Contacts of the helix formed by residues 182 - 192 (chain C) in PDB entry 1USK
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 PHE 182 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175C ILE* 3.9 31.9 - - + -
179C GLU* 3.3 39.5 - - + -
180C LYS 4.1 0.4 - - - -
181C ASP* 1.3 75.6 - - - +
183C SER* 1.3 59.4 + - - +
184C ALA 3.3 3.1 - - - +
185C LEU* 3.2 25.0 + - + +
186C ILE* 2.9 44.0 + - + +
205C GLU* 4.0 18.8 - - + -
208C GLN* 3.5 22.2 - - + -
209C MET* 4.1 25.6 - - + -
212C GLN* 3.1 26.2 + - - +
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Residues in contact with SER 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ASP* 3.4 24.3 + - - -
182C PHE* 1.3 77.6 - - - +
184C ALA* 1.3 59.2 + - - +
186C ILE* 4.0 8.2 - - - +
187C ALA* 3.1 29.5 + - - +
212C GLN* 3.9 4.4 + - - -
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Residues in contact with ALA 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ASP* 5.2 1.9 + - - +
182C PHE* 3.3 0.8 - - - +
183C SER* 1.3 79.8 + - - +
185C LEU* 1.3 63.4 + - - +
187C ALA* 3.4 7.0 + - - +
188C ARG* 3.2 20.8 + - - +
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Residues in contact with LEU 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ILE* 3.8 40.2 - - + -
171C PHE* 4.4 16.2 - - + -
173C ASP* 4.8 9.6 - - - +
175C ILE* 4.4 10.8 - - + -
182C PHE* 3.2 28.9 + - + +
184C ALA* 1.3 79.2 - - - +
186C ILE* 1.3 62.5 + - + +
188C ARG* 3.3 10.5 + - + +
189C LEU* 3.1 36.4 + - + +
209C MET* 4.2 26.0 - - + -
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Residues in contact with ILE 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C PHE* 2.9 32.1 + - + +
183C SER* 4.0 7.2 - - - +
185C LEU* 1.3 73.9 - - + +
187C ALA* 1.3 65.1 + - - +
189C LEU* 3.2 16.2 + - + +
190C LYS* 3.1 22.9 + - + +
209C MET* 4.2 8.3 - - + +
212C GLN* 3.4 43.1 - - + +
213C ALA* 3.6 13.7 - - + +
216C VAL* 3.4 32.3 - - + -
218C LEU* 4.2 8.7 - - + +
222C PHE* 6.2 0.2 - - + -
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Residues in contact with ALA 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C SER 3.1 18.1 + - - +
184C ALA* 3.7 7.0 - - - +
185C LEU 3.3 0.2 - - - -
186C ILE* 1.3 73.6 - - - +
188C ARG* 1.3 60.5 + - - +
190C LYS* 3.2 9.3 + - - +
191C LYS* 3.0 38.4 + - + +
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Residues in contact with ARG 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C PHE* 3.6 55.1 - - + +
172C PHE 5.5 1.2 + - - -
173C ASP* 4.1 20.4 + - - +
184C ALA 3.2 13.6 + - - +
185C LEU* 3.4 15.3 - - - +
186C ILE 3.3 0.2 - - - -
187C ALA* 1.3 78.2 - - - +
189C LEU* 1.3 57.3 + - - +
191C LYS* 4.7 4.0 - - - -
192C GLU* 3.1 53.9 + - + +
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Residues in contact with LEU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ALA* 3.9 3.1 - - + -
144C ILE* 5.5 1.6 - - + -
171C PHE* 3.7 25.6 - - + -
185C LEU* 3.1 30.4 + - + +
186C ILE* 3.6 14.6 - - + +
187C ALA 3.2 0.4 - - - -
188C ARG* 1.3 74.2 - - - +
190C LYS* 1.3 62.7 + - - +
193C ASN* 3.2 1.9 + - - -
194C ILE* 3.0 47.1 + - + +
197C VAL* 3.8 31.9 - - + -
209C MET* 5.8 1.6 - - + -
218C LEU* 4.0 28.6 - - + +
220C THR* 4.7 1.8 - - - +
222C PHE* 4.6 10.3 - - + -
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Residues in contact with LYS 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C ILE* 3.1 12.5 + - + +
187C ALA* 3.2 11.2 + - - +
189C LEU* 1.3 75.6 - - - +
191C LYS* 1.3 67.8 + - + +
193C ASN* 3.2 14.4 + - - +
216C VAL* 2.6 51.4 + - - +
217C GLY 4.8 0.9 - - - -
218C LEU* 3.3 27.1 - - + +
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Residues in contact with LYS 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C ALA* 3.0 24.7 + - + +
188C ARG* 4.1 5.4 - - - +
190C LYS* 1.3 78.2 - - + +
192C GLU* 1.3 64.7 + - + +
193C ASN* 3.3 5.9 + - - +
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Residues in contact with GLU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ARG* 2.9 33.2 + - - +
170C VAL* 3.2 23.0 - - - +
171C PHE* 3.8 13.9 - - + +
188C ARG* 3.1 44.5 + - + +
189C LEU 4.0 0.2 - - - -
191C LYS* 1.3 79.4 - - + +
193C ASN* 1.3 62.3 + - - +
194C ILE* 3.4 15.9 + - + +
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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