Contacts of the helix formed by residues 282 - 296 (chain C) in PDB entry 1ZUM
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 282 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C ASP 3.8 0.8 + - - -
281C ALA* 1.3 69.4 - - - +
283C MET* 1.3 59.7 + - - +
284C ASP* 3.3 11.1 + - - +
285C TRP* 3.1 35.8 + - + +
286C ALA* 2.9 30.3 + - - +
432C PHE* 5.6 0.2 - - - -
434C LYS* 4.3 26.1 + - + +
454C ASN* 5.9 0.4 + - - -
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Residues in contact with MET 283 (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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281C ALA 3.1 8.5 + - - +
282C ASP* 1.3 71.7 + - - +
284C ASP* 1.3 60.3 + - - +
286C ALA* 3.3 3.8 + - - +
287C VAL* 2.9 55.3 + - - +
314C ILE* 3.8 44.2 - - + +
317C GLU* 3.9 27.6 - - + +
318C PHE* 3.9 16.8 - - - +
321C ARG* 3.6 31.0 - - - +
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Residues in contact with ASP 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ASP* 3.3 7.7 + - - +
283C MET* 1.3 79.2 - - - +
285C TRP* 1.3 62.3 + - - +
287C VAL* 3.9 1.6 - - - +
288C GLU* 3.2 24.6 + - - +
321C ARG* 2.7 43.0 + - - +
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Residues in contact with TRP 285 (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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282C ASP* 3.1 26.8 + - + +
284C ASP* 1.3 79.5 - - - +
286C ALA* 1.3 56.3 + - - +
288C GLU* 3.4 8.3 + - + +
289C GLN* 2.9 72.3 + - + +
432C PHE* 3.6 20.1 - + - -
454C ASN* 2.8 28.4 + - + -
455C CYS* 4.9 3.1 - - + -
150D PHE* 6.3 1.3 - + - -
494D LYS* 3.7 37.3 - - + +
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Residues in contact with ALA 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ILE* 3.8 31.5 - - + +
281C ALA* 4.3 4.5 - - + -
282C ASP 2.9 24.2 + - - +
283C MET* 3.3 4.7 + - - +
285C TRP* 1.3 74.7 - - - +
287C VAL* 1.3 57.9 + - - +
289C GLN* 4.1 0.3 - - - +
290C ALA* 2.9 32.2 + - - +
318C PHE* 3.8 5.5 - - + -
432C PHE* 4.0 22.6 - - + -
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Residues in contact with VAL 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C MET* 2.9 30.0 + - - +
284C ASP 3.9 4.0 - - - +
286C ALA* 1.3 77.9 - - - +
288C GLU* 1.3 63.5 + - - +
290C ALA* 3.4 1.7 + - - +
291C HIS* 3.1 22.5 + - - +
318C PHE* 3.7 28.7 - - + +
321C ARG* 3.7 54.5 - - + +
322C SER* 4.1 8.9 + - - +
325C ARG* 4.6 9.9 - - + -
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Residues in contact with GLU 288 (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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284C ASP 3.2 15.3 + - - +
285C TRP* 3.9 8.7 - - + +
287C VAL* 1.3 81.6 - - - +
289C GLN* 1.3 67.7 + - + +
291C HIS* 3.3 8.7 + - - +
292C PHE* 3.0 29.2 + - + +
325C ARG* 2.8 47.4 + - - +
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Residues in contact with GLN 289 (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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275C ASN* 4.7 1.1 - - - -
285C TRP* 2.9 66.8 + - + +
286C ALA 4.1 0.4 - - - +
288C GLU* 1.3 83.0 + - - +
290C ALA* 1.3 55.7 + - - +
292C PHE* 3.6 16.5 - - - +
293C ALA* 2.7 36.1 + - - +
432C PHE* 3.4 25.4 - - + -
455C CYS* 4.0 3.1 - - - +
456C TYR* 3.7 28.8 + - + +
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Residues in contact with ALA 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ASN* 3.5 23.2 + - - +
277C ILE* 4.8 2.2 - - + -
286C ALA 2.9 19.6 + - - +
