Contacts of the helix formed by residues 179 - 186 (chain E) in PDB entry 5FHK
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 HIS 179 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177E PRO* 3.7 6.9 - - - +
178E THR* 1.3 106.6 + - - +
180E ALA* 1.3 65.4 + - - +
181E GLU* 3.4 18.6 - - + +
182E ASP* 3.0 31.1 + - - +
254E LEU* 3.7 4.9 - - - -
257E TRP* 4.9 7.9 - + + +
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Residues in contact with ALA 180 (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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179E HIS* 1.3 73.3 - - - +
181E GLU* 1.3 64.2 + - - +
183E LEU* 3.1 24.7 + - - +
184E HIS* 5.6 0.2 - - - -
199E LEU* 4.1 15.0 - - + -
207E VAL* 3.8 30.5 - - + +
209E ASN* 5.3 1.4 + - - +
254E LEU* 3.9 14.4 - - + +
257E TRP* 3.8 32.9 - - + -
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Residues in contact with GLU 181 (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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179E HIS* 3.1 20.4 - - + +
180E ALA* 1.3 75.7 + - - +
182E ASP* 1.3 64.9 + - - +
183E LEU 3.1 1.4 + - - -
184E HIS* 3.1 37.8 + - + +
207E VAL* 3.7 32.3 - - + +
257E TRP* 5.5 1.0 - - - -
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Residues in contact with ASP 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E PRO* 3.6 15.2 - - + +
178E THR* 3.1 31.2 + - - -
179E HIS* 3.0 27.2 + - - +
181E GLU* 1.3 79.3 - - - +
183E LEU* 1.4 56.3 + - - +
184E HIS 3.0 0.4 - - - -
185E ASP* 2.8 36.6 + - - +
186E HIS* 3.3 14.2 - - + +
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Residues in contact with LEU 183 (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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164E LEU* 4.3 2.2 - - + -
177E PRO* 4.1 3.6 - - + -
180E ALA 3.4 16.6 - - - +
181E GLU 3.1 1.6 - - - -
182E ASP* 1.4 77.2 - - - +
184E HIS* 1.3 62.5 + - - +
185E ASP 3.0 0.2 - - - -
186E HIS* 3.1 22.1 + - - +
188E LEU* 3.6 20.3 - - + +
197E TRP* 4.1 15.9 - - + -
199E LEU* 3.6 29.6 - - + -
209E ASN* 3.8 17.7 - - + +
211E ASP* 4.1 0.2 - - - +
233E ILE* 4.0 40.8 - - + -
254E LEU* 3.9 25.6 - - + -
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Residues in contact with HIS 184 (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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180E ALA 5.6 0.2 - - - -
181E GLU* 3.1 33.3 + - + +
182E ASP 3.0 0.4 - - - -
183E LEU* 1.3 77.2 - - - +
185E ASP* 1.3 66.6 + - - +
186E HIS 3.5 3.8 + - - +
208E VAL 5.2 8.6 + - - -
209E ASN* 3.9 13.0 + - + -
210E VAL 5.7 0.2 - - - -
211E ASP* 2.9 42.7 + - - +
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Residues in contact with ASP 185 (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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182E ASP* 2.8 28.7 + - + +
184E HIS* 1.3 84.5 - - - +
186E HIS* 1.3 66.2 + - + +
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Residues in contact with HIS 186 (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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170E TYR* 3.0 25.1 + - - +
174E HIS* 4.4 8.4 - - + +
175E PRO 3.1 27.8 + - - -
176E MET* 4.0 10.3 - - + -
177E PRO* 3.7 24.8 - - + +
182E ASP* 3.3 29.2 + - - +
183E LEU* 3.1 17.2 + - - +
184E HIS 3.3 3.8 - - - +
185E ASP* 1.3 86.7 + - + +
187E PHE* 1.3 64.6 + - - +
188E LEU* 3.5 16.4 + - + +
211E ASP* 5.7 0.2 - - - +
233E ILE* 4.0 12.0 - - + +
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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