Contacts of the helix formed by residues 283 - 294 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ASN* 3.5 37.1 - - - +
222B LEU* 5.2 0.4 - - - +
282B ALA* 1.3 75.3 - - - +
284B SER* 1.3 75.9 + - - +
285B LYS* 3.9 16.5 + - - +
286B ALA* 3.1 19.7 + - + +
287B LEU* 3.2 14.4 + - - +
312B TYR* 3.8 16.1 - - - -
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Residues in contact with SER 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B ALA 3.6 3.9 + - - -
283B ASP* 1.3 78.5 + - - +
285B LYS* 1.3 62.8 + - - +
287B LEU* 3.5 9.0 + - - +
288B ASP* 3.3 23.2 + - - +
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Residues in contact with LYS 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B ASP* 3.3 11.7 + - - +
284B SER* 1.3 78.4 + - - +
286B ALA* 1.3 65.2 + - - +
288B ASP* 3.8 2.9 + - - -
289B LEU* 3.5 5.4 + - - +
310B HIS* 3.2 24.6 + - - +
311B PRO* 3.3 30.1 + - + +
312B TYR* 3.4 25.3 - - + +
314B GLU* 2.8 30.5 + - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ASN* 4.6 0.4 - - - +
218B LEU* 3.8 9.8 - - + +
222B LEU* 4.4 21.5 - - + -
283B ASP* 3.1 21.5 + - + +
285B LYS* 1.3 80.2 - - - +
287B LEU* 1.3 58.7 + - + +
289B LEU* 3.5 5.0 + - - +
290B LEU* 3.1 24.3 + - - +
312B TYR* 3.6 36.3 - - + +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU* 4.2 9.6 - - + -
275B TRP* 4.0 16.2 - - + +
276B ASN* 4.0 32.1 - - + +
279B PHE* 3.8 43.3 - - + +
282B ALA* 4.2 9.4 - - + +
283B ASP 3.2 16.4 + - - +
284B SER* 3.5 8.0 + - - +
285B LYS 3.4 0.2 - - - -
286B ALA* 1.3 73.5 - - - +
288B ASP* 1.3 60.1 + - - +
289B LEU 3.2 1.6 - - - -
290B LEU* 3.1 17.2 + - + +
291B ASP* 2.8 31.6 + - - +
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Residues in contact with ASP 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B SER 3.3 14.8 + - - +
285B LYS* 4.2 6.1 - - - +
287B LEU* 1.3 78.6 - - - +
289B LEU* 1.3 60.6 + - - +
291B ASP* 3.7 9.5 + - - +
292B LYS* 3.3 44.4 + - - +
310B HIS* 3.3 22.0 + - + +
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 3.7 30.5 - - + -
134B LEU* 5.0 2.0 - - + -
218B LEU* 5.0 1.8 - - + -
285B LYS 3.5 4.8 + - - +
286B ALA 3.6 8.5 - - - +
287B LEU 3.2 0.4 - - - -
288B ASP* 1.3 77.6 - - - +
290B LEU* 1.3 64.4 + - - +
292B LYS* 3.1 7.4 + - - +
293B MET* 3.1 38.7 + - + +
302B ILE* 4.2 9.0 - - + -
307B ALA* 4.1 23.6 - - + +
310B HIS* 3.6 47.6 - - + +
312B TYR* 4.0 15.0 - - + -
313B LEU* 4.7 7.6 - - + -
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLY* 3.1 30.3 - - - +
218B LEU* 3.7 20.6 - - + +
219B ALA* 3.8 11.2 - - + +
222B LEU* 4.4 5.2 - - + -
275B TRP* 3.7 32.1 - - + -
279B PHE* 4.1 10.3 - - + -
286B ALA 3.1 14.3 + - - +
287B LEU* 3.1 27.3 + - + +
289B LEU* 1.3 76.7 - - - +
291B ASP* 1.3 55.2 + - - +
293B MET* 3.0 6.3 + - - +
294B LEU* 2.8 46.2 + - + +
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Residues in contact with ASP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LYS* 4.2 15.2 + - - -
275B TRP* 2.8 39.8 + - + +
287B LEU 2.8 18.4 + - - +
288B ASP* 3.7 12.5 - - - +
290B LEU* 1.3 71.9 - - - +
292B LYS* 1.3 65.3 + - - +
294B LEU 3.8 9.4 - - - +
295B THR* 3.0 14.7 + - - -
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Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B ASP* 3.3 43.3 + - - +
289B LEU 3.1 7.2 + - - +
291B ASP* 1.3 82.9 + - - +
293B MET* 1.3 62.0 + - - +
295B THR* 3.2 14.3 + - - -
300B LYS 6.0 0.4 - - - +
301B ARG* 3.4 2.9 - - - +
302B ILE* 3.1 56.9 + - + +
310B HIS* 4.3 11.4 - - - +
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Residues in contact with MET 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 4.8 9.0 - - - -
134B LEU* 3.8 21.1 - - + -
211B ILE* 3.8 27.6 - - + +
212B TRP* 3.6 15.4 + - - -
214B VAL* 3.6 27.8 - - + -
215B GLY* 3.8 23.6 - - - -
218B LEU* 5.0 5.8 - - - -
289B LEU* 3.2 31.9 - - + +
290B LEU 3.0 6.4 + - - +
292B LYS* 1.3 77.4 - - - +
294B LEU* 1.3 60.0 + - - +
295B THR 3.4 0.9 - - - -
301B ARG* 3.0 18.9 - - - +
302B ILE* 3.8 13.7 - - + -
307B ALA* 4.5 7.4 - - + -
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B TRP* 3.4 51.4 - - + +
215B GLY* 3.7 11.2 - - - +
216B CYS* 3.6 21.3 - - - +
219B ALA* 4.6 7.0 - - + -
227B ILE* 4.8 1.3 - - + -
228B PHE* 4.4 11.0 - - + -
244B LEU* 3.2 25.5 - - + +
275B TRP* 3.7 29.3 - - + -
290B LEU* 2.8 35.5 + - + +
291B ASP 3.8 5.9 - - - +
292B LYS 3.4 0.2 - - - -
293B MET* 1.3 76.5 - - - +
295B THR* 1.3 61.4 + - - +
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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