Contacts of the strand formed by residues 153 - 159 (chain A) in PDB entry 2BZN
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A PHE* 3.4 35.9 - - + -
41A SER* 2.8 18.0 + - - -
43A GLN* 3.4 11.1 - - - +
124A LYS 3.0 9.3 + - - -
125A TYR* 3.3 32.2 - - + +
126A ILE* 2.9 26.5 + - - +
151A GLN 3.9 0.6 + - - -
152A HIS* 1.3 70.0 - - - +
154A ILE* 1.3 62.4 + - - +
155A MET 4.0 0.3 + - - -
174A ASP* 3.4 15.7 - - + +
175A ILE* 3.9 10.3 - - + -
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Residues in contact with ILE 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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126A ILE* 3.5 16.6 - - + +
128A LEU* 3.8 20.6 - - + -
142A VAL* 4.5 3.8 - - + +
145A VAL* 3.9 15.5 - - + +
146A ARG* 3.7 50.5 - - + +
149A PHE 5.0 0.2 - - - +
152A HIS* 3.7 12.6 - - + +
153A THR* 1.3 75.1 - - - +
155A MET* 1.3 73.4 + - - +
156A ALA* 4.4 1.6 - - + -
172A GLY 4.2 2.9 - - - +
173A ALA* 3.8 16.9 - - + -
174A ASP* 2.8 38.9 + - - +
175A ILE 3.0 9.4 + - - +
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Residues in contact with MET 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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51A ILE* 3.8 26.0 - - + -
73A PHE* 3.9 28.5 - - + -
75A ALA* 5.2 4.0 - - - -
100A ALA* 4.4 9.9 - - - -
125A TYR* 4.5 7.4 - - + -
126A ILE 2.7 12.8 + - - +
127A CYS* 4.1 29.6 - - + -
128A LEU 2.8 26.2 + - - -
153A THR 4.0 1.8 + - - +
154A ILE* 1.3 75.2 - - - +
156A ALA* 1.3 63.1 + - - +
175A ILE* 3.1 31.4 - - + +
177A LYS* 4.7 2.0 - - + -
217A ILE* 3.9 21.1 - - + -
238A PHE* 5.4 3.6 - - + -
240A MET* 5.2 1.3 - - - -
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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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128A LEU* 3.3 6.7 - - + +
138A PHE* 4.0 17.5 - - + -
142A VAL* 4.0 11.7 - - + -
154A ILE* 4.4 3.4 - - + -
155A MET* 1.3 75.9 - - - +
157A GLY* 1.3 54.4 + - - +
168A LEU* 4.5 3.1 - - + +
173A ALA* 3.7 25.1 - - + -
175A ILE 2.8 9.7 + - - -
176A ILE* 3.2 14.0 - - + +
177A LYS* 2.8 30.3 + - - +
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Residues in contact with GLY 157 (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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128A LEU 3.1 10.1 + - - +
129A ASP* 3.6 0.7 - - - -
130A VAL* 2.9 36.1 + - - +
133A GLY* 4.4 0.2 - - - -
138A PHE* 3.6 10.9 - - - -
156A ALA* 1.3 77.2 - - - +
158A ASN* 1.3 73.2 + - - -
168A LEU* 4.8 4.7 - - - -
176A ILE* 5.1 0.2 - - - -
177A LYS* 3.8 6.1 - - - +
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Residues in contact with ASN 158 (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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129A ASP* 4.0 1.4 - - - +
130A VAL 3.1 15.6 + - - +
131A ALA* 3.9 3.9 - - - +
133A GLY 2.9 23.4 + - - +
134A TYR* 4.4 0.2 - - - -
157A GLY* 1.3 69.2 + - - -
159A VAL* 1.3 64.2 - - - +
177A LYS* 2.5 40.9 + - - +
178A VAL 4.2 0.2 - - - -
179A GLY 2.8 33.5 + - - +
180A ILE* 3.8 12.8 - - + +
219A ASP* 2.9 28.5 + - - +
1338A IMP 3.9 6.7 + - - -
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Residues in contact with VAL 159 (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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133A GLY 3.7 10.1 - - - +
134A TYR* 3.6 17.9 - - + +
158A ASN* 1.3 80.6 - - - +
160A VAL* 1.3 65.2 + - - +
161A THR 4.4 2.7 - - - +
164A MET* 3.5 27.4 - - + -
165A VAL* 3.9 22.0 - - + +
168A LEU* 3.7 15.9 - - + -
176A ILE* 3.6 29.6 - - + -
177A LYS 3.2 1.8 + - - +
178A VAL* 3.2 10.9 - - + +
179A GLY 3.1 19.1 + - - -
180A ILE* 4.2 1.8 - - - -
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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