Contacts of the helix formed by residues 281 - 297 (chain C) in PDB entry 1Z1G
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 SER 281 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C CYS* 4.5 1.6 - - - -
280C LEU* 1.3 82.1 - - - +
282C SER* 1.3 69.0 + - - +
283C GLY* 3.0 3.8 - - - -
284C THR* 2.7 41.3 + - - -
285C VAL* 3.5 8.1 + - - +
3K G 6.2 0.3 - - - +
4K C 5.6 4.6 + - - -
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Residues in contact with SER 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C VAL* 3.8 15.6 - - - +
214C GLY* 4.4 18.4 - - - -
217C CYS* 4.3 16.8 - - - +
280C LEU 3.9 3.0 + - - -
281C SER* 1.3 70.9 - - - +
283C GLY* 1.3 69.6 + - - +
284C THR 3.4 0.3 + - - -
285C VAL* 3.4 9.2 + - - +
286C SER* 3.6 10.0 + - - -
22L G 4.2 18.6 + - - -
23L C 6.1 0.7 - - - -
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Residues in contact with GLY 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C SER* 2.8 7.5 + - - -
282C SER* 1.3 78.7 + - - +
284C THR* 1.3 59.2 + - - -
286C SER* 3.7 3.0 + - - -
287C ARG* 3.0 34.6 + - - +
23L C 5.2 10.8 - - - -
24L T 4.4 14.7 - - - +
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Residues in contact with THR 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C TRP* 5.3 3.1 - - + -
280C LEU* 4.4 20.1 - - + +
281C SER* 2.7 35.7 + - - -
283C GLY* 1.3 69.9 - - - -
285C VAL* 1.3 65.3 - - - -
287C ARG* 2.8 23.1 + - + +
288C TYR* 2.8 43.9 + - + +
2K T 6.6 0.2 - - + -
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Residues in contact with VAL 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C TRP* 4.6 20.6 - - + -
199C LEU* 4.3 6.5 - - + +
202C ALA* 4.2 14.8 - - + -
213C VAL* 4.7 5.8 - - + -
216C LEU* 5.1 2.7 - - + -
217C CYS* 3.8 28.7 - - - -
272C ILE* 5.1 8.5 - - + -
280C LEU* 4.8 11.0 - - + -
281C SER 3.5 4.9 + - - +
282C SER 3.4 7.1 + - - +
283C GLY 3.4 0.6 - - - -
284C THR* 1.3 76.4 - - - +
286C SER* 1.3 62.9 + - - +
288C TYR* 3.4 2.3 + - - +
289C PHE* 3.1 18.9 + - - +
307C PHE* 3.1 33.0 - - + -
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Residues in contact with SER 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C VAL* 5.2 1.2 - - - +
282C SER 3.6 8.5 + - - -
283C GLY* 4.4 4.9 - - - -
284C THR 3.4 0.4 - - - -
285C VAL* 1.3 76.6 - - - +
287C ARG* 1.3 57.8 + - - +
289C PHE* 3.0 2.6 + - - +
290C MSE 2.8 29.3 + - - +
306C THR* 2.8 17.5 + - - -
307C PHE* 3.6 14.3 - - - +
22L G 5.4 0.2 - - - -
23L C 2.7 52.6 + - - -
24L T 3.9 1.2 + - - -
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Residues in contact with ARG 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C GLY 3.0 19.5 + - - +
284C THR* 2.8 32.1 + - + +
286C SER* 1.3 75.4 - - - +
288C TYR* 1.3 58.4 + - + +
290C MSE 2.9 50.9 - - + +
291C ARG* 3.4 15.7 + - - +
3K G 4.8 5.9 + - - -
4K C 3.1 24.6 - - - +
23L C 5.2 3.3 - - - +
24L T 4.4 20.9 - - + +
25L G 3.3 32.0 + - - -
26L G 2.8 29.7 + - - -
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Residues in contact with TYR 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C SER* 4.7 7.5 + - - -
196C PRO* 3.5 37.2 - - + +
198C TRP* 3.4 29.2 - + + -
199C LEU* 3.6 17.8 - - + +
284C THR* 2.8 35.2 + - + +
285C VAL 4.3 1.8 - - - +
287C ARG* 1.3 69.2 - - + +
289C PHE* 1.3 67.8 + - - +
290C MSE 3.0 1.8 - - - -
291C ARG* 2.8 41.6 + - + +
292C ALA 3.2 9.4 + - - -
2K T 4.0 21.1 + - - +
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Residues in contact with PHE 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C LEU* 4.3 7.4 - - + -
