Contacts of the helix formed by residues 294 - 312 (chain C) in PDB entry 1ZBU
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 CYS 294 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C GLU* 3.7 1.3 - - - -
153C GLU* 3.9 9.9 - - - +
171C GLN* 4.6 3.8 - - - -
173C TYR* 5.8 2.2 - - - -
190C THR 4.2 4.3 - - - +
192C ILE* 6.3 0.2 - - - -
291C ARG* 3.6 32.3 + - + +
292C PRO 3.1 2.2 - - - -
293C HIS* 1.3 78.4 - - - +
295C GLY* 1.3 59.3 + - - +
296C LEU* 3.9 9.4 - - - -
297C ASP* 3.2 31.4 + - - +
298C ASP* 2.8 29.6 + - - +
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Residues in contact with GLY 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ASP* 3.6 20.5 - - - +
136C GLU* 3.3 15.7 + - - -
153C GLU* 2.9 23.5 + - - -
155C PRO* 3.4 7.6 - - - -
294C CYS* 1.3 71.2 - - - +
296C LEU* 1.3 51.1 + - - +
299C SER* 2.7 39.3 + - - -
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Residues in contact with LEU 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C GLU* 2.9 8.6 + - - +
155C PRO* 3.7 8.5 - - + +
157C VAL* 4.4 9.0 - - + -
169C THR* 3.9 28.7 - - - +
170C PHE 4.4 11.0 - - - +
171C GLN* 3.4 47.8 - - + +
294C CYS* 3.3 4.6 - - - -
295C GLY* 1.3 72.6 - - - +
297C ASP* 1.3 57.6 + - - +
299C SER* 3.3 3.4 + - - -
300C LYS* 2.8 53.1 + - - +
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Residues in contact with ASP 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C ASP 4.4 1.8 - - - +
290C GLY* 3.4 14.2 - - - -
291C ARG* 2.8 49.5 + - - +
294C CYS* 3.2 16.8 + - - +
296C LEU* 1.3 79.5 - - - +
298C ASP* 1.3 57.4 + - - +
300C LYS* 3.3 26.3 + - - +
301C ASN* 3.0 35.2 + - - +
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Residues in contact with ASP 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ASP* 3.1 19.7 - - - +
230C ASP* 5.8 0.9 - - - +
277C LEU* 3.7 17.9 - - + +
288C TYR* 3.2 24.3 + - - -
291C ARG 3.6 7.4 - - - +
292C PRO* 3.9 0.2 - - - +
293C HIS* 3.3 18.9 + - - -
294C CYS 2.8 16.3 + - - +
297C ASP* 1.3 77.3 - - - +
299C SER* 1.3 55.3 + - - +
301C ASN* 3.1 6.9 + - - +
302C ILE* 2.9 35.2 + - + +
3001C MG 2.7 19.3 - - - -
3002C AMP 3.7 5.0 + - - -
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Residues in contact with SER 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ILE* 3.6 18.4 - - - +
133C ILE* 3.9 2.1 - - - -
134C ASP* 3.2 29.7 + - - +
155C PRO* 3.6 8.4 - - - +
157C VAL* 3.7 19.5 - - - +
295C GLY 2.7 25.7 + - - -
296C LEU* 3.5 6.7 - - - -
298C ASP* 1.3 74.0 - - - +
300C LYS* 1.3 56.3 + - - +
302C ILE* 3.5 4.3 + - - +
303C ALA* 3.0 28.2 + - - +
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Residues in contact with LYS 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C VAL* 4.4 5.6 - - + -
166C ILE* 5.1 5.0 - - + +
169C THR* 4.2 26.9 - - + -
289C ASP* 5.7 3.4 - - - +
296C LEU* 2.8 35.1 + - + +
297C ASP* 3.6 28.1 + - - +
299C SER* 1.3 71.5 - - - +
301C ASN* 1.3 64.2 + - - +
303C ALA* 3.2 8.8 + - - +
304C ARG* 3.0 31.2 + - - +
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Residues in contact with ASN 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C LEU* 4.0 15.3 - - + -
281C LEU* 4.3 11.3 - - + +
288C TYR* 3.4 23.5 + - - -
289C ASP* 2.9 33.7 + - - +
297C ASP* 3.0 22.6 + - - +
298C ASP* 3.5 9.0 - - - +
300C LYS* 1.3 74.0 - - - +
302C ILE* 1.3 64.8 + - - +
304C ARG* 2.7 46.9 + - - +
305C ILE* 3.1 19.7 + - - +
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Residues in contact with ILE 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ILE* 4.0 10.3 - - + -
134C ASP* 5.1 3.6 - - + +
228C LEU* 3.4 31.9 - - + -
230C ASP* 3.5 39.7 - - + +
260C ILE* 4.0 12.2 - - + +
277C LEU* 3.6 25.8 - - + -
280C MSE 4.4 7.9 - - + -
298C ASP* 2.9 24.3 + - + +
299C SER* 3.6 8.1 - - - +
301C ASN* 1.3 74.9 - - - +
303C ALA* 1.3 62.9 + - - +
305C ILE* 3.1 10.6 + - + +
306C ALA* 3.0 19.9 + - - +
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Residues in contact with ALA 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ILE* 3.7 26.5 - - + -
157C VAL* 3.8 8.5 - - + -
159C LEU* 3.9 1.4 - - + +
166C ILE* 3.4 25.8 - - + -
299C SER 3.0 15.1 + - - +
300C LYS 3.4 9.2 - - - +
301C ASN 3.2 0.2 - - - -
