Contacts of the helix formed by residues 101 - 109 (chain E) in PDB entry 3E2A
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 CYS 101 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E CYS* 3.9 5.4 - - - -
44E ASP* 3.8 1.1 - - - -
67E ALA* 4.4 6.1 - - - -
68E ASN* 4.8 2.2 - - - -
98E HIS* 3.4 23.6 - - - +
99E THR 3.2 0.2 - - - -
100E ASN* 1.3 74.8 - - - +
102E GLY* 1.3 65.6 + - - +
103E GLY* 3.6 4.5 - - - -
104E ILE* 3.3 37.7 + - + +
105E HIS* 3.1 27.5 + - - -
147E THR* 4.8 4.1 + - + +
230E ZN 2.3 36.8 - - - -
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Residues in contact with GLY 102 (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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83C TYR* 3.8 12.1 + - - -
44E ASP* 3.3 17.3 + - - -
100E ASN 3.5 5.4 + - - -
101E CYS* 1.3 70.8 - - - +
103E GLY* 1.3 56.9 + - - +
105E HIS* 3.3 9.0 + - - +
106E ALA* 2.8 31.2 + - - +
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Residues in contact with GLY 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C TYR* 4.8 2.0 - - - -
44E ASP* 2.9 14.1 + - - -
66E VAL* 3.9 25.1 - - - -
67E ALA* 4.5 5.8 - - - -
101E CYS* 3.2 6.0 - - - -
102E GLY* 1.3 72.8 - - - +
104E ILE* 1.3 64.9 + - - +
106E ALA* 3.2 7.1 + - - +
107E ALA* 2.9 23.6 + - - +
120E LEU* 3.9 7.3 - - - +
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Residues in contact with ILE 104 (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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67E ALA* 4.3 8.7 - - + -
68E ASN* 6.1 0.7 - - - +
101E CYS* 3.3 25.9 + - + +
103E GLY* 1.3 74.8 - - - +
105E HIS* 1.3 58.1 + - + +
107E ALA* 3.2 5.9 + - - +
108E MET* 2.9 35.4 + - - +
123E ILE* 4.0 21.1 - - + -
143E ALA* 3.8 17.7 - - + +
146E LEU* 4.1 17.3 - - + +
147E THR* 3.7 31.2 - - + +
150E ASN* 4.0 31.2 - - + +
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Residues in contact with HIS 105 (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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100E ASN* 4.1 28.8 - - + -
101E CYS 3.1 21.6 + - - +
102E GLY* 3.6 7.6 + - - +
104E ILE* 1.3 76.3 - - + +
106E ALA* 1.3 62.0 + - - +
108E MET* 3.3 12.1 + - + +
109E ALA* 3.1 23.4 + - - +
143E ALA* 3.5 32.0 - - + +
144E ASP* 6.1 0.2 - - - -
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Residues in contact with ALA 106 (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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83C TYR* 4.3 13.9 - - + +
102E GLY 2.8 21.0 + - - +
103E GLY* 3.6 2.0 - - - +
105E HIS* 1.3 72.6 - - - +
107E ALA* 1.3 62.8 + - - +
109E ALA* 3.3 23.4 + - - +
111E LYS 5.3 0.7 - - - +
113E LEU* 3.9 23.8 - - + +
117E ASN* 4.9 4.0 + - - -
120E LEU* 3.6 22.2 - - + +
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Residues in contact with ALA 107 (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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103E GLY 2.9 13.6 + - - +
104E ILE 3.4 9.2 - - - +
106E ALA* 1.3 76.5 - - - +
108E MET* 1.3 58.2 + - + +
109E ALA 3.8 0.3 - - - +
120E LEU* 3.7 25.0 - - + +
123E ILE* 3.8 35.2 - - + -
124E ARG* 2.8 36.1 + - + +
127E TRP* 5.2 0.4 - - - -
146E LEU* 5.5 0.2 - - + -
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Residues in contact with MET 108 (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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104E ILE* 2.9 18.8 + - - +
105E HIS* 3.3 17.5 + - + +
107E ALA* 1.3 74.2 - - - +
109E ALA* 1.3 63.9 + - - +
110E ASP* 3.6 2.4 + - - +
124E ARG* 3.7 1.8 + - - -
127E TRP* 3.5 38.8 - - + -
139E PRO 5.9 1.1 - - - +
142E ARG* 4.4 10.5 - - + -
143E ALA* 3.2 45.5 - - + +
146E LEU* 3.5 31.2 - - + -
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Residues in contact with ALA 109 (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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105E HIS 3.1 16.0 + - - +
106E ALA* 3.3 17.3 + - - +
107E ALA 3.8 0.2 - - - +
108E MET* 1.3 77.0 - - - +
110E ASP* 1.3 60.2 + - - +
111E LYS* 3.3 26.7 + - + +
113E LEU* 6.3 1.3 - - + -
117E ASN* 5.8 0.2 + - - -
124E ARG* 3.4 11.4 + - - -
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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