Contacts of the strand formed by residues 144 - 152 (chain E) in PDB entry 2J3W
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 MET 144 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68E CYS* 5.1 5.4 - - + -
69E HIS 4.5 10.3 - - - +
71E PHE* 3.8 33.0 - - - +
74E THR* 3.3 31.0 - - + +
136E ARG 5.0 0.3 - - - +
139E LEU* 3.0 43.2 + - + +
140E GLU 3.7 1.6 + - - -
142E VAL* 4.1 18.8 - - + +
143E GLN* 1.3 77.9 - - - +
145E ALA* 1.3 64.4 + - - +
146E VAL* 3.4 5.3 + - + +
167E PHE* 3.5 27.8 - - + -
169E ARG 3.9 1.8 - - - -
170E ARG* 4.9 0.2 - - - +
171E ILE* 3.9 3.4 - - - +
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Residues in contact with ALA 145 (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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136E ARG* 6.2 0.4 - - - -
140E GLU* 5.3 2.9 - - - +
144E MET* 1.3 69.8 - - - +
146E VAL* 1.3 63.1 + - - +
167E PHE* 4.6 0.9 - - - -
168E ILE* 2.8 34.5 + - + +
169E ARG* 2.9 41.1 + - + +
171E ILE* 3.9 21.1 - - + +
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Residues in contact with VAL 146 (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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71E PHE* 4.2 7.6 - - + -
136E ARG* 3.7 43.6 + - + +
139E LEU* 3.7 22.9 - - + -
144E MET* 3.4 20.1 + - + +
145E ALA* 1.3 80.8 - - - +
147E GLU* 1.3 63.8 + - - +
148E ALA* 4.7 0.7 - - + +
165E MET* 3.5 25.1 - - + -
166E ARG 3.2 14.8 - - - +
167E PHE* 4.1 9.0 - - - -
168E ILE* 3.8 11.2 - - - +
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Residues in contact with GLU 147 (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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136E ARG* 5.5 1.3 - - - +
146E VAL* 1.3 77.8 - - - +
148E ALA* 1.3 67.9 + - - +
149E LYS* 3.5 28.9 + - + +
164E ARG 3.5 4.2 - - - +
165E MET* 3.5 1.0 - - - -
166E ARG* 3.0 74.6 + - + +
168E ILE* 4.0 6.5 - - + +
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Residues in contact with ALA 148 (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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45E ASP* 4.9 2.1 - - - +
132E CYS* 3.3 43.9 - - + +
135E LEU* 4.2 13.5 - - + -
136E ARG* 4.9 9.4 + - + +
146E VAL* 4.1 2.1 + - + +
147E GLU* 1.3 78.3 - - - +
149E LYS* 1.3 63.2 - - - +
163E ILE* 4.7 0.7 - - + -
164E ARG 3.5 4.5 - - - -
165E MET* 3.8 21.1 - - + -
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Residues in contact with LYS 149 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129E ASN* 5.7 0.4 - - - -
132E CYS* 3.5 10.0 - - - -
147E GLU* 3.5 34.7 + - + +
148E ALA* 1.3 77.3 - - - +
150E PHE* 1.3 66.2 + - - +
151E VAL* 3.5 10.9 + - + -
163E ILE* 4.3 2.0 - - - +
164E ARG* 2.7 67.7 + - + +
166E ARG* 4.7 7.1 - - - +
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Residues in contact with PHE 150 (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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107E LEU* 4.7 2.5 - - + -
126E ILE* 3.7 31.7 - - + +
128E SER* 3.3 50.0 - - - -
129E ASN* 3.9 2.8 + - - -
131E LEU* 4.3 2.7 - - + -
132E CYS* 3.4 25.6 - - - -
149E LYS* 1.3 77.6 - - - +
151E VAL* 1.3 62.0 + - - +
152E GLN 4.1 7.9 - - - +
153E ASP* 5.1 11.0 - - + -
161E THR* 3.6 28.5 - - + -
162E GLU 3.3 7.2 - - - -
163E ILE* 3.5 31.4 - - + -
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Residues in contact with VAL 151 (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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149E LYS* 4.1 11.4 - - + +
150E PHE* 1.3 76.2 - - - +
152E GLN* 1.3 61.9 + - + +
158E ASP* 4.7 1.6 - - - +
162E GLU* 2.6 37.3 + - - +
164E ARG* 3.4 41.5 - - + +
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Residues in contact with GLN 152 (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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150E PHE* 3.6 4.1 - - - -
151E VAL* 1.3 87.3 - - + +
153E ASP* 1.3 62.3 + - - +
158E ASP* 3.5 25.8 + - - +
159E GLY* 4.9 3.5 + - - +
160E VAL* 3.5 30.4 + - - +
161E THR* 3.1 7.3 - - - +
162E GLU* 2.6 53.6 + - + +
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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