Contacts of the helix formed by residues 168 - 199 (chain X) in PDB entry 5KHU
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 THR 168 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167X ARG* 3.8 29.6 - - - +
169X PRO* 3.8 28.9 - - - -
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Residues in contact with PRO 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168X THR* 3.8 28.3 - - - -
170X LYS* 3.8 29.2 - - - -
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Residues in contact with LYS 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169X PRO* 3.8 24.9 - - - -
171X ILE* 3.8 29.4 - - - +
173X MET* 4.4 15.9 - - - +
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Residues in contact with ILE 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170X LYS* 3.8 26.5 - - - +
172X ASN* 3.7 29.6 - - - +
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Residues in contact with ASN 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171X ILE* 3.7 29.6 - - - +
173X MET* 3.8 25.8 - - - +
175X LEU* 4.3 16.8 - - - +
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Residues in contact with MET 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170X LYS* 4.4 17.3 - - - +
172X ASN* 3.8 26.7 - - - +
174X MET* 3.8 29.4 - - - +
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Residues in contact with MET 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173X MET* 3.8 29.2 - - - +
175X LEU* 3.8 25.4 - - - +
177X ASN* 4.6 15.5 - - - +
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Residues in contact with LEU 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172X ASN* 4.3 17.7 - - - +
174X MET* 3.8 25.8 - - - +
176X ALA* 3.8 29.4 - - - +
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Residues in contact with ALA 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175X LEU* 3.8 29.6 - - - +
177X ASN* 3.8 25.8 - - - +
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Residues in contact with ASN 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174X MET* 4.6 16.4 - - - +
176X ALA* 3.8 25.4 - - - +
178X LEU* 3.8 29.8 - - - +
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Residues in contact with LEU 178 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177X ASN* 3.8 29.2 - - - +
179X TYR* 3.8 26.7 - - - +
181X LYS* 4.5 18.4 - - - +
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Residues in contact with TYR 179 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178X LEU* 3.8 23.6 - - - +
180X LYS* 3.8 29.8 - - - +
182X ALA* 4.3 16.8 - - - +
184X GLN* 4.4 16.4 - - - +
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Residues in contact with LYS 180 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179X TYR* 3.8 29.4 - - - +
181X LYS* 3.8 26.0 - - - +
183X GLY* 4.5 14.4 - - - +
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Residues in contact with LYS 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178X LEU* 4.5 13.9 - - - +
180X LYS* 3.8 29.4 - - - +
182X ALA* 3.8 24.5 - - - +
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Residues in contact with ALA 182 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179X TYR* 4.3 16.8 - - - +
181X LYS* 3.8 24.7 - - - +
183X GLY* 3.7 29.8 - - - +
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Residues in contact with GLY 183 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180X LYS* 4.5 16.4 - - - +
182X ALA* 3.7 29.6 - - - +
184X GLN* 3.8 23.8 - - - +
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Residues in contact with GLN 184 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179X TYR* 4.4 19.7 - - - +
183X GLY* 3.8 27.4 - - - +
185X GLU* 3.7 30.1 - - - +
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Residues in contact with GLU 185 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184X GLN* 3.7 30.3 - - - +
186X ARG* 3.8 29.6 - - - +
188X SER* 4.4 17.5 - - - +
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Residues in contact with ARG 186 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185X GLU* 3.8 29.6 - - - +
187X PRO* 3.8 23.8 - - - -
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Residues in contact with PRO 187 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186X ARG* 3.8 29.4 - - - -
188X SER* 3.8 26.9 - - - -
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Residues in contact with SER 188 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185X GLU* 4.4 16.8 - - - +
187X PRO* 3.8 26.5 - - - -
189X VAL* 3.8 28.9 - - - +
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Residues in contact with VAL 189 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188X SER* 3.8 29.4 - - - +
190X THR* 3.8 27.4 - - - +
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Residues in contact with THR 190 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189X VAL* 3.8 24.7 - - - +
191X SER* 3.8 29.4 - - - +
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Residues in contact with SER 191 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190X THR* 3.8 28.7 - - - +
192X TYR* 3.8 26.2 - - - +
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Residues in contact with TYR 192 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191X SER* 3.8 29.4 - - - +
193X LYS* 3.8 26.2 - - - +
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Residues in contact with LYS 193 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192X TYR* 3.8 28.0 - - - +
194X GLU* 3.8 29.4 - - - +
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Residues in contact with GLU 194 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193X LYS* 3.8 29.4 - - - +
195X VAL* 3.8 27.6 - - - +
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Residues in contact with VAL 195 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194X GLU* 3.8 26.9 - - - +
196X LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 196 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195X VAL* 3.8 26.7 - - - +
197X ARG* 3.8 29.6 - - - +
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Residues in contact with ARG 197 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196X LEU* 3.8 29.6 - - - +
198X GLN* 3.8 26.2 - - - +
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Residues in contact with GLN 198 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197X ARG* 3.8 29.4 - - - +
199X CYS* 3.8 25.8 - - - +
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Residues in contact with CYS 199 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198X GLN* 3.8 29.2 - - - +
200X PRO* 3.8 29.2 - - - -
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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