Contacts of the strand formed by residues 200 - 205 (chain H) in PDB entry 1BGX
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 200 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120H ALA* 4.0 11.8 - - + +
121H PRO* 4.2 28.5 - - + +
193H VAL* 4.3 1.7 - - - +
194H ALA* 4.1 2.1 - - - -
195H HIS* 3.4 24.8 + - - +
198H SER* 3.2 28.0 + - - -
199H SER* 1.3 73.6 - - - +
201H LYS* 1.3 64.8 + - - +
202H VAL* 4.1 12.4 + - + +
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Residues in contact with LYS 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193H VAL 4.0 4.3 - - - +
194H ALA* 4.0 26.9 - - + -
195H HIS 3.3 23.9 + - - +
196H PRO* 4.3 8.8 - - - +
199H SER* 3.6 25.5 + - - +
200H THR* 1.3 75.1 - - - +
202H VAL* 1.3 62.4 + - - +
203H ASP* 5.1 3.1 - - - +
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Residues in contact with VAL 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H PRO* 5.6 5.8 - - + +
123H VAL* 4.0 27.2 - - + +
191H CYS 4.3 0.7 - - - +
193H VAL* 3.4 31.4 + - + +
200H THR* 4.1 15.7 - - + +
201H LYS* 1.3 74.6 - - - +
203H ASP* 1.3 77.0 + - - +
204H LYS* 4.3 11.1 + - + +
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Residues in contact with ASP 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H THR* 4.6 7.5 + - - +
191H CYS 4.0 4.3 - - - -
192H ASN* 2.7 30.4 + - - +
201H LYS* 5.1 1.9 - - - +
202H VAL* 1.3 90.2 + - - +
204H LYS* 1.3 63.8 + - - +
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Residues in contact with LYS 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H VAL* 3.5 43.6 + - + -
125H PRO* 4.0 21.5 - - + -
136H CYS* 6.0 0.2 - - - -
190H THR* 3.0 16.5 + - - -
191H CYS* 3.0 29.0 + - + +
202H VAL* 5.4 10.0 - - + +
203H ASP* 1.3 78.2 + - - +
205H LYS* 1.3 69.2 + - - +
206H ILE* 4.2 2.9 + - + +
123L GLU* 2.9 40.8 + - - +
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Residues in contact with LYS 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H PRO* 3.9 14.9 - - - +
188H SER* 3.8 30.4 + - - +
189H ILE 4.3 11.7 - - - +
190H THR* 4.3 7.0 - - - +
203H ASP 4.4 0.2 - - - -
204H LYS* 1.3 79.2 - - - +
206H ILE* 1.3 68.8 + - - +
207H GLU* 3.4 43.5 + - + +
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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
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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