Contacts of the helix formed by residues 179 - 186 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177D PRO* 3.9 0.3 - - - +
178D THR* 1.3 106.2 + - - +
180D ALA* 1.3 67.4 + - - +
181D GLU* 3.0 10.6 + - + +
182D ASP* 3.0 30.7 + - - +
254D LEU* 3.5 14.9 - - - +
257D TRP* 5.2 2.5 - - - +
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Residues in contact with ALA 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D HIS* 1.3 73.4 - - - +
181D GLU* 1.3 62.7 + - + +
183D LEU* 3.3 25.0 - - - +
184D HIS* 5.5 0.3 + - - -
199D LEU* 4.6 6.7 - - + -
207D VAL* 3.8 31.4 - - + +
209D ASN* 5.4 0.5 + - - -
254D LEU* 3.9 14.7 - - - +
257D TRP* 3.8 38.3 - - + +
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Residues in contact with GLU 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D HIS* 3.1 6.7 - - + +
180D ALA* 1.3 76.4 - - + +
182D ASP* 1.3 60.7 + - - +
183D LEU 2.9 10.8 + - - -
184D HIS* 3.1 46.2 + - + +
185D ASP* 4.6 1.4 - - - +
205D GLU* 5.5 0.2 - - - +
207D VAL* 3.1 40.5 - - - +
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Residues in contact with ASP 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D PRO* 3.3 22.5 - - + +
178D THR* 2.8 32.2 + - - -
179D HIS* 3.0 22.2 + - - +
181D GLU* 1.3 76.7 - - - +
183D LEU* 1.3 55.9 + - - +
184D HIS 3.2 0.4 - - - -
185D ASP* 2.9 33.1 + - - +
186D HIS* 3.0 19.2 - - + +
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Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D LEU* 4.0 14.8 - - + -
177D PRO* 4.4 4.7 - - + -
179D HIS 4.3 0.2 + - - -
180D ALA 3.3 16.4 - - - +
181D GLU 2.9 0.8 - - - -
182D ASP* 1.3 72.0 - - - +
184D HIS* 1.3 61.9 + - - +
185D ASP 3.0 6.6 + - - -
186D HIS* 3.3 17.8 + - - +
188D LEU* 3.9 22.2 - - + +
197D TRP* 4.0 17.3 - - + -
199D LEU* 3.7 30.1 - - + -
207D VAL* 6.1 0.4 - - + -
209D ASN* 3.6 21.1 - - + +
211D ASP* 4.1 0.3 - - - +
233D ILE* 4.1 26.5 - - + -
253D ILE* 4.9 0.2 - - + -
254D LEU* 3.8 20.6 - - + -
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Residues in contact with HIS 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D GLU* 3.1 45.9 + - + +
183D LEU* 1.3 76.4 - - + +
185D ASP* 1.3 66.3 + - - +
186D HIS 3.4 3.5 + - - +
207D VAL* 6.3 1.6 - - + -
208D VAL 5.2 3.4 - - - -
209D ASN* 3.7 23.5 + - - -
210D VAL 5.6 0.4 - - - -
211D ASP* 2.7 36.8 + - - +
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Residues in contact with ASP 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D HIS* 5.5 4.5 - - - -
181D GLU 4.6 0.6 - - - +
182D ASP* 2.9 29.8 + - - +
184D HIS* 1.3 87.8 - - - +
186D HIS* 1.3 67.9 + - + +
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Residues in contact with HIS 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D TYR* 2.9 27.3 + + - +
174D HIS* 3.8 19.1 - + + +
175D PRO* 3.1 30.9 + - + +
176D MET* 4.5 0.4 - - - -
177D PRO* 3.7 23.5 - - + +
182D ASP* 3.0 30.4 + - - +
183D LEU 3.3 15.0 + - - +
184D HIS 3.4 3.0 - - - +
185D ASP* 1.3 85.9 + - + +
187D PHE* 1.3 64.7 + - - +
188D LEU* 3.6 7.9 + - + +
233D ILE* 3.8 19.7 - - + +
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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