Contacts of the helix formed by residues 200 - 209 (chain C) in PDB entry 2JG1
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 SER 200 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198C ASP* 3.0 17.6 + - - -
199C GLU* 1.3 80.3 - - - +
201C LEU* 1.3 65.5 + - - +
202C GLU* 3.8 15.9 + - - +
203C SER* 3.2 17.2 + - - -
204C LEU* 3.0 21.8 + - - +
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Residues in contact with LEU 201 (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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199C GLU 3.7 1.5 + - - +
200C SER* 1.3 74.0 - - - +
202C GLU* 1.3 71.7 + - - +
204C LEU* 3.5 6.5 + - + +
205C LYS* 2.9 36.6 + - - +
229C PHE* 4.1 20.4 - - + -
238C ARG* 4.3 27.1 - - + +
310C VAL* 3.6 41.5 - - + -
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Residues in contact with GLU 202 (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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200C SER* 3.2 17.3 - - - +
201C LEU* 1.3 91.6 + - - +
203C SER* 1.3 59.3 + - - +
205C LYS* 3.6 10.6 + - + +
206C GLN* 3.2 23.0 + - - +
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Residues in contact with SER 203 (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 TYR* 3.1 19.7 + - - -
195C GLN* 5.1 3.3 + - - +
198C ASP* 3.3 26.5 + - - +
200C SER* 3.2 21.0 + - - -
202C GLU* 1.3 77.0 - - - +
204C LEU* 1.3 60.7 + - - +
206C GLN* 3.5 5.4 + - - +
207C ALA* 3.1 29.3 + - - +
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Residues in contact with LEU 204 (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* 4.2 17.0 - - + -
189C LEU* 3.9 22.9 - - + -
190C TYR* 3.9 11.9 - - - +
198C ASP 4.0 6.3 - - - +
199C GLU* 3.7 21.5 - - - +
200C SER 3.0 13.9 + - - +
201C LEU* 3.8 6.1 - - + +
203C SER* 1.3 73.7 - - - +
205C LYS* 1.3 65.3 + - - +
207C ALA* 3.6 1.9 + - - +
208C VAL* 3.2 30.7 + - - +
221C VAL* 4.3 9.4 - - + -
223C LEU* 4.4 13.5 - - + -
229C PHE* 3.8 41.7 - - + -
238C ARG* 5.4 2.5 - - - +
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Residues in contact with LYS 205 (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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201C LEU* 2.9 24.0 + - + +
202C GLU* 3.7 10.8 - - + +
204C LEU* 1.3 76.5 - - - +
206C GLN* 1.3 59.1 + - - +
208C VAL* 4.0 0.7 - - - +
209C SER* 2.6 33.0 + - - -
229C PHE* 3.9 3.6 - - + -
236C PHE* 3.6 46.8 - - + -
310C VAL* 2.7 48.4 + - - +
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Residues in contact with GLN 206 (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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202C GLU 3.2 14.8 + - - +
203C SER* 3.5 5.8 + - - +
204C LEU 3.4 0.2 - - - -
205C LYS* 1.3 77.9 - - - +
207C ALA* 1.3 63.1 + - - +
209C SER* 3.5 5.3 + - - -
210C GLN* 3.5 19.4 + - - +
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Residues in contact with ALA 207 (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 LEU* 4.3 11.9 - - + -
190C TYR* 4.2 14.1 - - + +
193C LEU* 3.6 26.7 - - + +
195C GLN* 4.9 5.4 - - - +
203C SER 3.1 18.0 + - - +
204C LEU 3.8 4.3 - - - +
206C GLN* 1.3 77.4 - - - +
208C VAL* 1.3 60.9 + - - +
210C GLN* 3.4 13.5 - - - +
213C PHE* 3.2 25.4 - - - -
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Residues in contact with VAL 208 (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 LEU* 4.3 11.2 - - + -
204C LEU 3.2 17.7 + - - +
205C LYS 4.2 1.8 - - - +
207C ALA* 1.3 76.3 - - - +
209C SER* 1.3 58.2 + - - +
210C GLN 3.3 1.9 + - - -
213C PHE* 3.6 19.6 - - - +
219C ILE* 3.5 25.1 - - + +
221C VAL* 4.0 23.3 - - + -
229C PHE* 4.0 15.7 - - + -
231C LYS* 3.0 47.3 + - + -
236C PHE* 4.7 1.1 - - + -
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Residues in contact with SER 209 (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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205C LYS 2.6 23.4 + - - -
206C GLN* 3.5 6.3 + - - -
207C ALA 3.3 0.6 - - - -
208C VAL* 1.3 74.2 - - - +
210C GLN* 1.3 63.0 + - - +
211C PRO* 3.8 3.3 - - - +
231C LYS* 4.0 12.0 + - - +
236C PHE* 3.3 22.9 - - - -
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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