Contacts of the helix formed by residues 187 - 198 (chain B) in PDB entry 4U8T
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 SER 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B SER* 2.7 25.6 + - - -
186B SER* 1.3 87.3 - - - +
188B LEU* 1.3 60.7 + - - +
189B GLU* 2.9 17.7 + - - +
190B HIS* 2.8 37.2 + - - -
191B VAL* 3.3 9.7 - - - +
229B VAL* 4.1 5.6 - - - +
0P 6MZ 4.9 0.2 - - - -
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Residues in contact with LEU 188 (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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187B SER* 1.3 71.2 - - - +
189B GLU* 1.3 64.3 + - - +
191B VAL* 3.3 4.7 + - + -
192B LYS* 3.1 44.1 + - + +
229B VAL* 4.0 28.5 - - + +
236B CYS* 4.9 3.6 - - + -
323B PHE* 3.7 35.4 - - + -
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B SER* 2.9 11.3 + - - +
188B LEU* 1.3 79.8 - - - +
190B HIS* 1.3 72.2 + - - +
192B LYS* 3.5 8.4 + - - +
193B LYS* 2.8 61.6 + - + +
254B TRP 6.0 0.2 - - - -
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Residues in contact with HIS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B SER* 3.8 15.3 - - - +
186B SER* 5.7 0.4 - - - -
187B SER* 2.8 20.4 + - - +
188B LEU 3.3 0.2 - - - -
189B GLU* 1.3 93.7 + - - +
191B VAL* 1.3 58.3 + - - +
193B LYS* 3.4 1.0 + - + -
194B SER 2.9 22.5 + - - -
200B TRP* 3.5 12.7 - - + -
253B ILE 5.0 0.4 - - - -
254B TRP* 3.3 61.9 + + + +
260B TYR* 4.1 9.0 - + - -
0P 6MZ 2.8 36.7 + + - +
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B SER* 3.7 19.5 - - - +
187B SER 3.3 17.5 - - - +
188B LEU* 3.6 9.2 - - + +
189B GLU 3.3 0.2 - - - -
190B HIS* 1.3 74.9 - - - +
192B LYS* 1.3 63.9 + - - +
194B SER* 3.2 7.7 + - - -
195B PHE* 3.2 18.2 + - - +
200B TRP* 4.2 3.6 - - + -
227B PHE* 4.3 12.3 - - + -
228B SER 5.8 0.4 - - - -
229B VAL* 3.9 14.6 - - + +
236B CYS* 4.0 12.8 - - - -
268B TRP* 3.8 20.1 - - + -
323B PHE* 3.7 27.9 - - + -
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Residues in contact with LYS 192 (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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188B LEU* 3.1 41.5 + - + +
189B GLU* 3.9 7.2 - - - +
190B HIS 3.4 0.2 - - - -
191B VAL* 1.3 73.2 - - - +
193B LYS* 1.3 67.1 + - + +
195B PHE* 3.0 14.1 + - - +
196B TYR* 3.0 37.1 + - + +
323B PHE* 3.3 47.5 + - + +
324B LEU* 5.7 0.9 - - + -
326B ASP* 4.0 17.8 + - - +
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Residues in contact with LYS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLU* 2.8 48.0 + - + +
190B HIS* 3.7 4.3 - - - +
192B LYS* 1.3 79.2 - - + +
194B SER* 1.3 62.6 + - - +
196B TYR* 4.4 9.0 - - + +
197B ASN* 3.1 34.0 + - - +
253B ILE* 3.0 43.8 + - + +
254B TRP* 4.2 11.0 - - + +
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Residues in contact with SER 194 (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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190B HIS 2.9 8.8 + - - -
191B VAL 3.4 10.5 - - - -
192B LYS 3.1 0.2 - - - -
193B LYS* 1.3 74.7 - - - +
195B PHE* 1.3 58.9 + - - +
197B ASN* 5.3 0.2 - - - -
198B GLY* 2.9 30.5 + - - -
199B ILE 2.8 26.5 + - - -
200B TRP* 3.4 28.8 - - - +
227B PHE* 4.4 0.5 - - - -
254B TRP* 4.6 3.3 - - - +
266B VAL* 3.8 5.0 - - - +
268B TRP* 3.1 23.4 + - - -
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Residues in contact with PHE 195 (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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167B ILE* 3.5 26.5 - - + -
191B VAL 3.2 8.3 + - - +
192B LYS 3.0 9.5 + - - +
194B SER* 1.3 82.1 - - - +
196B TYR* 1.3 89.7 + + - +
197B ASN 3.5 0.2 + - - -
198B GLY* 4.0 4.2 + - - -
268B TRP* 3.5 35.1 - + + +
271B VAL* 4.1 10.8 - - + -
323B PHE* 4.2 13.7 - + + -
324B LEU* 3.6 26.7 - - + -
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Residues in contact with TYR 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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192B LYS* 3.0 37.2 + - + +
193B LYS* 3.3 9.6 + - + +
195B PHE* 1.3 101.2 - + - +
197B ASN* 1.3 68.1 + - - +
198B GLY 3.7 0.2 - - - -
324B LEU* 3.9 18.7 - - + +
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Residues in contact with ASN 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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193B LYS* 3.1 29.1 + - - +
196B TYR* 1.3 85.2 - - - +
198B GLY* 1.3 65.0 + - - +
199B ILE* 3.3 16.6 + - + +
250B ASP* 4.9 8.0 - - + +
253B ILE* 3.5 38.6 - - + +
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Residues in contact with GLY 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B SER 2.9 12.5 + - - -
195B PHE 4.0 3.6 + - - -
196B TYR 3.7 1.6 - - - -
197B ASN* 1.3 78.1 - - - +
199B ILE* 1.3 64.1 + - - +
265B LYS* 3.4 7.3 - - - +
266B VAL* 2.9 38.3 + - - +
268B TRP* 5.2 2.0 - - - -
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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