Contacts of the strand formed by residues 152 - 156 (chain A) in PDB entry 1BXO
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 LEU 152 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A PHE* 3.6 14.6 - - - -
148A LEU* 3.9 0.7 - - - +
150A GLN* 2.9 40.9 + - + +
151A PRO* 1.3 74.4 - - + +
153A PHE* 1.3 73.7 + - - +
154A ALA* 5.0 0.7 - - + -
168A GLY* 2.9 25.1 + - - -
169A PHE 3.6 33.4 - - - +
170A ILE* 4.0 24.2 - - + -
309A VAL* 4.3 9.2 - - + -
310A PHE 3.3 15.9 - - - +
311A ASP* 3.8 22.2 - - + +
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Residues in contact with PHE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A THR* 3.8 14.6 - - + -
124A LEU* 3.8 41.3 - - + -
141A PHE* 3.7 36.8 - + + -
152A LEU* 1.3 78.4 - - - +
154A ALA* 1.3 65.0 + - - +
155A VAL* 4.0 10.5 - - + -
165A TYR* 4.5 5.2 - + + -
166A ASP 3.1 13.9 - - - +
167A PHE* 3.8 24.7 - + + -
191A TRP* 4.1 5.6 - + - -
309A VAL* 3.7 2.1 - - - +
310A PHE* 2.8 75.3 + + + +
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LEU* 5.0 1.1 - - + -
153A PHE* 1.3 76.2 - - - +
155A VAL* 1.3 63.9 + - - +
164A VAL 3.9 0.5 - - - +
165A TYR* 3.3 6.9 - - - +
166A ASP* 2.8 35.3 + - + +
169A PHE 4.7 4.5 - - - +
170A ILE* 5.3 0.7 - - - -
307A TYR* 3.3 38.4 - - + +
308A VAL 3.1 11.7 - - - +
309A VAL* 4.0 10.8 - - + -
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A PHE* 4.0 4.9 - - + -
154A ALA* 1.3 80.0 - - - +
156A ALA* 1.4 61.9 + - - +
157A LEU* 3.7 33.2 - - + -
164A VAL 3.5 4.0 - - - +
165A TYR* 3.5 33.0 - - + -
214A THR* 4.2 10.3 - - + -
303A LEU* 5.7 4.9 - - + -
306A GLN 3.9 2.6 - - - +
307A TYR* 3.6 10.2 - - - -
308A VAL* 2.9 33.8 + - + +
310A PHE* 3.5 30.1 - - + -
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASN* 3.4 2.6 + - - -
155A VAL* 1.4 71.4 - - - +
157A LEU* 1.3 60.5 + - - +
158A LYS* 4.6 7.2 - - - -
163A GLY* 3.3 8.5 - - - -
164A VAL* 2.9 47.9 + - + +
174A LYS* 4.5 10.3 - - + -
307A TYR* 4.1 12.5 - - + -
322A GLN* 3.8 24.9 - - + +
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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