Contacts of the helix formed by residues 115 - 123 (chain E) in PDB entry 5A15
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 LEU 115 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46E ILE* 3.8 28.3 - - + -
49E SER* 3.8 18.2 - - - +
51E LEU* 6.0 2.5 - - + -
85E ILE* 3.9 23.8 - - + -
88E TYR* 4.1 14.1 - - + +
89E LEU* 4.4 8.5 - - + -
110E ALA 3.0 9.4 + - - +
111E GLU* 5.1 0.2 - - - +
113E PHE* 3.8 15.7 - - + +
114E GLN* 1.3 83.7 - - - +
116E PRO* 1.3 65.7 - - - +
117E ASP 3.3 2.2 - - - -
118E LEU* 3.1 43.5 + - + +
119E VAL* 3.1 16.1 + - - +
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Residues in contact with PRO 116 (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 ILE* 6.0 3.8 - - + -
114E GLN* 3.4 12.6 - - + +
115E LEU* 1.3 83.4 - - - +
117E ASP* 1.3 68.4 + - - +
119E VAL* 3.2 13.5 + - + +
120E LYS* 3.1 21.7 + - - +
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Residues in contact with ASP 117 (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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88E TYR* 3.6 17.3 + - + +
92E ARG* 4.9 8.1 + - - -
115E LEU 3.3 0.6 - - - -
116E PRO* 1.3 80.8 - - - +
118E LEU* 1.3 61.7 + - - +
120E LYS* 3.2 11.6 + - - +
121E LEU* 3.2 27.2 + - + +
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Residues in contact with LEU 118 (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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84E TYR 5.2 1.1 - - - +
85E ILE* 3.5 32.5 - - + -
88E TYR* 3.7 37.3 + - + -
94E VAL* 3.3 35.2 - - + -
106E LEU* 5.6 1.6 - - + -
110E ALA* 3.9 11.4 - - + -
115E LEU* 3.1 27.8 + - + +
117E ASP* 1.3 75.8 - - - +
119E VAL* 1.3 66.6 + - - +
121E LEU* 3.3 3.4 + - + +
122E LEU* 3.2 35.0 + - + +
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Residues in contact with VAL 119 (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 LYS* 4.1 19.2 - - + +
110E ALA* 3.8 21.3 - - + +
111E GLU* 4.1 26.0 - - + +
115E LEU 3.1 17.2 + - - +
116E PRO* 3.2 11.9 + - + +
118E LEU* 1.3 77.4 - - - +
120E LYS* 1.3 54.2 + - + +
122E LEU* 3.3 2.4 + - - +
123E THR* 2.6 46.8 + - - +
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Residues in contact with LYS 120 (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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116E PRO 3.1 12.4 + - - +
117E ASP* 3.4 15.3 - - - +
118E LEU 3.2 0.4 - - - -
119E VAL* 1.3 78.9 - - + +
121E LEU* 1.3 61.6 + - + +
123E THR* 3.1 26.7 + - - +
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Residues in contact with LEU 121 (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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88E TYR* 4.2 17.0 - - + -
92E ARG 5.1 2.5 - - - +
93E GLN* 5.0 7.4 - - - -
94E VAL* 4.0 30.3 - - + +
103E LYS* 5.5 3.6 + - - -
117E ASP* 3.2 15.3 + - + +
118E LEU* 3.3 7.4 + - + +
120E LYS* 1.3 78.2 - - + +
122E LEU* 1.3 61.6 + - + +
123E THR 3.7 3.5 + - - +
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Residues in contact with LEU 122 (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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94E VAL* 4.4 15.7 - - + -
96E LEU* 4.4 4.9 - - + -
103E LYS* 4.4 41.2 - - + +
106E LEU* 3.6 42.6 - - + +
107E LYS* 4.0 32.2 - - + +
110E ALA* 4.7 1.1 - - + -
118E LEU* 3.2 36.3 + - + +
119E VAL 3.7 3.6 - - - +
120E LYS 3.2 0.6 - - - -
121E LEU* 1.3 77.7 - - - +
123E THR* 1.3 63.0 + - - +
124E PRO* 3.5 8.8 - - - +
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Residues in contact with THR 123 (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 LYS* 3.8 12.0 - - + +
119E VAL* 2.6 34.3 + - - +
120E LYS* 3.1 19.8 + - - +
121E LEU 4.2 3.1 - - - +
122E LEU* 1.3 77.5 - - - +
124E PRO* 1.3 81.0 - - + +
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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