Contacts of the helix formed by residues 101 - 110 (chain E) in PDB entry 3UDB
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 GLU 101 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99E GLY 4.7 1.0 - - - +
100E GLY* 1.3 72.7 - - - -
102E LEU* 1.3 64.7 + - - +
103E PHE* 3.9 20.0 - - + +
104E GLU* 2.9 41.4 + - + +
105E ARG* 3.4 5.2 + - - +
144E GLU 5.4 0.2 - - - +
145E ASN* 3.4 24.5 - - - +
146E THR 3.5 9.6 - - - +
147E LEU* 4.2 14.8 - - + -
148E LEU* 4.7 1.8 - - - +
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Residues in contact with LEU 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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100E GLY 3.3 3.0 + - - -
101E GLU* 1.3 70.5 - - - +
103E PHE* 1.3 63.1 + - - +
105E ARG* 3.1 11.7 + - + +
106E ILE* 3.1 31.7 + - + +
112E PHE* 4.6 4.5 - - + -
120E PHE* 4.3 36.3 - - + -
124E LEU* 6.4 2.5 - - + -
146E THR* 2.9 40.1 + - + +
147E LEU* 4.2 1.0 - - - +
148E LEU* 4.2 26.7 - - + -
156E LEU* 4.7 7.4 - - + -
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Residues in contact with PHE 103 (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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101E GLU* 3.0 17.2 - - + +
102E LEU* 1.3 80.0 - - - +
104E GLU* 1.3 72.2 + - - +
106E ILE* 3.2 20.9 + - + +
107E CYS* 3.0 46.3 + - + -
144E GLU 5.3 8.1 - - - +
145E ASN* 6.4 0.4 - - - -
146E THR 4.7 0.2 + - - -
182E TYR* 5.9 3.8 - + - +
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Residues in contact with GLU 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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100E GLY* 5.1 2.7 - - - -
101E GLU* 2.9 37.7 + - + +
103E PHE* 1.3 86.8 - - - +
105E ARG* 1.3 61.2 + - - +
107E CYS* 3.6 13.8 + - - -
108E ASN* 3.1 40.7 + - - +
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Residues in contact with ARG 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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101E GLU 3.4 1.4 + - - +
102E LEU* 3.1 10.4 + - - +
104E GLU* 1.3 77.9 - - - +
106E ILE* 1.3 66.0 + - - +
108E ASN* 3.5 7.7 + - - +
109E ALA* 3.2 23.4 + - + +
112E PHE* 3.6 14.3 - - + -
116E GLU* 2.6 39.0 + - - -
120E PHE* 3.9 10.8 - - - -
148E LEU* 3.7 27.7 - - + +
152E PRO 5.4 1.8 + - - -
154E PRO* 3.8 30.5 - - - +
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Residues in contact with ILE 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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102E LEU* 3.1 33.7 + - + +
103E PHE* 3.2 23.3 + - + +
105E ARG* 1.3 78.4 - - - +
107E CYS* 1.3 61.8 + - + +
109E ALA* 3.1 4.0 + - - +
110E GLY 3.0 35.7 + - - +
111E ARG* 3.9 4.8 + - - -
112E PHE* 3.4 31.9 - - + +
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Residues in contact with CYS 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 PHE* 3.0 51.4 + - + -
104E GLU* 4.3 15.0 - - - -
106E ILE* 1.3 81.5 - - + +
108E ASN* 1.3 62.7 + - - +
110E GLY* 3.4 13.8 + - - +
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Residues in contact with ASN 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 GLU* 3.1 35.8 + - - +
105E ARG* 3.8 8.0 - - + +
107E CYS* 1.3 78.7 - - - +
109E ALA* 1.3 59.5 + - - +
110E GLY 3.2 1.1 + - - -
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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 ARG* 3.2 16.5 + - + +
106E ILE 3.1 4.7 + - - +
108E ASN* 1.3 76.7 - - - +
110E GLY* 1.3 56.1 + - - +
111E ARG 2.9 22.7 + - - +
112E PHE* 4.1 13.0 - - + -
116E GLU* 5.8 1.1 - - - +
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Residues in contact with GLY 110 (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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106E ILE* 3.0 18.7 + - - +
107E CYS* 3.4 11.6 + - - +
108E ASN 3.2 4.0 + - - -
109E ALA* 1.3 74.7 - - - +
111E ARG* 1.3 61.4 + - - +
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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