Contacts of the helix formed by residues 193 - 197 (chain B) in PDB entry 4M83
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 PRO 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B ILE* 1.3 98.0 - - + +
194B LYS* 1.3 66.2 + - - +
195B ALA* 4.2 6.1 - - + +
196B LEU* 3.0 40.3 + - + +
197B GLN 3.8 0.5 + - - -
212B GLY* 3.9 4.4 - - - -
213B ALA 5.1 1.3 - - - +
312B GLN* 3.9 20.6 - - + -
315B LEU* 4.8 2.9 - - + -
380B MET* 3.6 38.8 - - + -
383B GLU* 3.3 17.3 - - - +
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Residues in contact with LYS 194 (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 ILE 3.6 2.0 + - - -
193B PRO* 1.3 70.8 - - - +
195B ALA* 1.3 63.6 + - - +
197B GLN* 3.0 21.0 + - - +
200B ALA* 3.8 33.7 - - + +
201B ASP* 5.8 1.1 - - - +
203B VAL* 6.2 0.2 - - - -
205B GLU* 3.2 31.0 + - - -
210B PHE* 3.6 45.8 - - + -
379B GLU* 4.0 22.7 + - - +
383B GLU* 2.9 17.3 + - - +
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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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193B PRO* 3.1 6.3 - - + +
194B LYS* 1.3 78.8 - - - +
196B LEU* 1.3 58.8 + - - +
197B GLN 3.3 2.2 + - - +
315B LEU* 4.5 6.7 - - + -
336B MET* 3.6 12.5 - - - +
340B LEU* 3.7 34.8 - - + +
375B ARG* 6.0 0.4 - - - +
376B ILE* 4.0 33.2 - - + -
379B GLU* 5.1 9.2 + - - +
380B MET* 5.7 0.7 - - + -
383B GLU* 4.7 0.4 + - - -
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Residues in contact with LEU 196 (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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134B LEU* 5.0 1.6 - - - +
192B ILE* 3.9 17.2 - - + +
193B PRO* 3.0 34.8 + - + +
195B ALA* 1.3 76.5 - - - +
197B GLN* 1.3 57.6 + - - +
198B PRO* 3.4 11.1 - - - +
308B ALA* 5.1 2.0 - - - +
311B SER* 3.9 24.9 - - - -
312B GLN* 4.3 5.8 - - + +
315B LEU* 3.9 15.9 - - + -
333B ASN* 4.8 4.5 - - + +
336B MET* 3.4 36.9 - - + +
337B LEU* 4.0 24.0 - - + -
340B LEU* 4.5 2.5 - - + -
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Residues in contact with GLN 197 (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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134B LEU* 3.3 15.3 - - - +
135B VAL* 2.8 54.4 + - - +
137B TRP* 3.8 5.7 - - - -
192B ILE* 4.3 3.1 - - + +
193B PRO 3.8 0.6 + - - -
194B LYS 3.0 15.2 + - - +
195B ALA 4.4 1.2 - - - +
196B LEU* 1.3 78.4 - - - +
198B PRO* 1.3 84.1 - - - +
199B HIS 3.6 0.3 + - - -
200B ALA* 3.4 19.7 + - + +
203B VAL* 3.8 16.7 - - + +
210B PHE* 3.6 30.5 - - + -
336B MET* 3.7 5.4 - - - +
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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
------------------------------------------------------------
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