302C ILE* 1.3 75.3 - - - +
304C ARG* 1.3 61.6 + - - +
306C ALA* 3.3 6.4 + - - +
307C VAL* 3.1 26.0 + - - +
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Residues in contact with ARG 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ILE* 5.2 10.1 - - + -
281C LEU* 4.3 5.6 - - - +
286C MSE 4.1 17.6 - - - +
287C ASP* 2.8 43.0 + - - +
289C ASP* 3.1 26.2 + - - -
300C LYS* 3.0 21.5 + - - +
301C ASN* 2.7 39.2 + - - +
303C ALA* 1.3 77.7 - - - +
305C ILE* 1.3 56.9 + - + +
307C VAL* 3.3 11.5 + - - +
308C ARG* 3.0 24.9 + - - +
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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
----------------------------------------------------------
260C ILE* 4.6 7.6 - - + -
264C TYR* 4.3 13.9 - - + -
277C LEU* 3.8 28.9 - - + -
280C MSE 4.0 26.2 - - + -
281C LEU* 3.8 11.0 - - + -
284C LEU* 4.3 2.7 - - + -
286C MSE 3.6 24.2 - - + -
301C ASN 3.4 11.2 - - - +
302C ILE* 3.1 9.8 + - + +
304C ARG* 1.3 73.6 - - - +
306C ALA* 1.3 56.0 + - - +
308C ARG* 3.1 6.9 + - - +
309C MSE 2.7 55.8 + - + +
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Residues in contact with ALA 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ILE* 5.3 0.9 - - + -
132C ILE* 5.3 2.2 - - + -
159C LEU* 3.9 15.7 - - + -
228C LEU* 4.3 9.6 - - + -
260C ILE* 4.1 11.4 - - + +
302C ILE 3.0 11.5 + - - +
303C ALA* 3.3 12.5 + - - +
305C ILE* 1.3 76.1 - - - +
307C VAL* 1.3 62.0 + - - +
309C MSE 3.4 2.4 + - - +
310C LEU* 3.0 32.5 + - + +
316C LEU* 4.0 23.0 - - + +
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Residues in contact with VAL 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LEU* 3.7 29.4 - - + -
164C LEU* 3.8 29.3 - - + +
166C ILE* 4.6 6.5 - - + -
303C ALA 3.1 17.0 + - - +
304C ARG* 3.4 11.2 - - - +
305C ILE 3.1 0.2 - - - -
306C ALA* 1.3 73.4 - - - +
308C ARG* 1.3 66.1 + - - +
310C LEU* 3.3 5.8 + - - +
311C GLN* 3.0 47.3 + - - +
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Residues in contact with ARG 308 (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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268C TYR* 4.1 0.2 - - - +
284C LEU* 2.8 62.4 + - + +
286C MSE 3.8 21.4 - - - +
304C ARG 3.0 14.2 + - - +
305C ILE* 3.4 8.3 - - - +
307C VAL* 1.3 77.4 - - - +
309C MSE 1.3 57.3 + - - +
311C GLN* 3.2 20.6 + - - +
312C ASP* 2.8 53.9 + - - +
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Residues in contact with MSE 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ILE* 4.0 26.2 - - - -
263C SER 3.6 25.8 - - - +
264C TYR* 3.6 20.0 - - - +
267C PHE* 3.8 8.5 - - + -
268C TYR* 3.6 31.0 - - + +
284C LEU* 5.1 0.2 - - + -
305C ILE* 2.7 32.7 + - + +
306C ALA* 3.8 5.8 - - - +
307C VAL 3.2 0.2 - - - -
308C ARG* 1.3 69.4 - - + +
310C LEU* 1.3 62.7 + - - +
312C ASP* 3.2 8.0 + - - +
313C GLY 3.2 0.3 + - - -
314C CYS* 2.9 53.8 + - + +
316C LEU* 4.0 11.4 - - + -
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C TYR* 3.6 31.9 - - + +
130C ILE* 5.2 2.5 - - + -
159C LEU* 4.8 9.0 - - + -
161C THR* 4.7 19.5 - - + +
164C LEU* 3.8 29.6 - - + -
306C ALA 3.0 23.1 + - - +
307C VAL 3.8 3.1 - - - +
309C MSE 1.3 74.8 - - - +
311C GLN* 1.3 60.5 + - - +
313C GLY* 2.8 22.2 + - - -
314C CYS 3.4 18.8 - - - +
315C GLU* 4.7 1.3 - - - -
316C LEU* 4.2 11.4 - - + +
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Residues in contact with GLN 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C LEU* 3.7 21.9 - - + +
307C VAL* 3.0 28.8 + - - +
308C ARG* 3.3 29.4 - - - +
310C LEU* 1.3 75.9 - - - +
312C ASP* 1.3 61.9 + - - +
313C GLY* 3.1 3.3 + - - -
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Residues in contact with ASP 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C PHE* 3.3 23.7 - - + -
268C TYR* 2.7 32.9 + - - +
284C LEU* 4.6 0.2 - - - +
308C ARG* 2.8 45.5 + - - +
309C MSE 3.6 5.8 - - - +
310C LEU 3.1 0.6 - - - -
311C GLN* 1.3 77.6 - - - +
313C GLY* 1.3 57.2 + - - +
314C CYS 3.5 1.3 - - - -
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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
------------------------------------------------------------
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