Contacts of the helix formed by residues 283 - 294 (chain C) in PDB entry 4IZ5
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 283 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C ASN* 3.5 34.5 - - - +
222C LEU* 5.2 0.6 - - - +
282C ALA* 1.3 75.3 - - - +
284C SER* 1.3 76.2 + - - +
285C LYS* 3.3 17.6 + - - +
286C ALA* 3.2 19.7 + - + +
287C LEU* 3.3 13.9 + - - +
312C TYR* 3.7 19.8 - - - -
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Residues in contact with SER 284 (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 ALA 3.5 3.5 + - - -
283C ASP* 1.3 79.6 + - - +
285C LYS* 1.3 63.2 + - - +
287C LEU* 3.5 9.2 + - - +
288C ASP* 3.3 23.4 + - - +
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Residues in contact with LYS 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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283C ASP* 3.3 16.0 + - - +
284C SER* 1.3 79.0 + - - +
286C ALA* 1.3 64.6 + - - +
288C ASP* 4.8 2.7 - - - -
289C LEU* 3.5 5.4 + - - +
310C HIS* 3.2 24.8 + - - +
311C PRO* 3.3 29.2 + - + +
312C TYR* 3.4 22.7 - - + +
314C GLU* 2.8 30.3 + - - +
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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
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123C ASN* 4.6 0.2 - - - +
218C LEU* 3.8 9.7 - - + +
222C LEU* 4.4 23.6 - - + -
283C ASP* 3.2 19.5 + - + +
285C LYS* 1.3 80.0 - - - +
287C LEU* 1.3 59.1 + - + +
289C LEU* 3.6 4.7 + - - +
290C LEU* 3.1 25.1 + - - +
312C TYR* 3.7 36.8 - - + -
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Residues in contact with LEU 287 (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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222C LEU* 4.2 9.9 - - + -
275C TRP* 4.0 14.5 - - + +
276C ASN* 4.0 33.2 - - + +
279C PHE* 3.8 44.0 - - + +
282C ALA* 4.2 9.6 - - + +
283C ASP 3.3 16.0 + - - +
284C SER* 3.5 6.9 + - - +
285C LYS 3.4 0.2 - - - -
286C ALA* 1.3 74.3 - - - +
288C ASP* 1.3 55.9 + - - +
289C LEU 3.2 1.6 - - - -
290C LEU* 3.1 17.5 + - + +
291C ASP* 2.8 36.7 + - - +
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Residues in contact with ASP 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 SER 3.3 13.5 + - - +
285C LYS* 4.2 6.3 - - - +
286C ALA 3.5 0.4 - - - -
287C LEU* 1.3 79.2 - - - +
289C LEU* 1.3 60.5 + - - +
291C ASP* 3.7 10.2 + - - +
292C LYS* 3.3 44.1 + - - +
310C HIS* 3.3 21.9 - - + +
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LEU* 3.7 30.5 - - + -
134C LEU* 5.1 2.2 - - + -
218C LEU* 5.1 0.9 - - + -
285C LYS 3.5 5.1 + - - +
286C ALA 3.6 8.3 - - - +
287C LEU 3.2 0.2 - - - -
288C ASP* 1.3 76.1 - - - +
290C LEU* 1.3 65.2 + - - +
292C LYS* 3.1 15.6 + - - +
293C MET* 3.1 31.1 + - + +
302C ILE* 4.2 17.9 - - + -
307C ALA* 4.2 14.4 - - + +
310C HIS* 3.6 47.4 - - + +
312C TYR* 4.0 14.4 - - + -
313C LEU* 4.7 7.6 - - + -
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Residues in contact with LEU 290 (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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215C GLY* 3.1 30.7 - - - +
218C LEU* 3.8 15.9 - - + +
219C ALA* 3.7 15.7 - - + +
222C LEU* 4.4 5.4 - - + -
275C TRP* 3.7 32.1 - - + -
279C PHE* 4.1 10.1 - - + -
286C ALA 3.1 15.2 + - - +
287C LEU* 3.1 26.4 + - + +
289C LEU* 1.3 75.8 - - - +
291C ASP* 1.3 56.6 + - - +
293C MET* 2.9 6.2 + - - +
294C LEU* 2.8 47.3 + - + +
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Residues in contact with ASP 291 (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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244C LEU* 5.9 0.2 - - - +
272C LYS* 4.3 15.2 + - - -
275C TRP* 2.9 38.9 + - + +
287C LEU 2.8 19.9 + - - +
288C ASP* 3.7 13.6 - - - +
289C LEU 3.3 0.2 - - - -
290C LEU* 1.3 73.1 - - - +
292C LYS* 1.3 65.2 + - - +
294C LEU 3.9 8.7 + - - +
295C THR* 3.0 15.2 + - - -
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Residues in contact with LYS 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 ASP* 3.3 42.6 + - - +
289C LEU* 3.1 8.5 + - - +
291C ASP* 1.3 82.1 + - - +
293C MET* 1.3 61.6 + - - +
295C THR* 3.2 15.0 + - - -
301C ARG* 3.4 2.9 - - - +
302C ILE* 3.1 52.9 + - + +
310C HIS* 4.3 11.7 - - - +
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Residues in contact with MET 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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130C LEU* 4.8 7.9 - - - -
134C LEU* 3.8 20.4 - - + -
211C ILE* 3.8 27.6 - - + +
212C TRP* 3.6 15.8 + - - -
214C VAL* 3.6 28.9 - - + +
215C GLY* 3.8 24.0 - - - -
218C LEU* 5.0 6.5 - - - -
289C LEU* 3.2 30.3 - - + +
290C LEU 2.9 7.5 + - - +
292C LYS* 1.3 77.5 - - - +
294C LEU* 1.3 58.7 + - - +
295C THR 3.4 1.3 - - - -
301C ARG* 3.1 19.2 - - - -
302C ILE* 3.8 13.9 - - + -
307C ALA* 4.6 8.1 - - + -
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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
----------------------------------------------------------
212C TRP* 3.4 50.9 - - + +
215C GLY* 3.7 10.3 - - - +
216C CYS* 3.6 20.6 - - - +
219C ALA* 4.6 6.5 - - + -
227C ILE* 4.8 1.8 - - + -
228C PHE* 4.4 11.2 - - + -
244C LEU* 3.2 26.4 - - + +
275C TRP* 3.7 29.6 - - + -
290C LEU* 2.8 36.6 + - + +
291C ASP* 3.9 5.9 - - - +
293C MET* 1.3 77.0 - - - +
295C THR* 1.3 58.4 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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