Contacts of the helix formed by residues 137 - 149 (chain E) in PDB entry 5ISO
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 SER 137 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E MET 3.6 10.8 - - - -
34E LYS* 3.8 19.2 - - - +
36E HIS 3.3 7.2 - - - -
37E ARG* 4.1 1.3 - - - +
38E CYS* 3.6 6.3 - - - -
132E ILE* 4.0 0.2 - - - +
135E ASN 3.9 0.8 + - - -
136E ALA* 1.3 79.3 - - - +
138E LEU* 1.3 63.4 + - - +
139E PHE* 3.2 7.4 + - - +
140E ASP* 2.9 43.0 + - - +
141E ALA 3.3 8.1 + - - -
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Residues in contact with LEU 138 (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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32E PHE* 4.6 2.7 - - + -
33E MET* 3.0 38.4 + - + +
36E HIS* 2.8 26.1 + - + +
38E CYS* 3.9 22.9 - - - -
41E LEU* 3.5 48.5 - - + -
137E SER* 1.3 70.3 - - - +
139E PHE* 1.3 66.0 + - - +
141E ALA* 3.0 8.3 + - + +
142E VAL* 3.0 26.3 + - - +
172E ILE* 4.8 4.9 - - + +
175E PHE* 3.7 21.8 - - + -
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Residues in contact with PHE 139 (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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30E THR* 4.1 14.4 - - + -
33E MET* 3.1 21.5 + - + +
34E LYS* 3.7 50.3 - - + +
137E SER* 3.2 8.9 - - - +
138E LEU* 1.3 77.0 - - - +
140E ASP* 1.3 62.6 + - - +
142E VAL* 3.4 4.0 + - - +
143E SER* 2.6 51.3 + - - -
323E VAL* 4.0 35.9 - - + -
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Residues in contact with ASP 140 (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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132E ILE* 3.8 12.6 - - + +
136E ALA* 4.1 7.8 - - + +
137E SER* 2.9 36.6 + - - +
138E LEU 3.2 0.2 - - - -
139E PHE* 1.3 88.8 - - - +
141E ALA* 1.3 57.2 + - - +
143E SER* 3.6 7.7 + - - -
144E SER* 2.9 29.8 + - - -
147E ARG* 4.7 2.3 + - - +
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Residues in contact with ALA 141 (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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38E CYS* 3.8 16.6 - - - -
132E ILE* 3.5 20.3 - - + +
137E SER 3.3 2.8 + - - -
138E LEU* 3.0 11.5 + - + +
140E ASP* 1.3 75.7 - - - +
142E VAL* 1.3 60.5 + - - +
144E SER* 3.1 5.3 + - - -
145E LEU* 2.8 35.6 + - + +
153E LEU* 5.4 4.1 - - + +
167E LEU* 4.0 16.8 - - + -
172E ILE* 4.4 9.4 - - + -
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Residues in contact with VAL 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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33E MET* 3.5 31.9 - - + -
138E LEU 3.0 6.2 + - - +
139E PHE 3.9 2.7 - - - +
141E ALA* 1.3 74.2 - - - +
143E SER* 1.3 63.4 + - - +
145E LEU* 3.3 8.0 + - + +
146E ILE* 3.0 43.4 + - + +
169E HIS* 5.6 1.3 - - + -
172E ILE* 3.9 22.4 - - + -
319E LEU* 4.1 21.8 - - + -
323E VAL* 3.8 26.2 - - + -
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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
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139E PHE* 2.6 45.7 + - - -
140E ASP* 3.6 8.5 + - - -
142E VAL* 1.3 77.3 - - - +
144E SER* 1.3 55.9 + - - +
146E ILE* 3.8 4.7 - - - +
147E ARG* 2.9 50.8 + - - +
323E VAL* 6.0 2.9 - - - +
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Residues in contact with SER 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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130E VAL* 3.4 25.5 - - - +
131E CYS 4.5 7.3 + - - -
132E ILE* 5.2 6.3 - - - -
140E ASP 2.9 18.3 + - - -
141E ALA* 3.5 6.7 - - - -
143E SER* 1.3 75.4 - - - +
145E LEU* 1.3 64.2 + - - +
147E ARG* 3.5 16.7 + - - +
148E ASN* 2.9 34.1 + - - +
150E ILE* 4.5 2.4 - - - +
153E LEU* 5.5 7.7 - - - +
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Residues in contact with LEU 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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141E ALA* 2.8 18.5 + - + +
142E VAL* 3.3 7.6 + - - +
144E SER* 1.3 77.6 - - - +
146E ILE* 1.3 58.8 + - - +
149E LYS* 3.0 21.8 + - - -
150E ILE* 3.1 37.6 + - + +
151E HIS 4.2 2.0 - - - +
152E ARG 4.1 5.4 - - - +
153E LEU* 3.9 32.3 - - + +
167E LEU* 4.7 2.5 - - + +
168E THR* 4.3 2.2 - - - -
169E HIS* 3.5 46.4 + - + +
172E ILE* 3.9 25.4 - - + -
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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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142E VAL* 3.0 32.8 + - + +
143E SER* 4.0 3.6 - - - +
145E LEU* 1.3 78.5 - - + +
147E ARG* 1.3 69.5 + - + +
149E LYS* 3.1 19.8 + - - +
169E HIS* 4.8 9.4 - - + -
316E SER* 5.2 2.9 - - - +
319E LEU* 5.4 0.4 - - + -
320E GLN* 3.6 60.1 - - + +
323E VAL* 4.5 7.4 - - + -
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Residues in contact with ARG 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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140E ASP 4.7 1.6 + - - -
143E SER* 2.9 28.5 + - - +
144E SER* 3.5 28.7 + - - +
146E ILE* 1.3 80.8 - - + +
148E ASN* 1.3 76.4 + - - +
149E LYS* 3.7 12.5 + - - -
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Residues in contact with ASN 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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130E VAL* 3.5 39.1 - - + +
144E SER* 2.9 29.6 + - - +
147E ARG* 1.3 96.5 + - - +
149E LYS* 1.3 73.6 + - - +
150E ILE* 3.5 18.7 - - + +
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Residues in contact with LYS 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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145E LEU 3.0 9.9 + - - -
146E ILE* 3.1 14.9 + - - +
147E ARG 4.2 11.0 + - - +
148E ASN* 1.3 81.9 + - - +
150E ILE* 1.3 61.6 + - - +
151E HIS* 5.0 6.6 + - - -
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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