Contacts of the helix formed by residues 208 - 213 (chain C) in PDB entry 3CQ6
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 208 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C THR* 3.6 17.0 + - - +
180C LEU* 4.2 1.6 - - - -
198C GLU* 2.7 29.1 + - - -
206C SER 3.7 1.2 + - - -
207C PRO* 1.3 73.6 - - - +
209C ALA* 1.3 52.3 + - - +
210C THR* 2.9 34.5 + - - +
211C THR* 2.7 38.3 + - - +
224C ARG* 3.6 1.2 + - - -
404C PO4 3.5 18.9 + - - -
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Residues in contact with ALA 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C LEU* 3.7 22.2 - - + +
183C VAL* 5.2 0.9 - - + -
196C VAL* 4.0 24.2 - - + -
198C GLU* 2.7 20.2 + - - +
208C SER* 1.3 65.4 - - - +
210C THR* 1.3 57.7 - - - +
211C THR* 3.0 3.8 - - - -
212C LEU* 2.8 30.2 + - + +
220C LEU* 3.5 12.5 - - + +
222C VAL* 3.8 16.6 - - + -
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Residues in contact with THR 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ILE* 4.5 8.7 - - + -
83C THR* 3.2 33.2 + - + -
85C VAL* 3.6 21.0 - - - +
87C VAL* 6.0 0.2 - - - -
208C SER* 2.9 22.2 + - - +
209C ALA* 1.3 76.1 - - - +
211C THR* 1.3 62.3 + - - +
213C LEU* 3.2 30.3 + - - +
214C GLU 4.7 0.7 + - - -
222C VAL* 3.8 21.7 - - + +
224C ARG* 5.1 0.4 - - - +
241C VAL* 4.2 23.3 - - + -
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Residues in contact with THR 211 (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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83C THR 4.3 11.0 - - - +
85C VAL* 3.7 22.0 - - + -
180C LEU* 3.2 20.8 - - - +
207C PRO* 4.6 13.0 - - + -
208C SER 2.7 22.8 + - - +
210C THR* 1.3 78.5 - - - +
212C LEU* 1.3 63.0 + - - +
213C LEU 3.4 0.2 - - - -
214C GLU* 4.7 8.4 + - - +
215C LYS* 5.3 0.9 + - - +
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Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C LEU* 4.0 25.8 - - + +
183C VAL* 3.9 26.7 - - + -
184C GLU* 3.7 44.4 - - + +
187C ILE* 4.1 7.6 - - + -
209C ALA* 2.8 14.1 + - - +
211C THR* 1.3 88.4 - - - +
213C LEU* 1.3 61.9 + - - +
214C GLU 3.3 1.8 - - - -
215C LYS* 3.2 10.9 + - + +
216C TYR* 3.2 30.7 + - + -
220C LEU* 3.6 10.7 - - + +
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C VAL* 5.8 2.0 - - + -
87C VAL* 5.2 6.3 - - + -
91C ASN* 6.0 0.2 - - - +
209C ALA 3.7 0.2 + - - -
210C THR* 3.2 32.3 + - + +
212C LEU* 1.3 74.7 - - - +
214C GLU* 1.3 66.6 + - - +
215C LYS 3.4 0.2 + - - -
216C TYR 3.4 8.8 + - - +
217C PRO* 3.4 18.4 - - + +
220C LEU* 3.4 45.5 - - + +
222C VAL* 4.2 2.9 - - + -
241C VAL* 3.6 48.0 - - + +
242C ALA* 3.9 13.2 - - - +
243C ASN* 4.7 2.4 - - - +
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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