Contacts of the helix formed by residues 168 - 199 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167Y ARG* 3.8 28.9 - - - +
169Y PRO* 3.8 28.9 - - - -
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Residues in contact with PRO 169 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168Y THR* 3.8 28.9 - - - -
170Y LYS* 3.8 26.7 - - - -
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Residues in contact with LYS 170 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169Y PRO* 3.8 25.6 - - - -
171Y ILE* 3.8 29.4 - - - +
173Y MET* 4.5 15.3 - - - +
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Residues in contact with ILE 171 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170Y LYS* 3.8 26.0 - - - +
172Y ASN* 3.8 30.1 - - - +
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Residues in contact with ASN 172 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171Y ILE* 3.8 25.8 - - - +
173Y MET* 3.8 28.7 - - - +
175Y LEU* 4.3 16.8 - - - +
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Residues in contact with MET 173 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170Y LYS* 4.5 16.8 - - - +
172Y ASN* 3.8 29.2 - - - +
174Y MET* 3.8 24.5 - - - +
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Residues in contact with MET 174 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173Y MET* 3.8 25.4 - - - +
175Y LEU* 3.8 29.4 - - - +
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Residues in contact with LEU 175 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172Y ASN* 4.3 17.3 - - - +
174Y MET* 3.8 27.8 - - - +
176Y ALA* 3.8 29.2 - - - +
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Residues in contact with ALA 176 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175Y LEU* 3.8 28.9 - - - +
177Y ASN* 3.8 26.7 - - - +
188Y SER* 4.0 27.1 - - - +
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Residues in contact with ASN 177 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176Y ALA* 3.8 25.8 - - - +
178Y LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 178 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177Y ASN* 3.8 28.7 - - - +
179Y TYR* 3.8 27.6 - - - +
181Y LYS* 4.6 16.4 - - - +
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Residues in contact with TYR 179 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178Y LEU* 3.8 24.7 - - - +
180Y LYS* 3.8 28.7 - - - +
182Y ALA* 4.6 13.5 - - - +
184Y GLN* 4.3 20.2 - - - +
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Residues in contact with LYS 180 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179Y TYR* 3.8 29.2 - - - +
181Y LYS* 3.8 25.8 - - - +
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Residues in contact with LYS 181 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178Y LEU* 4.6 14.4 - - - +
180Y LYS* 3.8 26.5 - - - +
182Y ALA* 3.8 28.7 - - - +
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Residues in contact with ALA 182 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179Y TYR* 4.6 15.3 - - - +
181Y LYS* 3.8 25.1 - - - +
183Y GLY* 3.8 29.4 - - - +
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Residues in contact with GLY 183 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182Y ALA* 3.8 28.9 - - - +
184Y GLN* 3.8 27.1 - - - +
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Residues in contact with GLN 184 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179Y TYR* 4.3 21.8 - - - +
183Y GLY* 3.8 28.5 - - - +
185Y GLU* 3.7 29.4 - - - +
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Residues in contact with GLU 185 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184Y GLN* 3.7 29.4 - - - +
186Y ARG* 3.8 29.4 - - - +
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Residues in contact with ARG 186 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185Y GLU* 3.8 29.2 - - - +
187Y PRO* 3.8 24.5 - - - -
189Y VAL* 4.4 18.2 - - - +
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Residues in contact with PRO 187 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186Y ARG* 3.8 24.0 - - - -
188Y SER* 3.8 28.9 - - - -
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Residues in contact with SER 188 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176Y ALA* 4.0 27.1 - - - +
187Y PRO* 3.8 29.4 - - - -
189Y VAL* 3.8 26.9 - - - +
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Residues in contact with VAL 189 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186Y ARG* 4.4 18.6 - - - +
188Y SER* 3.8 28.3 - - - +
190Y THR* 3.8 29.4 - - - +
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Residues in contact with THR 190 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Y VAL* 3.8 29.4 - - - +
191Y SER* 3.8 25.4 - - - +
193Y LYS* 4.3 17.9 - - - +
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Residues in contact with SER 191 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190Y THR* 3.8 25.8 - - - +
192Y TYR* 3.8 29.4 - - - +
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Residues in contact with TYR 192 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191Y SER* 3.8 29.4 - - - +
193Y LYS* 3.8 25.1 - - - +
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Residues in contact with LYS 193 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190Y THR* 4.3 16.4 - - - +
192Y TYR* 3.8 28.7 - - - +
194Y GLU* 3.8 26.5 - - - +
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Residues in contact with GLU 194 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193Y LYS* 3.8 26.2 - - - +
195Y VAL* 3.8 29.4 - - - +
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Residues in contact with VAL 195 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194Y GLU* 3.8 26.5 - - - +
196Y LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 196 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195Y VAL* 3.8 29.6 - - - +
197Y ARG* 3.8 26.9 - - - +
----------------------------------------------------------
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Residues in contact with ARG 197 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196Y LEU* 3.8 24.5 - - - +
198Y GLN* 3.8 29.6 - - - +
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Residues in contact with GLN 198 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197Y ARG* 3.8 28.3 - - - +
199Y CYS* 3.7 29.4 - - - +
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Residues in contact with CYS 199 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198Y GLN* 3.7 27.1 - - - +
200Y PRO* 3.2 34.5 - - - -
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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
------------------------------------------------------------
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