Contacts of the helix formed by residues 192 - 198 (chain D) in PDB entry 5D0A
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 192 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D LYS* 4.6 5.8 - - - +
190D SER 3.8 8.8 + - - +
191D CYS* 1.3 79.9 - - - +
193D LYS* 1.3 61.5 + - - +
194D CYS 3.3 2.7 - - - -
195D LEU* 3.1 28.6 + - + -
196D ASP* 3.0 47.7 + - - -
206D PRO* 6.0 0.4 - - + -
501D SF4 4.3 2.7 - - - -
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Residues in contact with LYS 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D CYS* 3.4 22.9 - - - -
192D THR* 1.3 79.3 - - - +
194D CYS* 1.3 57.9 + - - +
196D ASP* 3.5 6.8 + - - +
197D ALA* 2.9 31.9 + - - +
246D VAL* 3.8 25.1 + - + +
248D PRO* 3.9 19.9 - - + +
501D SF4 3.8 10.0 - - - -
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Residues in contact with CYS 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D LYS 4.0 0.2 - - - -
155D ASN* 3.6 31.6 - - + -
193D LYS* 1.3 76.6 - - - +
195D LEU* 1.3 84.2 + - - +
197D ALA 3.8 0.5 - - - -
198D CYS* 3.0 25.8 + - - +
203D LEU* 3.8 4.5 - - + +
243D CYS* 3.7 29.6 - - + +
246D VAL* 4.0 10.1 - - - -
501D SF4 2.3 41.0 - - - -
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Residues in contact with LEU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D LYS* 3.7 29.4 - - + +
192D THR* 3.1 35.6 + - + +
194D CYS* 1.3 85.7 - - - +
196D ASP* 1.3 65.7 + - - +
198D CYS* 3.8 11.4 + - - +
201D GLY* 5.3 4.7 - - - -
203D LEU* 3.8 33.5 - - + +
205D ASN* 4.1 4.3 - - - +
206D PRO* 4.0 34.3 - - + -
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Residues in contact with ASP 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D THR* 3.0 38.2 + - - +
193D LYS* 3.9 6.5 + - - +
195D LEU* 1.3 81.3 - - - +
197D ALA* 1.3 59.8 + - - +
198D CYS 3.5 2.9 - - - +
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Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D LYS 2.9 18.5 + - - +
194D CYS* 3.3 2.2 + - - +
196D ASP* 1.3 76.7 - - - +
198D CYS* 1.3 66.2 + - - +
199D PRO* 3.1 10.2 - - - +
242D THR* 3.8 14.3 - - + +
243D CYS* 5.9 0.2 - - - -
246D VAL* 4.0 28.5 - - + -
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Residues in contact with CYS 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D CYS 3.0 16.3 + - - +
195D LEU 4.1 8.5 - - - +
196D ASP 3.5 4.3 - - - +
197D ALA* 1.3 75.9 - - - +
199D PRO* 1.3 69.9 - - - +
200D THR* 3.1 9.0 + - - -
201D GLY* 3.2 12.6 + - - +
202D ALA 3.3 29.4 - - - +
203D LEU* 4.0 10.5 - - + +
502D SF4 2.3 42.4 - - - -
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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