Contacts of the helix formed by residues 203 - 210 (chain Z) in PDB entry 5GJQ
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 GLU 203 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195Z ASN* 5.3 8.0 - - + +
202Z HIS* 1.3 76.9 - - - +
204Z ALA* 1.3 64.0 + - + +
205Z CYS 3.3 4.4 - - - +
206Z ASP* 3.3 17.3 - - - +
207Z LEU* 3.2 17.3 + - - +
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Residues in contact with ALA 204 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188Z VAL* 5.1 1.6 - - + +
191Z ILE* 4.2 11.9 - - + +
192Z VAL* 3.5 40.0 - - + +
195Z ASN* 4.6 8.0 - - + +
203Z GLU* 1.3 76.3 - - + +
205Z CYS* 1.3 55.6 + - - +
206Z ASP 3.3 0.4 - - - -
207Z LEU* 3.1 17.4 - - + +
208Z LEU* 2.6 32.6 + - - +
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Residues in contact with CYS 205 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192Z VAL* 4.9 2.7 - - - +
195Z ASN* 5.8 1.2 - - - +
202Z HIS* 5.0 7.0 - - - +
203Z GLU 4.1 8.0 - - - +
204Z ALA* 1.3 76.0 - - - +
206Z ASP* 1.3 50.5 + - - +
208Z LEU* 2.5 13.9 + - - +
209Z MET* 2.5 36.8 + - - +
233Z LEU* 6.5 0.9 - - - -
236Z CYS* 5.1 15.9 - - + -
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Residues in contact with ASP 206 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203Z GLU* 3.3 16.9 + - - +
204Z ALA 3.3 0.2 - - - -
205Z CYS* 1.3 78.8 - - - +
207Z LEU* 1.3 63.7 + - - +
209Z MET* 3.3 18.3 + - - +
210Z GLU* 3.4 12.0 + - - +
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Residues in contact with LEU 207 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167Z ALA 6.0 1.6 - - - +
170Z TRP* 5.5 6.0 - - + +
188Z VAL* 5.1 13.5 - - + -
203Z GLU 3.2 7.7 + - - +
204Z ALA* 3.1 27.3 + - + +
205Z CYS 3.1 0.6 - - - -
206Z ASP* 1.3 75.4 - - - +
208Z LEU* 1.3 59.8 + - - +
210Z GLU* 3.2 19.8 - - - +
211Z ILE* 3.8 5.0 + - - +
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Residues in contact with LEU 208 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192Z VAL* 5.6 5.6 - - + -
204Z ALA 2.6 12.8 + - - +
205Z CYS* 2.5 20.1 + - - +
207Z LEU* 1.3 67.7 - - - +
209Z MET* 1.3 54.3 + - - +
210Z GLU 3.0 2.0 - - - -
211Z ILE* 2.6 36.0 + - + +
212Z GLU 4.0 2.4 + - - -
216Z MET* 5.9 7.6 - - + -
241Z PRO* 5.2 1.0 - - - +
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Residues in contact with MET 209 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205Z CYS 2.5 15.2 + - - +
206Z ASP* 3.3 15.2 + - - +
208Z LEU* 1.3 71.2 - - - +
210Z GLU* 1.3 62.1 + - - +
211Z ILE 3.2 1.0 + - - -
212Z GLU 4.1 0.3 + - - -
236Z CYS* 5.2 8.5 - - + +
240Z VAL* 3.9 30.4 - - + +
241Z PRO* 3.0 33.0 - - - +
242Z GLU 3.9 2.6 + - - -
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Residues in contact with GLU 210 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170Z TRP 5.5 7.2 - - - +
206Z ASP 3.4 7.6 + - - +
207Z LEU* 3.2 16.6 - - - +
209Z MET* 1.3 79.5 - - - +
211Z ILE* 1.3 61.6 + - - +
212Z GLU* 3.4 6.8 + - - +
242Z GLU* 5.4 2.6 + - - +
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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