Contacts of the helix formed by residues 282 - 290 (chain E) in PDB entry 1R4N
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 PRO 282 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280E GLN 3.3 9.6 - - - +
281E ILE* 1.3 88.4 - - + +
283E SER* 1.3 67.5 + - - +
284E SER* 4.0 13.7 - - - +
285E ILE* 2.7 22.0 + - + +
286E GLU 3.2 7.8 + - - -
323E LEU* 3.7 15.3 - - + -
388E ALA* 3.9 29.6 - - + +
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Residues in contact with SER 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E ILE 3.4 4.7 + - - -
282E PRO* 1.3 68.3 - - - +
284E SER* 1.3 64.4 + - - +
286E GLU* 3.0 21.4 + - - +
287E ASP* 3.0 25.7 + - - +
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Residues in contact with SER 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282E PRO* 4.0 12.6 - - - +
283E SER* 1.3 78.3 + - - +
285E ILE* 1.3 67.5 + - - +
287E ASP* 3.5 13.8 + - - +
288E ILE* 3.3 22.9 + - - +
388E ALA 4.7 3.3 + - - -
390E LEU 4.2 12.3 + - - -
391E ARG* 5.4 10.7 - - - +
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Residues in contact with ILE 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E ILE* 4.1 6.7 - - + -
282E PRO* 2.7 19.2 + - + +
284E SER* 1.3 83.0 + - - +
286E GLU* 1.3 68.4 + - - +
288E ILE* 2.7 20.9 + - + +
289E PHE* 2.8 45.1 + - + +
323E LEU* 3.6 17.7 - - + -
387E SER 2.8 31.0 - - - +
388E ALA* 3.2 25.4 - - - +
390E LEU* 4.7 15.3 - - + +
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Residues in contact with GLU 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E ILE* 4.1 30.2 - - + +
282E PRO 3.2 7.7 + - - +
283E SER* 3.0 13.3 + - - +
285E ILE* 1.3 76.7 - - - +
287E ASP* 1.3 57.9 + - - +
289E PHE* 2.9 25.3 + - - +
290E ASN* 2.8 48.4 + - - +
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Residues in contact with ASP 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E SER* 3.0 27.2 + - - +
284E SER* 3.5 12.3 - - - +
285E ILE 3.1 0.2 - - - -
286E GLU* 1.3 78.4 - - - +
288E ILE* 1.3 60.8 + - + +
290E ASN* 3.6 9.1 + - - +
291E ASP* 3.3 20.4 + - - +
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Residues in contact with ILE 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284E SER 3.3 16.2 - - - +
285E ILE* 2.7 21.4 + - + +
287E ASP* 1.3 70.7 - - - +
289E PHE* 1.3 70.6 + - + +
291E ASP* 2.7 23.4 + - - +
294E CYS* 3.4 8.3 - - - +
304E PHE* 4.4 5.8 - - + -
305E TRP* 3.2 30.3 - - + -
308E ALA* 4.2 15.3 - - + -
390E LEU* 3.7 44.0 - - + +
391E ARG* 4.4 1.8 - - - +
392E VAL* 4.4 18.4 - - + +
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Residues in contact with PHE 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E ILE* 4.5 10.1 - - + -
285E ILE* 2.8 34.8 + - + -
286E GLU* 3.2 29.2 - - - +
288E ILE* 1.3 83.5 - - + +
290E ASN* 1.3 59.6 + - - +
291E ASP 3.2 2.8 + - - -
294E CYS* 3.3 22.1 - - - +
295E ILE* 3.8 2.8 - - - +
308E ALA* 3.4 13.9 - - - -
311E LEU* 3.8 11.0 - - + -
312E LYS* 3.3 69.2 + - + -
315E VAL* 3.8 25.8 - - + -
323E LEU* 4.1 5.6 - - + -
390E LEU* 6.1 1.3 - - + -
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Residues in contact with ASN 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E GLU* 2.8 41.9 + - - +
287E ASP* 3.8 9.2 + - - +
289E PHE* 1.3 72.8 - - - +
291E ASP* 1.3 61.4 + - - +
292E ASP 3.7 1.4 + - - -
295E ILE* 3.8 16.2 - - - +
312E LYS* 4.9 7.1 + - - -
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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