Contacts of the helix formed by residues 292 - 301 (chain A) in PDB entry 2IZV
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 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A MET* 1.3 80.2 - - - +
293A LYS* 1.3 63.1 + - - +
294A TYR* 3.2 25.1 + - + +
295A ALA* 3.0 25.6 + - - +
296A ALA* 3.1 19.6 + - - +
311A ARG* 3.9 4.4 + - - +
314A ALA* 4.8 17.9 - - + -
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Residues in contact with LYS 293 (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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292A ASP* 1.3 76.8 - - + +
294A TYR* 1.3 90.7 + - + +
296A ALA* 3.5 0.6 + - - -
297A GLU* 2.8 62.0 + - - +
311A ARG* 3.6 20.0 - - - +
314A ALA* 5.9 0.2 - - - +
332A HIS* 3.5 31.3 + - + +
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Residues in contact with TYR 294 (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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292A ASP* 3.2 23.3 - - + +
293A LYS* 1.3 107.2 - - + +
295A ALA* 1.3 56.2 + - - +
297A GLU* 3.4 18.3 + - - +
298A ALA* 3.1 25.3 + - - +
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Residues in contact with ALA 295 (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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291A MET* 3.6 25.8 - - + -
292A ASP* 3.0 17.0 + - - +
294A TYR* 1.3 74.1 - - - +
296A ALA* 1.3 63.9 + - - +
298A ALA* 3.3 8.3 + - - +
299A LEU* 3.1 27.2 + - - +
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Residues in contact with ALA 296 (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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291A MET* 3.8 10.8 - - - -
292A ASP 3.1 13.4 + - - +
293A LYS 3.6 8.1 - - - +
294A TYR 3.4 0.2 - - - -
295A ALA* 1.3 76.0 - - - +
297A GLU* 1.3 58.1 + - - +
299A LEU* 3.2 2.1 + - - +
300A LEU* 2.9 35.5 + - - +
309A LEU* 4.2 7.2 - - + -
311A ARG* 3.8 13.0 - - - +
323A SER* 3.5 32.1 - - - +
332A HIS* 4.2 1.3 - - + -
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Residues in contact with GLU 297 (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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293A LYS* 2.8 45.9 + - - +
294A TYR* 3.5 21.4 - - - +
296A ALA* 1.3 71.7 - - - +
298A ALA* 1.3 60.9 + - - +
300A LEU* 3.8 0.3 - - - +
301A GLU* 2.9 30.5 + - - +
330A SER* 3.9 29.4 + - - +
332A HIS* 2.6 30.9 + - + +
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Residues in contact with ALA 298 (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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294A TYR 3.1 13.8 + - - +
295A ALA* 3.6 11.4 - - - +
296A ALA 3.2 0.2 - - - -
297A GLU* 1.3 76.1 - - - +
299A LEU* 1.3 64.5 + - + +
300A LEU 3.4 0.3 + - - -
301A GLU* 3.4 27.9 - - - +
303A LYS* 5.0 1.4 + - - -
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Residues in contact with LEU 299 (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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288A TRP* 3.9 30.3 - - + -
291A MET* 3.4 33.4 - - + -
295A ALA 3.1 15.6 + - - +
296A ALA 3.6 6.3 - - - +
298A ALA* 1.3 76.4 - - + +
300A LEU* 1.3 58.2 + - - +
303A LYS* 2.8 29.6 + - - -
309A LEU* 3.9 14.6 - - + -
381A LEU* 3.7 19.4 - - + +
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Residues in contact with LEU 300 (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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296A ALA 2.9 17.9 + - - +
297A GLU* 3.8 1.1 - - - +
299A LEU* 1.3 75.6 - - - +
301A GLU* 1.3 66.7 + - - +
302A GLY 3.2 0.5 + - - -
303A LYS* 3.0 22.4 + - - +
307A THR* 3.6 43.3 - - + +
308A PHE* 4.3 5.2 - - - +
309A LEU* 4.8 5.2 - - + -
323A SER* 3.6 43.1 - - - +
324A PHE* 3.7 10.8 - - - +
325A ARG* 3.6 11.8 + - + -
330A SER* 4.0 18.4 - - - +
331A LEU 5.3 0.2 - - - +
332A HIS* 5.8 0.2 - - + -
381A LEU* 4.3 11.9 - - + -
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Residues in contact with GLU 301 (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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297A GLU 2.9 14.2 + - - +
298A ALA* 3.4 23.8 - - - +
299A LEU 3.4 1.2 - - - -
300A LEU* 1.3 77.0 - - - +
302A GLY* 1.3 59.9 + - - +
303A LYS* 3.1 19.1 + - - +
325A ARG* 4.5 5.8 - - - +
330A SER* 4.8 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
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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