Contacts of the helix formed by residues 291 - 299 (chain A) in PDB entry 3IE7
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 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280A SER* 2.8 19.1 + - - +
284A GLN* 4.4 10.8 - - - +
290A PHE* 1.3 71.9 - - - +
292A LEU* 1.3 60.0 + - - +
293A GLU* 2.6 42.8 + - - +
294A ALA* 3.5 20.6 + - + +
295A ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A LYS* 3.3 40.5 - - + +
50A PHE* 4.7 22.0 - - + +
277A CYS* 4.8 3.6 - - - -
290A PHE* 3.5 33.4 + - + -
291A ASP* 1.3 74.1 + - - +
293A GLU* 1.3 57.5 + - - +
295A ALA* 3.8 2.3 - - + +
296A GLY* 3.1 24.8 + - - -
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Residues in contact with GLU 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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291A ASP* 2.6 25.7 + - - +
292A LEU* 1.3 70.7 - - - +
294A ALA* 1.3 64.1 + - - +
295A ALA 3.4 0.2 + - - -
296A GLY* 3.4 9.5 + - - -
297A LYS* 3.5 24.2 + - + +
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Residues in contact with ALA 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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280A SER* 4.0 9.4 - - - +
283A MSE 5.4 8.5 - - + -
284A GLN* 6.1 0.7 - - - +
291A ASP* 3.2 25.2 + - + +
293A GLU* 1.3 80.5 - - - +
295A ALA* 1.3 57.9 + - - +
297A LYS* 3.1 12.3 + - - +
298A LEU* 2.8 38.8 + - + +
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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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273A VAL 5.6 0.2 - - - +
276A GLY* 3.7 12.2 - - - +
277A CYS* 3.7 41.7 - - - -
280A SER* 4.2 3.7 - - - -
290A PHE* 4.4 0.7 - - + -
291A ASP 2.9 18.2 + - - +
292A LEU* 3.8 8.3 - - + +
293A GLU 3.2 0.2 - - - -
294A ALA* 1.3 78.8 - - - +
296A GLY* 1.3 57.8 + - - +
298A LEU* 3.8 0.8 - - - +
299A LYS* 2.8 32.7 + - - +
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Residues in contact with GLY 296 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A LEU 3.1 16.0 + - - -
293A GLU 3.4 3.1 + - - -
294A ALA 3.4 0.4 - - - -
295A ALA* 1.3 75.8 - - - +
297A LYS* 1.3 61.6 + - - +
299A LYS* 4.0 13.9 - - - +
300A ASN* 3.7 18.4 + - - +
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Residues in contact with LYS 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 GLU* 3.5 25.8 - - + +
294A ALA* 3.1 8.7 + - - +
295A ALA 3.0 0.8 - - - -
296A GLY* 1.3 76.8 - - - +
298A LEU* 1.3 66.6 + - + +
299A LYS 3.1 1.8 - - - -
300A ASN* 3.0 25.9 + - - +
301A GLN* 3.7 17.5 + - - +
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Residues in contact with LEU 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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239A PRO* 3.7 22.0 - - + +
241A VAL* 4.1 11.2 - - + -
276A GLY* 3.8 15.3 - - - +
279A ALA* 3.9 8.1 - - + -
280A SER* 3.8 34.1 - - - +
283A MSE 4.2 13.9 - - - -
294A ALA* 2.8 23.9 + - + +
295A ALA 3.8 3.8 - - - +
297A LYS* 1.3 76.9 - - + +
299A LYS* 1.3 57.1 + - - +
301A GLN* 2.8 41.2 + - - +
302A VAL* 3.5 11.6 + - - +
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Residues in contact with LYS 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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265A MSE 5.2 1.4 - - - +
269A GLU* 3.0 34.6 + - - +
272A LYS* 3.7 45.6 - - + +
273A VAL* 3.5 30.9 - - + +
276A GLY* 3.9 2.8 - - - -
295A ALA 2.8 18.1 + - - +
296A GLY* 4.0 11.7 - - - +
297A LYS 3.1 0.2 - - - -
298A LEU* 1.3 76.3 - - - +
300A ASN* 1.3 71.6 + - - +
301A GLN 3.3 1.0 + - - -
302A VAL* 3.5 16.9 + - - +
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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