Contacts of the helix formed by residues 207 - 216 (chain E) in PDB entry 2RJF
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 SER 207 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206E TRP* 1.3 85.0 - - - +
208E TRP* 1.3 64.7 + - - +
209E GLU* 3.5 15.7 + - - +
210E SER* 2.6 34.9 + - - -
211E TYR* 3.2 20.8 + - - +
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Residues in contact with TRP 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206E TRP* 3.5 24.3 - + - -
207E SER* 1.3 72.5 - - - +
209E GLU* 1.3 69.3 + - - +
211E TYR* 3.3 5.5 + + - +
212E LEU* 2.9 50.6 + - + +
219E THR* 3.8 13.9 - - + -
454E LYS* 3.7 36.3 - - + -
455E LEU 3.5 27.8 - - - -
456E GLU* 2.8 35.3 + - + -
468E VAL* 3.6 27.4 - - + -
504E ALA* 3.6 15.7 - - + -
505E GLY* 3.6 14.9 - - - +
514E LEU* 3.7 8.7 - - + +
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Residues in contact with GLU 209 (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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207E SER* 3.2 14.7 - - - +
208E TRP* 1.3 94.3 + - - +
210E SER* 1.3 61.0 + - - +
212E LEU* 4.0 7.8 - - - +
213E GLU* 3.3 35.2 + - - +
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Residues in contact with SER 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E SER* 2.6 26.7 + - - -
209E GLU* 1.3 74.4 - - - +
211E TYR* 1.3 62.4 + - - +
213E GLU* 3.2 12.2 + - - +
214E GLU* 2.9 46.7 + - - +
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Residues in contact with TYR 211 (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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206E TRP* 3.5 32.5 - + + +
207E SER 3.2 16.4 + - - +
208E TRP* 3.7 13.9 - + - +
210E SER* 1.3 79.4 - - - +
212E LEU* 1.3 59.0 + - - +
214E GLU* 3.3 11.7 + - + +
215E GLN* 3.0 67.1 + - + +
454E LYS* 3.8 20.3 + - + -
468E VAL* 4.0 9.2 - - + -
484E ASP* 2.6 38.2 + - - +
517E PRO* 3.5 20.6 - - + +
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Residues in contact with LEU 212 (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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208E TRP* 2.9 40.5 + - + +
209E GLU* 4.0 6.5 - - - +
211E TYR* 1.3 76.9 - - + +
213E GLU* 1.3 54.4 + - + +
215E GLN* 4.7 1.6 - - - -
216E LYS* 2.8 30.0 + - - -
217E ALA* 3.1 38.6 + - + +
218E ILE* 4.0 5.6 - - - +
219E THR* 3.7 41.7 - - + +
454E LYS* 4.2 11.2 - - + -
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Residues in contact with GLU 213 (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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209E GLU* 3.3 24.7 + - - +
210E SER* 3.2 12.7 + - - +
212E LEU* 1.3 75.7 - - + +
214E GLU* 1.3 65.4 + - - +
216E LYS* 3.4 19.6 + - - +
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Residues in contact with GLU 214 (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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210E SER* 2.9 38.9 + - - +
211E TYR* 3.3 12.6 + - + +
213E GLU* 1.3 78.6 - - - +
215E GLN* 1.3 73.8 + - - +
216E LYS* 3.6 11.1 + - - -
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Residues in contact with GLN 215 (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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211E TYR* 3.0 58.9 + - + +
212E LEU 4.2 0.2 - - - +
214E GLU* 1.3 87.1 + - - +
216E LYS* 1.3 71.3 + - - +
217E ALA* 3.3 18.3 + - + +
454E LYS* 4.4 8.0 + - - -
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Residues in contact with LYS 216 (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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212E LEU 2.8 11.3 + - - -
213E GLU* 3.4 13.0 + - - +
214E GLU 3.3 11.6 - - - -
215E GLN* 1.3 80.8 - - - +
217E ALA* 1.3 56.9 + - - +
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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