Contacts of the helix formed by residues 182 - 190 (chain C) in PDB entry 3F78
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 ASP 182 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C PHE 3.7 6.9 - - - +
169C ALA* 3.9 6.1 - - + -
179C THR* 4.0 15.2 - - + +
181C PHE* 1.3 75.9 - - - +
183C PHE* 1.3 64.5 + - - +
184C SER* 2.6 28.9 + - - -
185C ASP* 2.8 27.1 + - - +
186C TYR 3.0 18.4 + - - -
219C VAL* 5.4 6.1 - - + +
224C LEU* 3.8 37.4 - - + +
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Residues in contact with PHE 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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131C ASP* 3.7 18.4 - - + -
132C LEU 3.5 29.4 - - - -
133C VAL* 3.6 23.8 - - + -
167C GLN* 3.7 24.2 - - + +
168C PHE 3.4 27.6 - - - -
169C ALA* 3.6 2.4 - - + +
182C ASP* 1.3 75.2 - - - +
184C SER* 1.3 63.5 + - - +
186C TYR* 3.2 3.3 + - - +
187C VAL* 3.0 28.7 + - - +
219C VAL* 3.9 18.8 - - + -
220C PHE* 3.7 22.0 - + - -
224C LEU 3.6 7.1 + - - +
225C GLY* 3.7 7.0 - - - -
226C ALA* 3.7 24.0 - - + -
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Residues in contact with SER 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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182C ASP* 2.6 22.9 + - - -
183C PHE* 1.3 76.5 - - - +
185C ASP* 1.3 66.1 + - - +
187C VAL* 3.4 7.6 + - - +
188C LYS* 3.0 25.1 + - - +
223C GLU 5.5 1.3 - - - -
224C LEU* 3.1 22.1 + - - +
225C GLY* 4.0 7.8 - - - -
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Residues in contact with ASP 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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179C THR* 5.6 0.2 - - - +
181C PHE* 3.5 16.9 - - + +
182C ASP* 2.8 46.2 + - - +
184C SER* 1.3 78.2 + - - +
186C TYR* 1.3 66.0 + - - +
188C LYS* 3.3 8.7 + - - +
189C TRP* 3.0 31.7 + - + +
195C LEU* 4.0 7.9 - - + -
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Residues in contact with TYR 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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158C MET* 4.4 13.1 + - + -
162C SER* 4.1 20.8 - - - -
163C ASN 5.0 0.3 + - - -
166C TYR 3.7 20.6 + - - -
167C GLN* 3.9 7.4 - - + -
168C PHE* 3.2 66.6 - + + +
181C PHE* 4.1 4.7 - + + -
182C ASP 3.0 5.8 + - - +
183C PHE 3.5 4.5 - - - +
185C ASP* 1.3 77.7 - - - +
187C VAL* 1.3 64.3 + - + +
190C LYS* 2.7 69.0 + - + +
192C PRO* 5.2 3.8 - - + -
195C LEU* 3.7 25.5 - - + +
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Residues in contact with VAL 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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167C GLN* 3.4 36.8 - - + +
183C PHE 3.0 18.4 + - - +
184C SER* 3.9 6.7 - - - +
185C ASP 3.3 0.2 - - - -
186C TYR* 1.3 79.3 - - + +
188C LYS* 1.3 64.2 + - - +
190C LYS* 3.5 29.1 + - - +
225C GLY* 6.5 0.2 - - - -
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Residues in contact with LYS 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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184C SER 3.0 17.1 + - - +
185C ASP* 3.7 9.2 - - - +
187C VAL* 1.3 81.4 - - - +
189C TRP* 1.3 78.5 + - + +
190C LYS* 5.1 0.5 - - - +
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Residues in contact with TRP 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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185C ASP* 3.0 15.2 + - + +
188C LYS* 1.3 105.7 - - + +
190C LYS* 1.3 70.7 + - - +
191C ASP* 3.0 14.2 + - + +
194C ALA* 3.9 37.9 - - + -
195C LEU* 3.8 24.7 - - + -
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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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163C ASN 6.0 3.5 - - - -
164C THR* 5.0 16.5 - - - +
166C TYR 5.7 0.9 - - - -
186C TYR* 2.7 61.1 + - + +
187C VAL* 3.5 33.3 + - - +
188C LYS 4.9 0.7 - - - +
189C TRP* 1.3 71.9 - - - +
191C ASP* 1.3 57.2 + - - +
192C PRO* 3.7 9.4 - - - +
195C LEU* 4.6 0.4 - - - +
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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