287C VAL 3.8 1.6 - - - +
289C GLN* 1.3 72.9 - - - +
291C HIS* 1.3 66.1 + - - +
293C ALA* 3.4 2.7 + - - +
294C LEU* 3.2 17.8 + - - +
305C GLY 5.0 0.5 - - - +
308C THR* 4.3 6.7 + - + +
318C PHE* 3.6 24.5 - - + -
322C SER* 5.5 0.2 - - - +
405C MET* 3.5 20.9 - - + +
432C PHE* 5.3 0.2 - - - -
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Residues in contact with HIS 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C VAL* 3.1 13.8 + - + +
288C GLU* 3.4 12.6 - - - +
290C ALA* 1.3 77.5 - - - +
292C PHE* 1.3 60.6 + - - +
295C PHE* 2.9 67.6 + + - +
322C SER* 5.0 3.2 + - - -
325C ARG* 3.6 60.6 + - + +
326C ALA* 3.8 9.6 + - - +
329C ARG* 2.9 43.4 + - - -
405C MET* 4.1 7.7 - - + +
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Residues in contact with PHE 292 (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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288C GLU* 3.0 17.5 + - - +
289C GLN* 3.6 24.2 - - - +
291C HIS* 1.3 82.2 - - - +
293C ALA* 1.3 67.1 + - - +
295C PHE* 5.2 0.4 - - - -
296C PHE* 3.0 73.4 + + + +
329C ARG* 5.8 1.3 - - - +
456C TYR* 3.8 12.3 - - + -
457C ASP* 3.7 32.1 - - + -
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Residues in contact with ALA 293 (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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275C ASN* 4.0 8.7 - - - +
289C GLN 2.7 21.4 + - - +
290C ALA 3.5 7.6 - - - +
292C PHE* 1.3 76.2 - - - +
294C LEU* 1.3 58.4 + - - +
296C PHE* 5.2 1.0 - - - +
301C CYS* 6.0 0.2 - - - +
304C ALA* 3.5 8.1 - - - -
305C GLY* 2.9 23.6 + - - +
456C TYR* 3.4 45.1 - - + -
457C ASP* 4.3 4.9 - - - +
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Residues in contact with LEU 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 ALA 3.2 12.2 + - - +
291C HIS 4.0 1.3 - - - +
292C PHE 3.2 0.2 - - - -
293C ALA* 1.3 81.8 - - - +
295C PHE* 1.3 81.3 + - + +
296C PHE 3.4 2.0 + - - +
299C GLY* 3.3 19.6 - - - -
304C ALA* 4.3 8.2 - - + +
305C GLY 3.5 24.2 - - - +
306C SER* 3.5 20.6 - - - -
399C GLU* 5.9 0.4 - - - +
402C GLY 4.3 5.4 - - - +
403C PRO 4.1 0.2 - - - -
404C VAL 3.4 48.0 - - - +
405C MET* 3.4 24.2 - - + +
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Residues in contact with PHE 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C HIS* 2.9 58.0 + + - +
294C LEU* 1.3 84.2 - - + +
296C PHE* 1.3 68.2 + - - +
297C ASN 3.3 0.5 + - - -
298C GLN* 3.1 15.4 + - - -
299C GLY* 3.3 4.9 + - - +
326C ALA* 4.3 10.3 - - + -
329C ARG* 3.3 32.6 + - - +
341C GLN* 4.0 7.8 - - - +
383C PRO* 3.7 21.8 - - + -
384C THR 3.9 15.0 - - - -
385C VAL* 4.5 0.2 - - + -
403C PRO* 3.4 41.5 - - + -
405C MET* 4.1 19.5 - - + -
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Residues in contact with PHE 296 (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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112C LYS* 6.1 0.2 - - - -
116C ILE* 4.0 28.5 - - + -
120C VAL* 4.1 24.5 - - + -
124C MET* 5.6 2.0 - - + -
170C PHE* 3.7 35.4 - + - -
292C PHE* 3.0 56.6 + + + +
293C ALA 5.2 1.3 - - - +
294C LEU 3.4 2.3 - - - +
295C PHE* 1.3 73.7 - - - +
297C ASN* 1.3 79.0 + - + +
299C GLY* 2.9 14.9 + - - -
300C GLN 3.8 1.4 + - - -
301C CYS* 4.6 10.6 - - + +
329C ARG* 4.4 4.9 - - - +
457C ASP* 3.9 22.4 - - + +
459C PHE* 6.5 0.9 - + - -
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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
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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