Contacts of the helix formed by residues 192 - 197 (chain B) in PDB entry 6PSI
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 GLY 192 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B HIS* 6.4 0.2 - - - -
190B CYS* 3.7 9.7 - - - -
191B TYR* 1.3 80.2 - - - +
193B PRO* 1.4 71.6 - - - +
194B SER 3.9 0.2 - - - -
195B ALA* 4.0 4.5 - - - -
196B THR* 3.0 24.8 + - - -
296B THR 3.7 2.2 + - - -
297B TYR 3.6 12.1 - - - -
298B HIS* 4.0 4.7 - - - -
120C ARG* 4.4 6.3 + - - -
156C GLY 4.8 0.7 - - - +
158C VAL* 4.7 0.5 - - - +
177C VAL* 5.7 0.5 - - - +
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Residues in contact with PRO 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B GLU* 3.4 16.5 - - - +
149B LYS 3.3 29.4 - - - +
150B ASP* 3.4 23.6 - - + +
192B GLY* 1.4 82.2 - - - +
194B SER* 1.3 64.2 + - - +
195B ALA 3.2 3.1 - - - -
196B THR* 3.7 1.4 + - - -
197B SER* 2.9 30.4 + - - +
297B TYR 4.3 5.4 - - - +
298B HIS* 4.7 6.3 - - + -
299B GLY 3.9 17.7 - - - +
301B ILE* 4.7 2.2 - - + -
120C ARG* 3.4 24.6 - - - +
158C VAL* 4.1 0.3 - - - +
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Residues in contact with SER 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLU* 3.8 16.1 + - - +
193B PRO* 1.3 76.9 - - - +
195B ALA* 1.3 62.2 + - - +
196B THR 3.5 0.2 - - - -
197B SER 3.2 12.6 - - - -
198B GLU* 3.2 33.5 + - - +
297B TYR* 5.2 3.4 - - - -
299B GLY 4.3 1.5 + - - -
300B ASN* 2.9 49.4 + - - -
303B LYS* 3.8 2.6 + - - -
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B GLY* 4.0 8.3 - - - +
193B PRO* 3.2 0.6 - - - +
194B SER* 1.3 80.5 - - - +
196B THR* 1.3 62.2 + - + +
295B ALA 5.5 1.3 - - - +
296B THR 3.2 27.1 - - - +
297B TYR* 3.4 33.3 + - + +
299B GLY 5.0 0.2 + - - -
377B PHE* 3.4 16.8 - - - -
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Residues in contact with THR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TYR* 3.7 31.2 - - + -
192B GLY 3.0 15.4 + - - +
193B PRO 3.7 2.0 + - - -
195B ALA* 1.3 78.2 - - + +
197B SER* 1.3 62.1 + - - +
377B PHE* 3.3 9.9 - - - -
154C ARG* 2.8 26.5 + - - -
155C GLU 5.1 2.5 - - - +
156C GLY* 3.0 37.2 + - - +
157C SER* 3.3 8.0 + - - -
158C VAL* 4.0 2.8 - - - +
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Residues in contact with SER 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLU* 3.1 20.3 - - - +
193B PRO 2.9 21.8 + - - +
194B SER* 3.2 4.2 - - - -
195B ALA 3.5 0.2 - - - -
196B THR* 1.3 82.7 + - - +
198B GLU* 1.3 57.7 + - - +
199B LYS 3.1 9.9 - - - +
200B CYS* 4.3 10.1 - - - -
377B PHE* 4.0 2.5 - - - -
154C ARG* 4.5 3.8 + - - +
157C SER* 3.2 6.6 - - - -
158C VAL* 2.9 40.6 + - - +
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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