Contacts of the helix formed by residues 189 - 194 (chain C) in PDB entry 2JC6
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 ALA 189 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188C VAL* 1.3 79.3 - - - +
190C PRO* 1.3 76.5 - - + +
191C GLU* 3.3 24.9 - - - +
192C VAL* 3.0 19.4 + - + +
193C LEU* 3.5 5.4 + - - +
202C VAL* 4.2 17.5 - - + +
205C TRP* 3.7 28.2 - - + -
206C SER* 5.7 0.4 + - - -
233C ILE* 4.6 0.4 - - - -
267C ARG* 4.1 0.7 - - - +
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Residues in contact with PRO 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C VAL 3.9 1.1 - - - +
189C ALA* 1.3 87.8 - - + +
191C GLU* 1.3 59.9 + - - +
193C LEU* 3.2 3.3 + - + +
194C ALA* 2.8 25.3 + - - +
205C TRP* 3.7 38.1 - - + -
233C ILE* 3.4 31.0 - - + +
234C LEU* 3.2 26.0 - - + +
236C ALA* 4.7 0.4 - - + -
262C LYS* 4.1 28.3 - - + +
267C ARG* 4.2 0.2 - - - +
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Residues in contact with GLU 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C ALA* 3.7 10.4 - - - +
190C PRO* 1.3 74.5 - - - +
192C VAL* 1.3 64.8 + - + +
194C ALA* 3.4 12.5 + - - -
196C LYS* 3.0 45.6 + - + +
197C PRO 4.7 11.9 - - - +
198C TYR* 5.2 0.4 - - - -
199C SER* 5.2 1.4 + - - +
201C ALA* 4.4 1.0 - - - +
202C VAL* 3.2 30.4 + - + +
262C LYS 4.2 1.1 + - - +
264C PRO* 3.9 29.1 - - + +
267C ARG* 3.0 38.8 + - - -
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Residues in contact with VAL 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C VAL* 3.4 30.3 - - + -
189C ALA 3.0 13.4 + - - +
191C GLU* 1.3 77.3 - - + +
193C LEU* 1.3 61.5 + - + +
195C GLN* 3.0 20.3 + - - -
196C LYS 4.2 7.1 + - - +
198C TYR* 4.7 10.1 - - + -
202C VAL* 3.8 32.3 - - + -
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Residues in contact with LEU 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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185C PRO 5.4 0.7 - - - +
188C VAL* 3.7 25.6 - - + -
189C ALA 3.5 4.7 + - - +
190C PRO 3.2 7.1 + - - +
192C VAL* 1.3 76.0 - - + +
194C ALA* 1.3 52.5 + - - +
195C GLN* 2.8 18.9 + - - +
230C PHE* 3.8 52.9 - - + +
233C ILE* 3.4 44.4 - - + -
234C LEU* 3.7 11.8 - - + +
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Residues in contact with ALA 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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190C PRO 2.8 20.3 + - - +
191C GLU* 3.6 12.1 - - - +
192C VAL 3.3 0.4 - - - -
193C LEU* 1.3 69.0 - - - +
195C GLN* 1.3 69.7 + - - +
196C LYS* 2.8 19.1 + - + +
234C LEU* 3.5 15.6 - - + +
262C LYS* 6.2 1.3 - - - +
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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