Contacts of the helix formed by residues 268 - 277 (chain A) in PDB entry 1IZ2
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 THR 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLU* 3.9 9.6 - - - +
35A PHE* 3.2 13.9 - - - -
39A ARG* 4.9 6.3 - - - +
265A ASN 5.4 1.8 - - - +
266A GLU* 3.2 16.5 + - - +
267A LEU* 1.3 80.2 - - - +
269A HIS* 1.3 65.4 + - - +
270A ASP* 4.0 9.2 + - - +
271A ILE* 3.1 33.1 + - + +
272A ILE* 3.2 18.6 + - - +
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Residues in contact with HIS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR 4.9 1.1 - - - -
28A PRO* 4.4 24.0 - - + +
31A ALA* 4.0 26.9 - - + -
32A GLU* 3.2 14.8 + - + +
35A PHE* 3.2 11.8 - - - -
268A THR* 1.3 73.1 - - - +
270A ASP* 1.3 78.7 + - - +
272A ILE* 3.2 10.2 + - + +
273A THR* 3.1 44.2 + - + -
380A LYS* 5.7 14.6 - - + +
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Residues in contact with ASP 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 3.3 8.3 + - - +
269A HIS* 1.3 88.5 + - - +
271A ILE* 1.3 69.6 + - + +
273A THR* 2.8 17.8 + - - -
274A LYS* 2.9 14.9 + - - +
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Residues in contact with ILE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A CYS* 5.0 2.5 - - - -
234A LYS* 4.5 9.4 - - + -
235A LEU* 3.5 39.5 - - + -
253A PHE* 5.9 0.4 - - + -
266A GLU* 3.0 41.5 - - + +
268A THR* 3.1 21.8 + - - +
270A ASP* 1.3 76.8 - - + +
272A ILE* 1.3 68.2 + - + +
274A LYS* 3.1 16.0 + - - +
275A PHE* 3.1 35.4 - - + -
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Residues in contact with ILE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 4.3 7.9 - - + -
251A ILE* 3.8 8.7 - - + -
253A PHE* 4.2 13.9 - - + -
267A LEU* 3.4 32.1 - - + -
268A THR 3.2 16.4 - - - +
269A HIS* 3.2 10.7 + - + +
270A ASP 3.2 0.8 - - - -
271A ILE* 1.3 80.4 - - + +
273A THR* 1.3 58.0 + - - +
275A PHE* 3.1 6.4 + - - -
276A LEU* 2.9 55.0 + - + +
373A LEU* 4.2 17.9 - - + -
375A ILE* 4.3 8.7 - - + -
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Residues in contact with THR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A HIS* 3.1 36.5 + - + -
270A ASP* 2.8 15.6 + - - -
272A ILE* 1.3 80.1 - - - +
274A LYS* 1.3 59.6 + - - +
275A PHE 3.0 1.3 + - - -
276A LEU* 3.2 18.8 + - + +
277A GLU* 3.3 24.0 + - - +
380A LYS* 6.4 0.2 - - - +
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Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLN* 5.3 0.5 + - - -
270A ASP 2.9 10.5 + - - +
271A ILE* 3.1 12.3 + - - +
273A THR* 1.3 76.9 - - - +
275A PHE* 1.3 74.8 + - + +
277A GLU* 3.6 26.3 + - - +
278A ASN* 4.6 3.8 - - - +
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Residues in contact with PHE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLN* 3.3 45.7 - - + +
231A HIS 4.8 2.2 - - - -
232A CYS* 3.1 49.8 - - + -
235A LEU* 4.9 2.5 - - + -
239A VAL* 3.5 32.5 - - + -
241A LEU* 3.5 16.0 - - + +
251A ILE* 6.0 0.9 - - + -
253A PHE* 5.6 1.8 - + + -
271A ILE* 3.1 24.2 - - + +
272A ILE* 3.1 10.4 + - - +
273A THR 3.0 0.8 - - - -
274A LYS* 1.3 101.0 - - + +
276A LEU* 1.3 62.2 + - + +
277A GLU 3.2 5.7 + - - -
278A ASN* 3.7 8.3 - - - +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LEU* 4.7 11.6 - - + +
249A THR* 5.9 4.9 - - + -
251A ILE* 3.3 33.2 - - + -
272A ILE* 2.9 35.0 + - + +
273A THR* 3.2 11.2 + - + +
275A PHE* 1.3 80.4 - - + +
277A GLU* 1.3 56.7 + - + +
278A ASN 3.4 4.1 + - - +
375A ILE* 5.0 9.9 - - + -
377A GLN* 6.4 2.5 - - + -
380A LYS* 6.2 5.8 - - + +
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Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A THR* 3.3 26.5 - - - +
274A LYS* 3.6 21.5 - - - +
276A LEU* 1.3 78.5 - - - +
278A ASN* 1.3 57.5 + - - +
279A GLU 4.1 1.1 + - - -
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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