D VAL* 4.1 19.0 - - + +
70D PHE* 3.9 16.2 - - + -
250D GLU* 4.9 0.6 + - - +
300D ASP* 3.2 9.8 - - + +
301D VAL* 1.3 81.6 - - - +
303D HIS* 1.3 63.7 + - + +
305D ILE* 3.3 4.4 + - - +
306D ARG* 3.1 55.9 + - - +
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Residues in contact with HIS 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B GLU* 4.3 23.1 + - - -
298D LYS 6.2 0.4 - - - +
300D ASP* 3.5 11.5 + - + +
301D VAL 3.3 0.4 - - - -
302D GLU* 1.3 81.9 - - + +
304D THR* 1.3 62.9 + - - +
306D ARG* 3.5 10.9 + - - +
307D ASP* 3.1 30.7 + - + +
262G LYS* 5.2 10.3 + - - -
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Residues in contact with THR 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D MET* 3.8 18.2 - - + +
245D LEU* 4.7 4.7 - - + -
248D HIS* 2.7 32.7 + - + +
298D LYS* 4.9 4.8 + - + +
300D ASP 4.2 0.7 + - - -
301D VAL 2.9 10.1 + - - -
303D HIS* 1.3 80.9 - - - +
305D ILE* 1.3 66.1 + - - +
307D ASP* 3.3 7.3 + - + +
308D ILE* 2.9 39.4 + - + +
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Residues in contact with ILE 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ILE* 6.3 0.4 - - + -
67D LEU* 3.9 26.7 - - + -
70D PHE* 3.6 43.5 - - + -
72D LEU* 4.2 21.3 - - + -
245D LEU* 3.7 30.5 - - + -
301D VAL* 2.9 24.1 + - + +
302D GLU* 3.7 8.3 - - - +
304D THR* 1.3 72.2 - - - +
306D ARG* 1.3 58.0 + - - +
308D ILE* 3.2 11.4 + - + +
309D LEU* 3.0 37.4 + - + +
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Residues in contact with ARG 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B ALA* 5.9 0.3 - - - +
70D PHE* 3.7 27.0 - - + -
302D GLU* 3.1 44.4 + - - +
303D HIS* 3.8 11.9 - - - +
305D ILE* 1.3 74.1 - - - +
307D ASP* 1.3 60.1 + - - +
309D LEU* 4.2 5.1 - - - +
310D GLY* 2.8 29.1 + - - -
313D ARG* 5.4 0.5 + - - -
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Residues in contact with ASP 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B LYS* 2.4 43.1 + - - +
272B GLU* 5.6 0.3 - - - +
287B ALA* 5.8 3.5 - - - +
288B SER 5.0 2.8 + - - -
225D PRO* 3.8 15.9 - - - +
303D HIS* 3.1 20.3 + - + +
304D THR* 3.3 10.7 + - + +
306D ARG* 1.3 75.1 - - - +
308D ILE* 1.3 64.2 + - + +
310D GLY* 3.9 1.2 - - - -
311D GLY* 3.0 20.3 + - - -
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Residues in contact with ILE 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ILE* 4.1 15.5 - - + -
72D LEU* 6.3 0.9 - - + -
225D PRO* 4.0 13.9 - - + +
228D VAL* 4.6 14.6 - - + -
241D LEU* 4.1 16.6 - - + -
244D MET* 3.7 28.3 - - + -
245D LEU* 4.5 3.4 - - + -
304D THR* 2.9 37.7 + - + +
305D ILE* 3.6 19.1 - - + +
307D ASP* 1.3 78.1 - - + +
309D LEU* 1.3 64.1 + - + +
311D GLY* 3.2 0.9 + - - -
312D ILE* 3.1 39.3 + - + +
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Residues in contact with LEU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 3.7 22.1 - - + +
48D VAL* 3.9 14.6 - - + -
50D ILE* 3.8 28.5 - - + -
70D PHE* 4.3 19.1 - - + +
72D LEU* 4.2 12.1 - - + -
305D ILE* 3.0 37.0 + - + +
306D ARG* 4.2 4.0 - - - +
308D ILE* 1.3 74.9 - - + +
310D GLY* 1.3 58.1 + - - +
312D ILE* 3.4 2.6 + - + +
313D ARG* 2.9 57.9 + - - +
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Residues in contact with GLY 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ALA* 4.3 25.1 - - - +
306D ARG 2.8 18.8 + - - -
307D ASP* 3.9 1.3 - - - -
309D LEU* 1.3 77.5 - - - +
311D GLY* 1.3 60.9 + - - +
313D ARG* 3.7 13.9 + - - +
314D SER* 3.2 22.5 + - - -
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Residues in contact with GLY 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LYS* 3.2 32.5 - - - +
192B THR* 3.7 2.1 - - - +
225D PRO* 4.4 0.7 - - - -
307D ASP 3.0 15.3 + - - -
308D ILE 3.7 2.7 - - - -
310D GLY* 1.3 75.7 - - - +
312D ILE* 1.3 58.8 + - - +
314D SER* 3.2 7.5 + - - -
315D THR* 3.0 28.2 + - - -
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Residues in contact with ILE 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 3.9 20.0 - - + -