185C TYR* 6.0 2.2 - + - -
188C ILE* 3.5 44.4 - - + -
199C LEU* 3.8 11.3 - - + +
203C MSE 3.6 36.1 - - + -
285C VAL 3.1 12.6 + - - +
286C SER* 3.0 9.5 + - - +
288C TYR* 1.3 77.5 - - - +
290C MSE 1.3 62.3 + - - +
292C ALA* 3.4 1.9 + - + -
293C ARG* 3.1 25.1 + - + +
305C PRO 5.1 3.1 - - - -
306C THR* 4.1 10.1 - - - -
307C PHE* 3.6 39.7 - + + -
310C LEU* 3.8 27.1 - - + -
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Residues in contact with MSE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C SER 2.8 11.9 + - - +
287C ARG* 2.9 49.8 - - + +
289C PHE* 1.3 78.6 - - - +
291C ARG* 1.3 90.1 + - - +
293C ARG* 3.0 35.7 + - - +
294C LYS* 3.1 25.3 + - - +
306C THR* 6.3 0.7 - - - -
23L C 6.3 0.2 - - + -
24L T 3.5 68.4 - - + +
25L G 5.4 2.0 - - - +
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Residues in contact with ARG 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C SER* 6.1 0.7 - - - +
287C ARG* 3.4 31.7 + - - +
288C TYR* 2.8 44.1 + - + +
290C MSE 1.3 95.5 - - - +
292C ALA* 1.3 56.4 + - - +
294C LYS* 3.3 8.7 + - + +
295C ALA* 2.9 29.7 + - - +
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Residues in contact with ALA 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ILE* 3.6 19.1 - - + +
191C ALA* 3.4 5.4 - - - +
192C ALA* 3.9 33.9 - - + +
195C SER* 4.3 6.4 + - - +
199C LEU* 4.8 3.1 - - + -
288C TYR 3.2 8.2 + - - +
289C PHE* 4.0 5.8 - - + +
291C ARG* 1.3 75.3 - - - +
293C ARG* 1.3 58.4 + - - +
295C ALA* 3.7 8.1 - - - -
296C SER* 2.9 30.5 + - - -
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Residues in contact with ARG 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ILE* 3.8 18.3 - - + +
289C PHE* 3.1 17.4 + - + +
290C MSE 3.0 18.4 + - - +
292C ALA* 1.3 74.6 - - - +
294C LYS* 1.3 69.4 + - + +
296C SER* 3.2 14.0 + - - -
297C GLY* 3.5 6.8 + - - -
298C LEU 4.5 4.0 + - - +
300C PHE* 5.0 16.6 - - + -
304C PRO* 3.3 45.0 + - + +
305C PRO* 2.6 37.9 + - - -
306C THR* 3.4 19.8 - - - +
24L T 2.5 39.9 + - - -
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Residues in contact with LYS 294 (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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290C MSE 3.1 28.7 + - - +
291C ARG* 3.7 9.4 - - + +
293C ARG* 1.3 79.7 - - + +
295C ALA* 1.3 59.1 + - - +
297C GLY* 3.1 20.6 + - - -
24L T 5.8 2.4 + - - -
25L G 4.9 9.1 + - - -
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Residues in contact with ALA 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C ALA* 4.2 13.3 - - + +
194C SER* 5.8 2.5 - - - +
291C ARG* 2.9 18.4 + - + +
292C ALA* 3.9 9.4 - - - +
294C LYS* 1.3 74.6 - - - +
296C SER* 1.3 61.8 + - - +
297C GLY* 3.3 1.0 + - - -
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Residues in contact with SER 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C LYS* 2.5 40.2 + - - +
188C ILE* 3.5 11.2 - - - -
191C ALA* 3.4 8.7 - - - +
292C ALA 2.9 17.1 + - - -
293C ARG 3.5 6.5 - - - -
294C LYS 3.2 0.4 - - - -
295C ALA* 1.3 77.1 - - - +
297C GLY* 1.3 61.8 + - - +
298C LEU* 3.4 17.5 + - - +
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Residues in contact with GLY 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C ARG 3.5 2.6 + - - -
294C LYS* 3.1 16.9 + - - -
295C ALA 3.3 1.3 - - - -
296C SER* 1.3 78.1 - - - +
298C LEU* 1.3 65.4 + - - +
299C SER* 3.9 1.4 + - - -
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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