Contacts of the strand formed by residues 146 - 150 (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 VAL 146 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121H PRO* 5.0 2.2 - - + -
138H VAL* 4.8 7.4 - - + -
141H TYR* 3.7 35.9 - - + +
145H PRO* 1.3 82.6 - - - +
147H THR* 1.3 63.5 + - - +
148H LEU* 3.6 5.0 + - + +
173H LEU* 3.8 30.0 - - + +
193H VAL* 4.2 21.8 - - + -
194H ALA 3.5 6.7 - - - +
195H HIS* 3.9 27.6 - - + -
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Residues in contact with THR 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145H PRO 4.5 0.4 + - - -
146H VAL* 1.3 70.8 - - - +
148H LEU* 1.3 60.4 + - - +
149H THR* 4.2 16.8 + - + +
192H ASN 3.4 5.2 - - - +
193H VAL* 3.6 1.7 - - - -
194H ALA* 3.1 41.0 + - - +
196H PRO* 5.2 8.1 - - - +
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Residues in contact with LEU 148 (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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136H CYS* 4.6 2.7 - - + +
138H VAL* 4.2 20.6 - - + -
146H VAL* 3.6 5.9 + - + +
147H THR* 1.3 75.0 - - - +
149H THR* 1.3 72.2 + - - +
150H TRP* 3.8 28.2 - - + +
159H VAL* 6.2 0.5 - - - +
161H THR* 5.3 11.4 + - + +
173H LEU* 4.0 24.5 - - + -
174H SER 5.0 0.2 - - - -
175H SER* 3.9 25.4 - - - +
191H CYS* 3.7 29.4 - - - -
192H ASN 3.4 5.6 - - - +
193H VAL* 4.2 5.8 - - + +
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Residues in contact with THR 149 (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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147H THR* 4.8 14.9 + - + +
148H LEU* 1.3 80.6 - - - +
150H TRP* 1.3 66.6 + - - +
152H SER* 4.4 3.7 - - - -
153H GLY* 3.9 25.8 + - - -
191H CYS* 4.3 0.3 - - - -
192H ASN* 3.1 44.5 + - - +
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Residues in contact with TRP 150 (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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134H LEU* 4.5 1.6 - - + -
135H GLY* 3.8 28.7 - - - -
136H CYS* 3.9 25.6 - - + -
148H LEU* 3.8 13.5 - - + +
149H THR* 1.3 71.8 - - - +
151H ASN* 1.3 71.9 + - - +
152H SER 3.4 0.2 - - - -
153H GLY* 3.3 8.9 + - - +
154H SER 3.4 0.3 + - - -
155H LEU* 3.4 39.0 + - + +
159H VAL* 3.9 28.8 - - + +
175H SER* 3.3 28.6 + - - -
176H SER 4.7 0.6 - - - +
177H VAL* 4.0 29.5 - - + +
189H ILE* 3.8 21.5 - - + -
190H THR 3.4 21.1 - - - -
191H CYS* 4.1 13.0 - - + -
206H ILE* 4.5 11.2 - - + -
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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