Contacts of the helix formed by residues 205 - 211 (chain E) in PDB entry 6BAA
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 205 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203E GLU* 3.9 4.5 + - + +
204E VAL* 1.3 73.2 - - - +
206E PRO* 1.4 64.9 - - + +
207E PRO 3.5 0.9 - - - -
208E GLU* 3.0 3.1 + - - -
209E ASP* 2.5 42.6 + - + +
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Residues in contact with PRO 206 (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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204E VAL* 4.1 2.5 - - + -
205E LYS* 1.4 90.7 - - + +
207E PRO* 1.3 58.5 - - + -
209E ASP* 4.5 3.8 - - + +
210E LEU* 2.6 37.5 + - - +
255E ILE* 3.6 36.8 - - + +
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Residues in contact with PRO 207 (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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65E TRP* 5.0 10.3 - - + +
204E VAL* 3.7 23.6 - - + -
206E PRO* 1.3 95.4 - - + +
208E GLU* 1.3 60.5 + - + +
210E LEU* 3.3 7.0 - - + +
211E GLN* 2.9 28.2 + - - +
221E PHE* 3.6 48.7 - - + -
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Residues in contact with GLU 208 (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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48A ASN* 2.9 30.3 - - + +
50A ARG* 6.2 1.6 - - + -
331B SER* 5.0 5.6 + - - -
63E SER 5.9 3.6 - - - +
65E TRP 5.8 4.0 + - - +
203E GLU* 4.5 6.5 - - - +
204E VAL* 3.3 23.6 - - + +
205E LYS* 3.0 4.1 + - - +
207E PRO* 1.3 82.3 - - - +
209E ASP* 1.3 61.2 + - - +
211E GLN* 3.3 12.6 + - - +
212E ASP* 3.7 1.4 + - - +
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Residues in contact with ASP 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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331B SER* 5.5 5.6 - - - -
205E LYS* 2.5 26.4 + - + +
206E PRO* 4.5 3.6 - - + +
208E GLU* 1.3 70.3 - - - +
210E LEU* 1.3 62.8 + - - +
211E GLN 3.3 0.2 - - - -
212E ASP* 3.3 21.0 - - - +
255E ILE* 5.8 4.7 - - + -
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Residues in contact with LEU 210 (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 PRO 2.6 24.5 + - - +
207E PRO* 3.3 11.0 - - + +
208E GLU 3.2 0.2 - - - -
209E ASP* 1.3 77.5 - - - +
211E GLN* 1.3 55.5 + - - +
212E ASP 3.1 6.5 + - - -
213E LEU* 3.8 3.1 + - - +
216E ARG* 3.0 37.4 + - - +
221E PHE* 4.7 10.8 - - + -
254E PRO* 4.9 11.9 - - + -
255E ILE* 4.7 11.6 - - + +
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Residues in contact with GLN 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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47A LYS* 5.4 5.5 - - - +
48A ASN* 3.9 10.5 + - - +
63E SER* 5.3 7.9 - - - +
207E PRO 2.9 12.1 + - - +
208E GLU* 3.3 16.4 - - - +
209E ASP 3.3 0.4 - - - -
210E LEU* 1.3 75.1 - - - +
212E ASP* 1.3 61.5 + - - +
213E LEU 3.2 0.9 - - - -
214E GLY* 3.2 17.1 + - - +
216E ARG* 4.0 14.8 - - + +
221E PHE* 5.2 4.9 - - + -
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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