Contacts of the helix formed by residues 275 - 283 (chain E) in PDB entry 5DO9
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 LYS 275 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E GLU* 2.7 32.3 + - - +
50E SER 4.3 7.6 - - - -
51E GLY* 5.0 2.7 - - - +
155E ASP* 2.5 35.3 + - - +
231E ALA* 3.9 13.9 - - + +
232E LEU* 4.1 5.1 - - - +
233E SER* 3.6 22.0 - - - +
274E ASN* 1.3 97.2 + - - +
276E LYS* 1.3 63.4 + - - +
277E ASP* 3.2 14.8 + - - +
278E LEU* 3.3 15.3 + - + +
279E LEU* 3.2 19.2 + - - +
329E THR 3.2 2.0 + - - -
330E CYS* 5.1 0.9 - - - +
331E ALA 5.6 0.7 - - - +
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Residues in contact with LYS 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E LEU* 3.9 23.3 - - + -
274E ASN 3.3 0.8 - - - -
275E LYS* 1.3 77.3 - - - +
277E ASP* 1.3 62.2 + - - +
279E LEU* 3.4 7.5 + - - +
280E GLU* 3.2 33.7 + - - +
306E ARG* 4.1 26.8 - - - +
328E PHE* 4.1 8.0 + - + +
329E THR 3.2 25.2 + - - +
330E CYS* 4.1 21.8 - - + +
333E ASP* 6.0 0.9 - - - -
336E ASN* 3.6 21.4 - - - +
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Residues in contact with ASP 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E ARG* 4.6 12.3 + - - -
275E LYS* 3.6 15.8 - - - +
276E LYS* 1.3 82.0 - - + +
278E LEU* 1.3 88.0 + - - +
280E GLU* 3.3 26.1 + - - +
281E GLU* 3.5 6.1 + - - +
330E CYS* 3.5 30.4 - - + -
332E THR* 4.5 4.2 + - - -
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Residues in contact with LEU 278 (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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155E ASP* 3.8 45.1 - - + +
181E ARG* 5.3 8.7 - - - +
233E SER* 3.8 13.7 - - - +
275E LYS* 3.3 27.5 + - + +
277E ASP* 1.3 95.2 + - - +
279E LEU* 1.3 62.0 + - - +
281E GLU* 3.4 9.0 + - + +
282E LYS* 3.0 28.4 + - + +
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Residues in contact with LEU 279 (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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232E LEU* 4.2 26.0 - - + +
233E SER* 4.3 3.8 - - - +
235E TYR* 3.8 28.3 - - + -
275E LYS 3.2 12.9 + - - +
276E LYS* 3.4 10.8 - - - +
277E ASP 3.2 0.4 - - - -
278E LEU* 1.3 74.8 - - - +
280E GLU* 1.3 65.2 + - - +
282E LYS* 4.5 3.1 - - - +
283E ILE* 3.0 39.2 + - + +
302E ALA* 3.5 34.3 - - + +
305E ALA* 4.6 4.5 - - + -
306E ARG* 3.9 24.0 - - + +
309E ILE* 5.2 3.6 - - + -
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Residues in contact with GLU 280 (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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276E LYS* 3.2 20.0 - - + +
277E ASP* 3.3 15.7 + - - +
279E LEU* 1.3 78.7 - - - +
281E GLU* 1.3 62.1 + - - +
283E ILE* 3.7 4.9 - - - +
284E MET* 3.7 21.7 - - - +
302E ALA* 3.7 23.2 - - - +
306E ARG* 4.4 14.9 + - - -
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Residues in contact with GLU 281 (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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145E TYR* 5.2 8.0 + - - -
148E ARG* 4.8 15.0 + - - +
158E LYS* 4.0 25.0 + - - +
277E ASP 3.5 5.9 + - - +
278E LEU* 3.4 11.7 + - + +
279E LEU 3.2 0.6 - - - -
280E GLU* 1.3 81.5 - - - +
282E LYS* 1.3 70.4 + - + +
284E MET* 3.0 23.6 + - - +
285E TYR* 3.6 28.8 + - - -
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Residues in contact with LYS 282 (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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148E ARG* 4.1 26.0 - - - +
149E ARG* 5.5 1.2 - - - +
233E SER* 2.8 37.9 + - - +
235E TYR* 3.3 22.9 - - + +
236E ASP* 2.9 29.4 + - - +
237E GLN* 3.2 13.3 + - - +
278E LEU* 3.0 18.1 + - - +
279E LEU* 4.1 2.7 - - - +
281E GLU* 1.3 83.1 - - + +
283E ILE* 1.3 56.3 + - - +
284E MET 2.9 5.9 + - - -
285E TYR* 2.9 19.4 + - - +
286E SER* 3.0 19.9 + - - -
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Residues in contact with ILE 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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235E TYR* 3.6 22.6 + - + +
279E LEU* 3.0 28.2 + - + +
280E GLU 3.7 11.9 - - - +
281E GLU 3.1 0.4 + - - -
282E LYS* 1.3 75.3 - - - +
284E MET* 1.3 72.6 + - + +
285E TYR 3.1 2.3 + - - -
286E SER 3.9 9.7 + - - +
287E HIS* 4.6 4.5 + - - -
288E LEU* 4.4 14.4 - - + +
295E TYR* 6.4 0.4 - - + -
300E ARG* 3.5 16.9 + - - +
301E ASP 4.0 24.2 - - - +
302E ALA* 4.0 21.1 - - + +
305E ALA* 4.0 21.1 - - + -
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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