Contacts of the helix formed by residues 182 - 194 (chain C) in PDB entry 3COA
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 182 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C LEU* 1.3 77.2 - - - +
183C LEU* 1.3 65.2 + - - +
184C SER* 3.7 7.7 + - - -
185C GLN* 3.0 35.9 + - - +
186C ILE* 3.1 19.8 + - - +
228C ASN* 4.0 19.5 - - - +
233C LYS* 6.2 0.4 - - + -
234C SER* 3.9 14.8 - - - +
235C SER 3.4 21.1 - - - +
236C TRP* 3.9 14.3 - - + -
237C TRP* 4.3 1.3 - - - -
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Residues in contact with LEU 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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2A T 3.6 45.1 - - + +
3A G 3.7 15.0 + - - +
182C THR* 1.3 73.4 - - - +
184C SER* 1.3 62.4 + - - +
186C ILE* 3.1 8.5 + - - +
187C TYR* 3.0 65.1 + - + +
213C ILE* 3.8 9.2 - - + -
214C ARG* 3.7 16.2 - - + -
217C LEU* 3.7 23.8 - - + -
234C SER* 4.5 3.8 + - - +
235C SER 4.4 1.2 + - - -
237C TRP* 3.9 10.9 - - - +
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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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2A T 4.0 18.6 + - - -
182C THR* 3.2 9.0 + - - -
183C LEU* 1.3 77.9 - - - +
185C GLN* 1.3 59.2 + - - +
187C TYR* 3.3 16.6 + - - +
188C GLU* 3.0 41.9 + - - +
234C SER* 5.4 1.1 + - - -
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Residues in contact with GLN 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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181C LEU* 3.5 32.1 - - + +
182C THR* 3.0 40.1 + - - +
184C SER* 1.3 75.1 - - - +
186C ILE* 1.3 61.8 + - - +
188C GLU* 3.4 17.3 + - - +
189C TRP* 2.9 28.4 + - - +
236C TRP* 3.5 16.9 - - - -
233F LYS* 5.7 6.9 - - - +
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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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169C ILE* 4.2 26.5 - - + -
172C ALA* 4.3 14.1 - - + -
173C ILE* 4.4 6.5 - - + -
181C LEU* 3.9 20.0 - - + +
182C THR 3.1 14.5 + - - +
183C LEU* 3.1 7.7 + - - +
185C GLN* 1.3 75.1 - - - +
187C TYR* 1.3 66.5 + - - +
189C TRP* 3.1 8.0 + - - +
190C MET* 3.1 33.6 + - + +
213C ILE* 4.1 20.0 - - + -
217C LEU* 4.0 24.0 - - + -
237C TRP* 4.2 17.3 - - + -
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Residues in contact with TYR 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A T 3.6 21.1 + - - +
183C LEU* 3.0 51.5 + - + +
184C SER* 3.5 13.2 - - - +
185C GLN 3.3 0.2 - - - -
186C ILE* 1.3 75.4 - - - +
188C GLU* 1.3 64.3 + - + +
190C MET* 3.0 15.2 + - - +
191C VAL* 3.1 17.6 + - + +
209C TRP* 3.8 19.5 - + + -
210C LYS* 3.6 56.1 - - + -
213C ILE* 4.0 11.7 - - + -
214C ARG* 2.9 28.6 + - - +
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Residues in contact with GLU 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 32.1 + - - +
185C GLN* 3.5 19.2 + - - +
187C TYR* 1.3 76.3 - - + +
189C TRP* 1.3 62.9 + - - +
191C VAL* 3.6 6.5 + - - +
192C LYS* 3.1 25.8 + - - +
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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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168C LEU* 3.7 10.3 - - + -
171C LYS* 3.7 44.4 - - + -
172C ALA* 3.5 22.2 - - + -
175C SER* 3.4 29.7 + - - -
181C LEU* 5.2 3.6 - - + -
185C GLN 2.9 14.0 + - - +
186C ILE 3.1 7.4 + - - +
188C GLU* 1.3 74.2 - - - +
190C MET* 1.3 94.1 + - + +
192C LYS* 4.7 2.2 - - - -
193C SER* 2.7 66.7 + - - -
194C VAL* 3.9 17.9 - - + -
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Residues in contact with MET 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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165C TYR* 5.6 0.7 - - - -
168C LEU* 3.3 44.0 - - + -
169C ILE* 4.1 5.2 - - - +
172C ALA* 4.5 2.0 - - + -
186C ILE* 3.1 21.4 + - + +
187C TYR 3.0 6.3 + - - +
189C TRP* 1.3 117.8 - - + +
191C VAL* 1.3 59.1 + - - +
194C VAL* 2.9 39.9 + - - +
197C PHE* 3.8 16.7 - - + +
209C TRP* 3.7 27.6 - - + -
213C ILE* 4.1 16.8 - - + -
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Residues in contact with VAL 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 TYR 3.1 11.5 + - - +
188C GLU* 4.1 5.8 - - - +
190C MET* 1.3 76.2 - - - +
192C LYS* 1.3 60.6 + - - +
194C VAL 4.6 0.7 - - - +
197C PHE* 3.8 11.2 - - + +
198C LYS* 3.4 38.0 - - - +
201C GLY* 3.7 28.9 - - - -
209C TRP* 3.7 20.6 - - + -
210C LYS* 6.1 0.2 - - - -
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Residues in contact with LYS 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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188C GLU 3.1 19.2 + - - +
189C TRP* 4.2 2.7 - - + +
191C VAL* 1.3 78.3 - - + +
193C SER* 1.3 64.5 + - - +
194C VAL 3.8 0.2 - - - -
28E A 5.9 4.1 - - - +
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Residues in contact with SER 193 (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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189C TRP* 2.7 64.2 + - - -
192C LYS* 1.3 78.6 - - - +
194C VAL* 1.3 59.1 + - - +
195C PRO* 3.6 8.7 - - - +
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Residues in contact with VAL 194 (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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160C TRP* 4.0 22.0 - - + +
168C LEU* 4.1 20.2 - - + -
189C TRP* 3.9 26.7 - - + -
190C MET* 2.9 19.8 + - - +
191C VAL 4.6 0.6 - - - +
192C LYS 3.8 0.4 - - - -
193C SER* 1.3 77.7 - - - +
195C PRO* 1.3 71.6 - - + +
196C TYR 4.1 2.9 - - - +
197C PHE* 2.9 46.4 + - + -
198C LYS* 3.2 10.5 + - - -
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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
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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