Contacts of the helix formed by residues 191 - 196 (chain B) in PDB entry 4B5G
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 MET 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B THR* 2.9 19.6 + - + -
190B ASP* 1.3 72.7 + - - +
192B TRP* 1.3 58.6 - - - +
194B THR* 3.3 10.8 + - + -
195B LEU* 2.9 46.3 + - + +
223B GLN* 3.3 27.8 + - + +
225B VAL* 3.6 22.0 - - + -
230B ALA* 3.3 38.1 - - + +
233B ALA* 3.6 17.5 - - + -
252B VAL* 4.0 19.1 - - + -
254B TYR* 4.0 10.3 - - - +
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Residues in contact with TRP 192 (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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46A ALA* 4.1 9.2 - - + -
190B ASP* 3.2 2.9 + - - +
191B MET* 1.3 77.5 - - - +
193B ARG* 1.3 69.9 + - - +
195B LEU* 3.2 6.8 + - - +
196B TYR* 2.8 43.5 + + - +
199B VAL* 3.2 41.5 + - + +
200B PRO 3.6 6.7 + - - -
201B GLY* 3.7 13.9 - - - -
219B ARG* 3.4 33.9 - - - +
223B GLN 6.0 1.0 - - - +
236B ALA* 3.3 49.3 - - + +
237B HIS* 3.5 15.5 - - - -
238B VAL* 4.2 10.8 - - + -
250B LEU* 3.9 24.8 - - + +
252B VAL* 5.9 1.5 - - + +
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Residues in contact with ARG 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B HIS* 6.0 4.3 - - + -
155B GLN* 4.8 10.3 + - - +
157B ILE* 3.6 22.5 - - - +
158B ASP* 2.6 30.5 + - - -
190B ASP* 3.1 28.9 + - + +
192B TRP* 1.3 87.0 - - - +
194B THR* 1.3 61.7 + - - +
196B TYR 2.7 28.9 + - - -
197B PRO* 3.2 43.4 - - - +
199B VAL 2.7 24.3 + - - -
200B PRO* 3.5 11.7 + - - +
219B ARG* 3.6 5.6 - - - +
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Residues in contact with THR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLY* 4.5 6.9 - - - -
189B THR* 3.5 21.8 + - + +
190B ASP* 3.1 15.0 + - - +
191B MET* 3.7 19.1 - - + -
193B ARG* 1.3 76.6 - - - +
195B LEU* 1.3 66.1 + - + +
197B PRO* 4.3 6.9 - - - +
230B ALA* 5.8 0.9 - - + +
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Residues in contact with LEU 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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50A ASN 3.9 0.2 - - - +
53A GLY* 3.4 25.3 + - - -
191B MET* 2.9 35.0 + - + +
192B TRP 3.7 3.4 - - - +
194B THR* 1.3 79.7 - - + +
196B TYR* 1.3 82.1 + - + +
197B PRO* 3.9 0.4 - - - -
230B ALA 5.4 0.2 - - - +
233B ALA* 3.9 37.9 - - + +
234B VAL 4.9 2.5 - - - -
235B SER* 3.9 17.7 - - - +
236B ALA* 3.6 30.5 - - + +
252B VAL* 4.6 0.4 - - + -
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Residues in contact with TYR 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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21A TYR* 6.0 0.2 - - - -
46A ALA* 3.4 31.0 - - + +
47A ASP* 2.8 29.0 + - - -
50A ASN* 3.6 23.3 - - + +
52A HIS 5.9 0.9 - - - -
192B TRP* 2.8 42.0 + + + +
193B ARG* 2.7 33.9 + - - +
195B LEU* 1.3 104.0 - - + +
197B PRO* 1.3 55.7 - - - +
198B ASP 3.2 5.5 + - - -
199B VAL* 3.6 15.3 + - + -
235B SER* 3.6 5.8 - - - -
236B ALA* 3.1 42.5 + - + -
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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