Contacts of the helix formed by residues 300 - 320 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C HIS* 3.8 4.4 - - - -
249C SER* 2.9 21.8 + - - -
250C GLU* 3.7 12.9 - - - +
298C LYS 3.9 2.5 + - - +
299C GLY* 1.3 72.0 - - - -
301C VAL* 1.3 66.2 + - - +
302C GLU* 3.2 17.2 + - + +
303C HIS* 3.4 39.5 + - + +
304C THR* 4.2 1.0 + - - -
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Residues in contact with VAL 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C MET* 3.8 29.6 - - - -
66C VAL* 3.7 23.1 - - + -
67C LEU* 4.3 3.4 - - + -
245C LEU* 4.0 16.2 - - + -
248C HIS* 3.4 34.3 - - + +
250C GLU* 2.7 32.1 + - + +
299C GLY 3.6 1.0 + - - -
300C ASP* 1.3 71.3 - - - +
302C GLU* 1.3 68.6 + - - +
304C THR* 2.9 5.1 + - - -
305C ILE* 2.9 25.7 + - + +
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Residues in contact with GLU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C VAL* 4.1 21.0 - - + +
70C PHE* 4.2 10.1 - - + -
250C GLU* 5.1 0.4 + - - -
300C ASP* 4.2 15.2 - - + +
301C VAL* 1.3 81.1 - - - +
303C HIS* 1.3 81.1 + - + +
305C ILE* 3.3 3.6 + - - +
306C ARG* 2.6 71.2 + - - +
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Residues in contact with HIS 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C LYS 5.7 1.2 + - - -
300C ASP* 3.4 38.9 + - + +
301C VAL 3.2 1.0 - - - -
302C GLU* 1.3 84.6 + - + +
304C THR* 1.3 65.4 + - - +
306C ARG* 3.5 25.0 + - - +
307C ASP* 3.1 23.0 + - - +
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Residues in contact with THR 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C MET* 3.7 24.5 - - + +
245C LEU* 4.5 5.4 - - + -
248C HIS* 2.6 30.4 + - + +
298C LYS* 4.9 4.2 + - + +
300C ASP 4.2 1.1 + - - -
301C VAL* 2.9 7.2 + - - -
303C HIS* 1.3 80.0 - - - +
305C ILE* 1.3 62.6 + - - +
307C ASP* 3.2 7.7 + - + +
308C ILE* 3.0 38.1 + - + +
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Residues in contact with ILE 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C VAL* 5.2 0.7 - - + -
67C LEU* 4.1 25.8 - - + -
70C PHE* 3.7 40.4 - - + -
72C LEU* 4.2 21.1 - - + -
241C LEU* 6.2 0.4 - - + -
245C LEU* 3.7 30.1 - - + -
301C VAL* 2.9 23.1 + - + +
302C GLU* 3.6 9.0 - - - +
304C THR* 1.3 76.6 - - - +
306C ARG* 1.3 62.4 + - - +
308C ILE* 3.2 11.7 + - + +
309C LEU* 3.0 33.9 + - + +
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Residues in contact with ARG 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C PHE* 3.9 32.7 - - + -
302C GLU* 2.6 55.0 + - - +
303C HIS* 3.5 25.2 - - - +
305C ILE* 1.3 74.3 - - - +
307C ASP* 1.3 57.7 + - - +
309C LEU* 4.1 5.4 - - - +
310C GLY* 2.9 26.7 + - - -
313C ARG* 5.5 0.3 + - - -
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Residues in contact with ASP 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C PRO* 3.8 14.7 - - - +
303C HIS 3.1 15.5 + - - +
304C THR* 3.2 11.8 + - + +
306C ARG* 1.3 75.0 - - - +
308C ILE* 1.3 65.0 + - + +
310C GLY* 4.0 0.4 - - - -
311C GLY* 3.1 19.6 + - - -
191D LYS* 2.9 40.6 + - - +
287D ALA* 5.6 3.6 - - - +
288D SER 5.0 3.5 + - - -
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Residues in contact with ILE 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 4.1 16.6 - - + -
225C PRO* 3.8 13.8 - - + +
228C VAL* 4.5 14.6 - - + -
241C LEU* 4.0 17.5 - - + -
244C MET* 3.8 26.9 - - + -
245C LEU* 4.5 3.1 - - + -
304C THR* 3.0 34.7 + - + +
305C ILE* 3.7 17.5 - - + +
307C ASP* 1.3 75.0 - - + +
309C LEU* 1.3 66.1 + - + +
311C GLY* 3.2 2.4 + - - -
312C ILE* 3.0 40.8 + - + +
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Residues in contact with LEU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.7 19.0 - - + +
48C VAL* 4.1 13.9 - - + -
50C ILE* 3.9 27.6 - - + -
70C PHE* 4.3 20.0 - - + +
72C LEU* 4.3 13.0 - - + -
305C ILE* 3.0 34.8 + - + +
306C ARG* 4.1 4.3 - - - +
308C ILE* 1.3 79.9 - - + +
310C GLY* 1.3 55.9 + - - +
312C ILE* 3.3 2.0 + - + -
313C ARG* 2.8 64.2 + - - +
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Residues in contact with GLY 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ARG 2.9 19.1 + - - -
307C ASP* 4.1 1.1 - - - -
309C LEU* 1.3 74.3 - - - +
311C GLY* 1.3 62.2 + - - +
313C ARG* 3.4 12.7 + - - +
314C SER* 3.0 25.5 + - - -
287D ALA* 4.6 22.4 - - - +
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Residues in contact with GLY 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C PRO* 4.3 1.1 - - - -