50D ILE* 3.8 21.3 - - + -
225D PRO* 4.2 16.3 - - - +
228D VAL* 3.7 25.8 - - + -
229D ALA* 4.4 9.2 - - + +
232D PHE* 4.0 9.9 - - + -
308D ILE* 3.1 20.9 + - + +
309D LEU* 3.9 7.6 - - + +
311D GLY* 1.3 72.2 - - - +
313D ARG* 1.3 65.6 + - - +
315D THR* 3.3 9.9 + - - -
316D CYS* 3.1 24.7 + - - -
324D LEU* 4.5 16.6 - - + -
327D LEU* 4.8 5.8 - - + -
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Residues in contact with ARG 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLU* 3.9 30.9 + - - -
30D VAL* 3.4 40.4 + - + +
32D LEU* 3.6 31.3 - - + +
306D ARG 5.4 0.4 + - - -
309D LEU* 2.9 47.2 + - - +
310D GLY* 3.8 12.0 - - - +
311D GLY 3.4 0.2 - - - -
312D ILE* 1.3 75.7 - - - +
314D SER* 1.3 57.9 + - - +
316D CYS* 3.3 6.2 + - - +
317D THR* 3.0 30.4 + - - -
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Residues in contact with SER 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B THR* 3.7 4.2 - - - +
287B ALA* 6.0 2.7 - - - -
289B GLU* 2.7 27.2 + - - -
310D GLY 3.2 16.2 + - - -
311D GLY* 3.6 5.6 - - - -
312D ILE 3.2 0.4 - - - -
313D ARG* 1.3 76.6 - - - +
315D THR* 1.3 64.9 + - - +
317D THR* 3.2 10.0 + - - +
318D TYR* 2.8 41.2 + - - -
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Residues in contact with THR 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B THR* 2.7 32.7 + - - +
194B VAL* 4.0 14.4 - - + -
17D LEU* 3.8 24.9 - - + -
229D ALA* 3.4 22.3 - - + +
311D GLY 3.0 16.5 + - - -
312D ILE 3.3 8.2 + - - -
314D SER* 1.3 74.9 - - - +
316D CYS* 1.3 62.2 + - - +
318D TYR* 3.1 4.3 + - - +
319D VAL* 3.1 23.3 + - - +
327D LEU* 4.1 9.9 - - + -
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Residues in contact with CYS 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D VAL* 3.7 19.7 - - + -
32D LEU* 4.5 7.9 - - - -
312D ILE* 3.1 21.4 + - - -
313D ARG 3.4 8.5 - - - +
314D SER 3.3 0.2 - - - -
315D THR* 1.3 74.5 - - - +
317D THR* 1.3 57.0 + - - +
319D VAL* 3.4 3.5 + - - -
320D GLY 2.9 9.0 + - - -
321D ALA* 2.7 61.2 + - + +
323D LYS 4.7 0.2 - - - -
324D LEU* 4.6 8.3 - - - -
327D LEU* 4.4 22.2 - - - -
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Residues in contact with THR 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ASN* 3.6 22.4 + - + +
22D SER* 4.1 7.4 + - - -
24D LEU* 3.8 18.1 - - + +
30D VAL* 3.7 12.5 - - - +
313D ARG* 3.0 16.0 + - - +
314D SER* 3.2 12.7 + - - +
316D CYS* 1.3 77.0 - - - +
318D TYR* 1.3 64.0 + - + +
319D VAL 3.3 0.3 + - - -
320D GLY* 3.4 10.2 + - - -
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Residues in contact with TYR 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ALA* 3.6 38.8 + - + +
132B ASN* 3.7 29.4 - - + +
180B ILE* 4.3 11.4 - - + +
188B THR* 3.9 12.5 + - + +
192B THR* 4.1 9.4 - - - -
194B VAL* 3.8 36.3 - - + -
289B GLU* 2.8 25.5 + - - -
19D PRO* 3.3 12.5 - - + +
20D LYS 2.9 27.2 + - - +
314D SER* 2.8 42.4 + - - -
315D THR 3.1 6.9 + - - +
317D THR* 1.3 78.7 - - + +
319D VAL* 1.3 58.2 + - + +
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Residues in contact with VAL 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B VAL* 5.0 0.7 - - + -
17D LEU* 4.3 25.4 - - + -
18D ARG 3.6 21.5 - - - +
19D PRO* 4.6 0.2 - - + -
20D LYS* 3.7 22.4 - - - +
21D ARG 4.8 0.9 - - - +
315D THR* 3.1 20.0 + - + +
316D CYS* 3.6 8.1 - - - +
318D TYR* 1.3 80.1 - - + +
320D GLY* 1.3 57.4 + - - +
321D ALA* 4.0 9.6 - - + +
327D LEU* 3.6 22.7 - - + -
330D ARG* 3.6 39.5 + - + +
331D THR* 5.3 0.2 - - - -
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Residues in contact with GLY 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG 4.6 2.0 - - - -
22D SER* 3.5 30.5 - - - -
23D THR 5.7 0.2 + - - -
24D LEU* 3.7 13.1 - - - +
316D CYS 2.9 4.4 + - - -
317D THR 3.4 5.9 + - - -
318D TYR 3.4 0.4 - - - -
319D VAL* 1.3 78.9 - - - +
321D ALA* 1.3 61.1 + - - +
322D ALA* 3.5 3.1 + - - +
330D ARG* 3.6 23.2 + - - -
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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