Contacts of the helix formed by residues 195 - 199 (chain B) in PDB entry 4HH3
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 ILE 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B VAL* 4.4 8.7 - - + -
165B VAL* 3.8 33.0 - - + -
170B GLY* 3.0 24.1 + - - +
172B ILE* 4.0 26.2 - - + -
183B LEU* 5.4 4.0 - - + -
193B ALA 3.3 3.1 + - - -
194B ALA* 1.3 72.2 - - - +
196B ALA* 1.3 67.8 + - + +
198B GLU* 3.1 22.8 + - + +
199B PHE* 3.5 31.3 - - + -
204B ARG* 6.4 0.9 - - + -
207B PHE* 4.1 13.7 - - + -
208B MET* 4.0 18.6 - - + -
249B LEU* 5.5 0.7 - - + -
251B CYS* 5.3 7.2 - - - -
253B ILE* 6.4 0.4 - - + -
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B ALA* 3.3 1.9 - - + +
195B ILE* 1.3 82.5 - - + +
197B GLN* 1.3 61.0 + - + +
199B PHE* 3.1 27.5 + - - +
202B ARG* 3.6 10.6 - - - +
203B ARG* 3.5 13.2 - - - +
204B ARG* 3.5 37.9 - - + +
207B PHE* 4.0 22.0 - - + -
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Residues in contact with GLN 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ARG* 6.0 1.2 - - - +
194B ALA* 3.3 29.0 + - + +
195B ILE 3.2 1.0 - - - -
196B ALA* 1.3 76.9 - - + +
198B GLU* 1.3 63.1 + - - +
199B PHE 3.2 4.6 + - - +
202B ARG 5.0 5.6 - - - +
203B ARG* 6.4 0.7 - - - -
204B ARG* 6.2 1.8 - - - +
228B ARG* 3.0 28.9 + - - +
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Residues in contact with GLU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 4.7 8.5 - - + -
183B LEU* 4.8 11.2 - - + +
190B LEU* 3.6 16.0 - - + +
193B ALA* 3.8 9.2 - - + +
194B ALA 3.7 12.9 + - - +
195B ILE* 3.1 16.2 + - + +
197B GLN* 1.3 77.9 - - - +
199B PHE* 1.3 67.7 + - + +
227B ALA* 3.4 6.1 - - - +
228B ARG* 2.7 47.4 + - - +
229B ARG* 2.8 52.4 + - - +
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Residues in contact with PHE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B LEU* 3.7 31.6 - - + -
195B ILE* 3.5 39.0 - - + -
196B ALA 3.1 14.0 + - - +
197B GLN* 3.2 4.1 - - - -
198B GLU* 1.3 87.9 - - + +
200B GLU* 1.3 67.6 + - - +
201B GLY 3.3 0.5 + - - -
202B ARG* 3.2 24.5 + - + +
207B PHE* 3.7 33.4 - + - -
225B VAL* 3.5 38.8 - - + -
226B LEU 3.4 3.6 - - - +
227B ALA* 4.0 8.1 - - - -
228B ARG* 5.3 0.7 - - - -
234B LEU* 4.5 6.1 - - + -
236B VAL* 4.5 11.7 - - + -
253B ILE* 5.2 4.0 - - + -
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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