Contacts of the helix formed by residues 206 - 210 (chain E) in PDB entry 4S0H
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 PHE 206 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55E LYS* 6.3 0.2 - - - -
56E VAL* 4.0 22.9 - - + -
57E PHE* 3.8 10.3 - + - -
58E LEU* 3.5 46.0 - - + -
61E ARG* 5.9 0.7 - - - -
87E TYR* 3.7 27.3 + + - -
89E VAL* 4.4 11.2 - - + -
180E GLN* 3.1 10.4 + - - +
181E PRO 4.8 1.0 + - - -
183E LEU* 6.1 0.2 - - + -
204E HIS* 5.2 8.5 - - + -
205E VAL* 1.3 76.7 - - - +
207E PRO* 1.4 63.7 - - + +
208E GLU* 2.9 32.0 + - + -
209E THR* 2.8 29.1 + - - +
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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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68E HIS* 3.5 18.5 + - - +
180E GLN* 3.8 11.9 - - - +
205E VAL* 3.7 11.4 - - + +
206E PHE* 1.4 83.1 - - + +
208E GLU* 1.3 70.1 + - - +
209E THR 3.4 0.6 + - - -
210E ALA* 3.8 12.7 - - - +
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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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58E LEU* 3.8 19.8 - - + +
61E ARG* 3.4 35.1 + - - -
64E TRP* 3.8 23.2 - - + +
65E LEU* 4.0 25.4 - - + -
68E HIS* 3.8 25.1 + - + +
72E THR* 4.8 1.6 + - - -
206E PHE* 3.6 21.8 - - + +
207E PRO* 1.3 90.5 - - - +
209E THR* 1.3 60.1 + - - +
210E ALA 3.2 8.5 + - - +
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Residues in contact with THR 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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58E LEU* 3.6 29.6 - - + -
64E TRP* 3.7 34.3 - - + -
87E TYR* 3.8 23.1 - - + -
180E GLN* 3.6 6.9 + - - -
181E PRO* 3.1 27.2 + - - +
206E PHE* 2.8 21.6 + - + +
208E GLU* 1.3 74.8 - - - +
210E ALA* 1.3 64.0 + - - +
211E PHE* 3.2 11.1 - - - -
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Residues in contact with ALA 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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68E HIS* 4.6 7.8 + - + -
72E THR* 3.7 16.5 + - - +
109E ALA* 5.3 1.8 - - + -
178E LYS* 4.2 20.4 - - - +
179E TYR 3.2 13.2 - - - +
180E GLN* 3.4 22.4 - - + +
181E PRO* 4.1 3.1 - - - +
207E PRO 3.8 11.6 + - - +
208E GLU 3.2 4.8 - - - +
209E THR* 1.3 83.5 + - - +
211E PHE* 1.3 61.5 + - - +
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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