Contacts of the helix formed by residues 211 - 217 (chain C) in PDB entry 6D6Q
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 211 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ARG* 4.1 15.7 - - - +
33C ARG* 4.2 11.0 - - - +
145C ASP* 2.3 44.9 + - - -
146C GLY* 4.0 2.9 - - - -
209C ASP 3.6 2.8 + - - -
210C PRO* 1.3 77.4 - - - +
212C GLY* 1.3 65.4 + - - +
213C GLU* 4.3 7.0 - - + +
214C GLU* 3.4 29.5 + - + +
215C GLU* 3.2 17.3 + - - +
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Residues in contact with GLY 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ARG* 5.1 13.5 + - - -
144C TYR* 5.0 5.2 - - - -
145C ASP* 2.4 24.2 + - - -
146C GLY* 4.6 2.0 - - - -
211C THR* 1.3 74.9 + - - +
213C GLU* 1.3 65.4 + - - +
215C GLU* 2.9 18.3 + - - +
216C HIS* 2.9 12.6 + - - +
48F GLN* 6.2 1.3 - - - -
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Residues in contact with GLU 213 (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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10C PRO* 4.2 15.7 - - + +
14C TYR* 6.2 2.5 - - + -
211C THR* 3.7 5.5 - - + +
212C GLY* 1.3 73.2 - - - +
214C GLU* 1.3 61.7 + - + +
216C HIS* 2.9 39.2 + - - +
217C LEU* 3.0 44.4 + - + +
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Residues in contact with GLU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TYR* 2.9 43.4 + - + +
23C ARG* 3.4 26.7 + - - +
24C PRO* 4.9 2.1 - - - +
25C ASP* 5.7 0.2 - - - -
27C ARG* 4.0 5.9 + - - -
199C ALA* 4.6 2.8 - - - +
201C PHE* 4.3 6.1 - - - -
207C ILE* 3.1 22.0 - - + +
210C PRO* 3.3 19.0 - - + +
211C THR* 3.4 26.7 + - + +
212C GLY 3.2 0.6 - - - -
213C GLU* 1.3 77.9 - - + +
215C GLU* 1.3 57.0 + - - +
217C LEU* 4.2 9.7 - - - -
218C ALA* 3.2 24.1 + - - +
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Residues in contact with GLU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ARG* 5.7 1.1 + - - +
144C TYR* 3.3 28.2 + - - -
146C GLY* 4.2 3.3 - - - -
147C ASN* 3.2 26.3 + - - -
197C SER* 6.1 0.2 - - - -
199C ALA* 5.5 1.1 - - + -
210C PRO* 3.3 26.4 - - + +
211C THR 3.2 14.6 + - - +
212C GLY* 2.9 9.1 + - - +
214C GLU* 1.3 77.0 - - - +
216C HIS* 1.3 67.0 + - - +
217C LEU 3.4 0.4 + - - -
218C ALA* 3.7 14.6 + - - +
221C THR* 5.0 18.7 + - + +
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Residues in contact with HIS 216 (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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92C ARG* 5.7 7.9 - - - +
212C GLY 2.9 10.7 + - - +
213C GLU* 2.9 30.8 + - - +
215C GLU* 1.3 81.4 - - - +
217C LEU* 1.3 57.5 + - + +
218C ALA 3.4 4.9 + - - +
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Residues in contact with LEU 217 (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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10C PRO* 4.6 16.6 - - + -
11C LEU* 4.0 33.9 - - + +
14C TYR* 4.2 17.5 - - + -
201C PHE* 3.7 28.5 - - + -
213C GLU* 3.0 49.6 + - + +
214C GLU* 4.2 4.0 - - - +
216C HIS* 1.3 77.0 - - + +
218C ALA* 1.3 56.3 + - - +
219C THR* 5.7 0.9 - - - +
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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