Contacts of the strand formed by residues 141 - 149 (chain E) in PDB entry 3N2N
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 141 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40E TYR* 4.0 7.7 - - - -
42E GLY* 3.3 17.9 - - - +
44E ASP* 3.2 36.2 + - - +
79E ARG* 5.4 1.6 + - - -
134E GLU* 6.0 1.5 - - - +
135E ASN* 6.1 0.9 - - - -
139E TYR* 3.3 20.8 + - - +
140E ARG* 1.3 78.2 + - - +
142E ALA* 1.3 69.8 + - - +
143E SER* 3.3 20.1 + - - +
172E GLY 5.2 3.3 - - - +
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Residues in contact with ALA 142 (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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40E TYR* 3.6 23.8 - - + -
42E GLY 2.9 9.5 + - - +
43E PHE* 3.4 9.9 - - + -
44E ASP 2.8 28.6 + - - +
141E THR* 1.3 69.4 - - - +
143E SER* 1.3 59.4 + - - +
144E VAL* 3.5 9.1 + - + -
174E ILE* 5.7 6.3 - - + -
215E ILE* 3.6 32.5 - - + -
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Residues in contact with SER 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E ASP* 3.5 9.3 + - - +
46E TYR* 4.4 13.8 + - - -
131E ILE* 4.3 16.6 - - - +
134E GLU* 6.1 0.7 - - - +
135E ASN* 5.1 3.6 + - - -
141E THR* 3.3 23.9 + - - +
142E ALA* 1.3 70.4 - - - +
144E VAL* 1.3 60.4 + - - +
172E GLY 4.1 8.9 + - - +
173E ALA* 3.2 18.6 - - - -
174E ILE* 2.9 27.5 + - - +
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Residues in contact with VAL 144 (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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43E PHE* 4.0 19.7 - - + -
44E ASP 2.9 9.4 + - - +
45E LEU* 3.4 24.6 - - + +
46E TYR* 2.8 33.1 + - - -
142E ALA* 4.2 8.1 - - + +
143E SER* 1.3 76.9 - - - +
145E ILE* 1.3 62.0 + - - +
146E ILE* 4.5 3.1 - - + -
174E ILE* 3.4 17.3 - - + +
176E TYR* 3.6 32.8 - - + -
208E LEU* 5.4 1.8 - - + -
211E ILE* 5.9 0.9 - - + -
212E ILE* 6.3 0.9 - - + -
215E ILE* 4.1 16.8 - - + -
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Residues in contact with ILE 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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46E TYR* 3.3 22.7 - - + +
48E ILE* 3.5 24.0 - - + -
124E PHE* 4.0 20.0 - - + -
127E ALA* 4.1 16.4 - - + -
131E ILE* 4.2 2.7 - - + -
144E VAL* 1.3 75.4 - - - +
146E ILE* 1.3 66.9 + - - +
147E ALA 4.2 1.8 - - - +
168E SER* 3.7 32.5 - - - +
173E ALA* 3.9 15.9 - - + -
174E ILE 2.8 13.6 + - - +
175E VAL* 4.1 11.4 - - + -
176E TYR* 2.7 35.2 + - - +
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Residues in contact with ILE 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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45E LEU* 3.7 27.1 - - + -
46E TYR 2.9 9.5 + - - -
47E PHE* 3.4 26.2 - - + -
48E ILE 2.8 26.0 + - - +
65E PHE* 4.0 4.7 - - + -
69E LEU* 4.3 11.0 - - + -
144E VAL* 4.1 2.9 + - + -
145E ILE* 1.3 78.4 - - - +
147E ALA* 1.3 59.0 - - - +
148E LEU* 3.6 26.2 + - + +
176E TYR* 3.5 6.7 - - + +
178E VAL* 3.8 20.9 - - + -
208E LEU* 3.9 31.4 - - + -
212E ILE* 4.6 2.7 - - + -
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Residues in contact with ALA 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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48E ILE* 3.2 13.7 - - + +
85E PHE* 5.9 0.2 - - + -
120E MET* 4.7 11.7 - - - -
124E PHE* 4.1 30.5 - - + -
145E ILE* 4.0 1.3 - - + -
146E ILE* 1.3 72.3 - - - +
148E LEU* 1.3 59.1 + - - +
149E THR* 4.0 4.0 + - + +
175E VAL* 5.2 0.4 - - + -
176E TYR 2.8 15.6 + - - +
177E ALA* 3.4 9.0 - - + +
178E VAL 2.7 31.7 + - - +
191E ILE* 5.3 1.8 - - + -
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Residues in contact with LEU 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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47E PHE* 4.8 1.3 - - + -
48E ILE 2.8 10.1 + - - +
49E LEU* 3.8 28.9 - - + -
50E ASP* 2.9 30.5 + - - +
62E ILE* 3.9 29.8 - - + +
65E PHE* 3.8 27.1 - - + -
85E PHE* 4.3 1.2 - - - -
146E ILE* 3.6 29.8 - - + +
147E ALA* 1.3 70.6 - - - +
149E THR* 1.3 62.6 + - - +
178E VAL* 3.4 32.5 - - + +
180E VAL* 4.6 2.0 - - + -
201E VAL* 4.2 15.0 - - + -
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Residues in contact with THR 149 (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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50E ASP* 2.7 27.9 + - - -
62E ILE* 5.3 0.4 - - - -
85E PHE* 4.4 0.7 - - - -
120E MET* 4.1 22.2 - - - -
147E ALA* 4.7 6.7 - - + +
148E LEU* 1.3 77.0 - - - +
150E ASP* 1.3 64.9 + - - +
151E GLY* 3.0 17.0 + - - +
153E LEU* 4.1 8.0 - - - +
177E ALA* 5.7 1.3 - - + -
178E VAL 3.2 5.3 + - - +
179E GLY* 3.2 9.0 - - - -
180E VAL* 2.9 29.9 + - - +
188E LEU* 3.7 27.1 - - + +
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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