307C ASP 3.1 15.2 + - - -
308C ILE 3.2 3.6 + - - -
309C LEU 3.2 0.2 - - - -
310C GLY* 1.3 77.6 - - - +
312C ILE* 1.3 56.9 + - - +
314C SER* 3.2 6.9 + - - -
315C THR* 2.9 29.1 + - - -
191D LYS* 3.4 28.9 - - - -
192D THR* 3.7 5.2 - - - +
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Residues in contact with ILE 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.9 20.9 - - + -
50C ILE* 4.0 12.6 - - + -
225C PRO 4.2 15.5 - - - +
228C VAL* 3.8 17.7 - - + -
229C ALA* 4.4 13.7 - - + +
232C PHE* 4.3 11.0 - - + -
308C ILE* 3.0 36.4 + - + +
309C LEU* 3.9 6.3 - - + +
311C GLY* 1.3 75.0 - - - +
313C ARG* 1.3 67.4 + - - +
314C SER 3.1 0.2 + - - -
315C THR* 3.1 7.5 + - - -
316C CYS* 3.0 24.3 + - - -
324C LEU* 4.4 16.4 - - + -
327C LEU* 4.8 2.9 - - + -
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Residues in contact with ARG 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLU* 3.9 33.6 + - - -
30C VAL* 3.2 45.6 + - + +
32C LEU* 3.5 30.5 - - + +
306C ARG 5.5 0.2 + - - -
309C LEU* 2.8 55.3 + - - +
310C GLY* 3.8 9.8 - - - +
312C ILE* 1.3 73.0 - - - +
314C SER* 1.3 57.8 + - - +
316C CYS* 3.3 3.6 + - - +
317C THR* 3.0 31.2 + - - -
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Residues in contact with SER 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C GLY 3.0 18.2 + - - -
311C GLY* 3.7 4.7 - - - -
312C ILE 3.0 0.2 - - - -
313C ARG* 1.3 75.5 - - - +
315C THR* 1.3 58.2 + - - +
317C THR* 3.3 9.2 + - - -
318C TYR* 2.9 40.5 + - - -
192D THR* 3.2 9.2 - - - +
287D ALA* 5.9 4.0 - - - -
289D GLU* 2.6 28.9 + - - -
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Residues in contact with THR 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 3.9 27.8 - - + -
229C ALA* 3.4 19.9 - - + +
311C GLY 2.9 15.2 + - - -
312C ILE* 3.1 7.6 + - - -
314C SER* 1.3 77.5 + - - +
316C CYS* 1.3 62.9 + - - +
318C TYR* 3.3 2.4 + - - +
319C VAL* 3.1 22.7 + - + +
327C LEU* 4.2 8.5 - - + -
192D THR* 2.6 38.5 + - - +
194D VAL* 3.9 9.6 - - + -
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Residues in contact with CYS 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 3.6 20.0 - - + -
32C LEU* 4.4 10.1 - - - -
312C ILE* 3.0 16.6 + - - -
313C ARG 3.4 9.2 - - - +
315C THR* 1.3 75.5 - - - +
317C THR* 1.3 57.6 + - - +
319C VAL* 3.2 5.1 + - - -
320C GLY 2.8 26.0 + - - -
321C ALA* 2.9 41.8 + - - +
324C LEU* 4.4 11.0 - - - -
327C LEU* 4.4 20.9 - - - -
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Residues in contact with THR 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C SER* 3.9 5.5 + - - +
24C LEU* 3.9 23.7 - - + +
30C VAL* 3.7 12.0 - - - +
313C ARG* 3.0 15.8 + - - +
314C SER* 3.5 11.7 - - - -
316C CYS* 1.3 74.9 - - - +
318C TYR* 1.3 64.6 + - + +
319C VAL 3.2 0.7 + - - -
320C GLY 3.3 8.0 + - - -
321C ALA 4.3 0.4 + - - -
132D ASN* 3.9 20.6 + - + +
135D SER* 6.3 0.9 - - - -
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Residues in contact with TYR 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PRO* 3.4 10.5 - - + +
20C LYS 2.9 28.8 + - - +
314C SER* 2.9 45.4 + - - -
315C THR 3.3 6.5 + - - +
317C THR* 1.3 75.9 - - + +
319C VAL* 1.3 57.8 + - + +
320C GLY 3.5 0.2 - - - -
131D ALA* 3.7 37.2 + - + +
132D ASN* 3.8 29.9 - - + +
180D ILE* 4.3 13.1 - - + +
188D THR* 3.7 12.2 + - + +
192D THR* 4.1 9.4 - - - -
194D VAL* 3.8 33.7 - - + -
289D GLU* 2.6 27.0 + - - -
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Residues in contact with VAL 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 4.4 24.7 - - + -
18C ARG 3.5 22.0 - - - +
20C LYS* 3.7 22.4 - - + +
21C ARG 4.6 1.0 - - - +
315C THR* 3.1 17.4 + - + +
316C CYS 3.7 4.9 - - - +
318C TYR* 1.3 80.7 - - + +
320C GLY* 1.3 61.0 + - - +
321C ALA* 4.1 4.7 - - + -
327C LEU* 3.6 27.1 - - + -
330C ARG* 3.8 41.0 + - + +
331C THR* 5.4 0.7 - - - -
194D VAL* 4.8 0.9 - - + -
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Residues in contact with GLY 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ARG 4.4 3.8 - - - -
22C SER* 3.6 29.1 - - - -
24C LEU* 3.9 14.3 - - - +
316C CYS 2.8 3.9 + - - -
317C THR 3.3 4.4 + - - -
318C TYR 3.5 0.2 - - - -
319C VAL* 1.3 77.0 - - - +
321C ALA* 1.3 60.3 + - - +
322C ALA 3.8 2.1 + - - -
326C GLU* 4.0 0.2 - - - +
330C ARG* 3.1 29.2 + - - -
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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