Contacts of the strand formed by residues 121 - 126 (chain E) in PDB entry 3BZE
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 LYS 121 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E ALA* 3.4 5.0 - - - +
118E TYR* 3.1 30.2 + - - +
119E ASP* 4.4 3.4 - - + +
120E GLY* 1.3 80.0 - - - +
122E ASP* 1.3 78.6 + - + +
123E TYR* 3.9 0.7 - - - +
136E VAL* 4.7 10.3 + - - +
137E ASP* 4.1 18.4 + - - +
0F MET* 5.8 6.5 - - - +
1F ILE* 4.6 24.9 - - + +
60F TRP* 4.6 0.7 - - - -
220G ASP* 6.1 0.9 - - - -
273G ARG* 6.3 2.0 - - - +
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Residues in contact with ASP 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E GLN* 4.0 14.8 - - - +
116E PHE 4.0 4.3 - - - -
121E LYS* 1.3 85.0 + - + +
123E TYR* 1.3 59.6 + - - +
125E THR* 4.5 7.4 + - - +
136E VAL* 4.7 23.7 - - + +
137E ASP* 4.6 10.6 - - - +
60F TRP* 2.5 38.2 + - - +
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Residues in contact with TYR 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E LEU* 3.0 32.1 - - + +
84E TYR* 3.1 13.5 - - - -
85E TYR* 3.4 32.3 - + - -
95E LEU* 6.1 0.2 - - + -
116E PHE* 2.9 19.4 + - + +
117E ALA* 3.8 11.7 - - - -
118E TYR* 3.9 19.3 - - + +
121E LYS 3.2 0.9 + - - +
122E ASP* 1.3 74.5 - - - +
124E LEU* 1.3 78.0 + - + +
125E THR* 5.3 0.2 - - - -
136E VAL* 3.3 25.4 + - - -
137E ASP* 4.3 3.0 + - + -
139E ALA 3.5 3.3 + - - -
140E ALA* 3.5 31.1 - - + +
143E SER* 2.9 31.3 + - - -
9R LEU* 4.1 17.3 - - + -
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Residues in contact with LEU 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E GLN* 3.4 1.9 - - - +
116E PHE* 2.7 43.5 + - + +
123E TYR* 1.3 92.1 - - + +
125E THR* 1.3 63.5 + - - +
133E TRP* 4.2 17.3 - - + -
134E THR 4.1 2.2 - - - -
135E ALA* 3.7 33.0 - - + +
140E ALA* 4.2 4.0 - - + +
143E SER* 4.4 7.4 - - - +
144E GLU* 4.1 18.2 - - + +
147E SER* 3.9 11.2 - - - +
7R LEU* 3.8 29.8 - - + -
9R LEU* 3.9 13.9 - - + -
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Residues in contact with THR 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E GLU 4.1 5.4 - - - +
115E GLN* 3.7 29.2 + - + +
116E PHE 5.1 0.5 + - - -
122E ASP* 4.5 9.0 + - - +
123E TYR 4.3 0.2 - - - -
124E LEU* 1.3 79.1 + - - +
126E LEU* 1.3 78.5 + - - +
127E ASN* 5.1 2.7 - - - +
133E TRP* 3.2 6.1 - - - -
134E THR* 2.7 46.8 + - - -
136E VAL* 4.3 12.3 - - - +
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Residues in contact with LEU 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E TYR* 6.1 0.2 - - - -
114E GLU* 2.9 41.8 + - + +
125E THR* 1.3 89.3 - - - +
127E ASN* 1.3 66.6 + - - +
128E GLU 4.0 0.3 + - - -
130E LEU* 3.4 37.9 - - + -
132E SER 3.5 12.1 - - - +
133E TRP* 3.4 44.5 - - + -
153E ALA* 3.8 15.9 - - + +
156E GLN* 4.2 7.2 - - + +
160E LEU* 3.9 9.9 - - + -
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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