Contacts of the helix formed by residues 109 - 120 (chain E) in PDB entry 5A0Q
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 VAL 109 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74E ILE* 3.8 19.7 - - + -
108E THR* 1.4 73.2 - - - +
110E GLU* 1.4 59.6 + - - +
112E VAL* 3.7 1.5 - - + +
113E THR* 2.8 42.1 + - - +
143E PHE* 3.9 19.7 - - + -
145E GLY* 3.3 45.3 - - - +
147E ASP* 3.9 7.3 + - + -
152E GLN* 3.5 14.6 - - + +
154E PHE* 3.9 21.8 - - + +
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Residues in contact with GLU 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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108E THR* 3.3 7.1 + - - +
109E VAL* 1.4 77.8 - - - +
111E SER* 1.3 71.7 + - - +
113E THR* 4.1 2.3 - - - -
114E GLN* 3.2 40.9 + - - +
152E GLN* 4.4 8.4 + - - +
154E PHE* 3.8 34.5 - - + -
162E PHE* 3.4 21.2 - - + -
78M SER 4.2 1.6 - - - +
79M ASN 4.0 14.6 - - - +
80M ASN* 5.1 5.7 + - - -
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Residues in contact with SER 111 (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 MET* 3.9 26.4 - - - +
108E THR* 3.2 13.3 + - - -
110E GLU* 1.3 82.3 + - - +
112E VAL* 1.3 59.2 + - - +
113E THR 3.2 1.6 - - - -
114E GLN* 3.6 10.8 + - - +
115E ALA* 3.0 30.1 + - - +
78M SER* 3.1 26.1 + - - -
79M ASN* 3.9 15.3 + - - -
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Residues in contact with VAL 112 (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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70E ILE* 4.7 7.4 - - + -
74E ILE* 3.5 17.0 - - + -
92E ALA* 4.9 4.3 - - + +
95E GLU* 6.1 1.1 - - - +
96E THR* 3.5 30.1 - - + -
107E MET* 3.4 28.5 - - - +
108E THR 3.1 17.7 + - - +
109E VAL 3.4 5.1 + - - +
111E SER* 1.3 75.4 - - - +
113E THR* 1.3 59.2 + - - +
115E ALA* 3.9 4.1 + - - +
116E VAL* 3.3 22.9 + - - +
143E PHE* 3.8 26.7 - - + -
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Residues in contact with THR 113 (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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109E VAL* 2.8 18.2 + - - +
110E GLU 4.1 3.6 - - - -
112E VAL* 1.3 74.4 - - - +
114E GLN* 1.3 60.3 + - - +
116E VAL* 3.3 4.0 + - - +
117E SER* 3.0 25.5 + - - -
143E PHE* 3.5 35.6 - - + -
154E PHE* 3.5 21.6 - - + +
156E MET* 3.8 18.1 - - + +
162E PHE* 3.4 27.1 - - + -
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Residues in contact with GLN 114 (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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110E GLU* 3.2 37.2 + - - +
111E SER* 3.6 9.4 + - - +
113E THR* 1.3 76.8 - - - +
115E ALA* 1.3 60.0 + - - +
117E SER* 3.1 3.6 + - - -
118E ASN* 2.9 39.2 + - - +
162E PHE* 4.1 24.8 - - + -
82F ARG* 4.1 6.0 + - - +
89F ARG* 5.6 6.2 + - - +
77M HIS 5.5 1.4 + - - -
78M SER* 3.8 31.5 + - - +
80M ASN* 5.8 2.2 - - - +
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Residues in contact with ALA 115 (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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95E GLU* 4.1 34.7 - - + +
107E MET* 5.2 4.7 - - + -
111E SER 3.0 17.4 + - - +
112E VAL* 4.1 6.3 - - - +
113E THR 3.3 0.2 - - - -
114E GLN* 1.3 77.1 - - - +
116E VAL* 1.3 62.2 + - + +
118E ASN* 3.4 23.8 - - - +
119E LEU* 3.6 14.5 - - - +
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Residues in contact with VAL 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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88E LEU* 4.2 25.6 - - + +
91E LYS 5.7 0.2 - - - -
92E ALA* 3.8 28.0 - - + -
95E GLU* 6.4 0.2 - - + -
112E VAL 3.3 17.7 - - - +
113E THR 3.3 7.6 + - - +
114E GLN 3.2 0.4 - - - -
115E ALA* 1.3 76.1 - - + +
117E SER* 1.3 63.9 + - - +
118E ASN 3.2 0.2 - - - -
119E LEU* 3.3 20.9 + - + +
120E ALA* 3.5 10.2 + - - +
141E LEU* 3.8 19.5 - - + -
143E PHE* 4.0 8.1 - - + -
156E MET* 3.6 20.7 - - + +
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Residues in contact with SER 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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113E THR 3.0 13.7 + - - -
114E GLN 3.1 10.7 + - - -
116E VAL* 1.3 74.6 - - - +
118E ASN* 1.4 61.3 + - - +
120E ALA* 3.2 20.2 + - - +
121E LEU 4.5 0.7 + - - -
156E MET* 3.5 21.2 - - - +
160E GLY 3.7 13.2 + - - -
162E PHE* 3.5 22.5 + - - +
82F ARG* 2.9 29.9 + - - -
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Residues in contact with ASN 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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114E GLN* 2.9 35.0 + - - +
115E ALA* 3.4 17.6 - - - +
116E VAL 3.2 0.4 - - - -
117E SER* 1.4 76.5 - - - +
119E LEU* 1.3 62.7 + - + +
120E ALA 3.5 0.3 + - - -
121E LEU 4.7 0.5 + - - -
122E GLN* 3.0 28.2 - - - +
82F ARG* 3.2 31.5 + - - +
83F LEU* 4.4 11.7 - - + +
86F ASN* 4.6 17.9 - - - +
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Residues in contact with LEU 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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88E LEU* 4.1 22.4 - - + +
91E LYS* 4.2 28.3 - - + -
95E GLU* 6.1 4.0 - - + -
115E ALA 3.6 17.0 - - - +
116E VAL* 3.3 12.9 + - + +
117E SER 3.2 0.4 - - - -
118E ASN* 1.3 80.6 - - + +
120E ALA* 1.3 63.2 + - - +
121E LEU 3.5 0.8 + - - -
122E GLN* 3.8 20.4 + - + +
137E PHE* 3.6 13.6 - - + -
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Residues in contact with ALA 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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88E LEU* 5.5 2.2 - - + -
116E VAL 3.5 7.2 + - - +
117E SER* 3.2 20.5 + - - +
118E ASN 3.2 0.2 - - - -
119E LEU* 1.3 79.4 - - - +
121E LEU* 1.3 73.2 + - + +
122E GLN 3.9 0.7 + - - -
123E PHE* 4.6 0.5 - - - -
136E PRO* 4.5 3.1 - - - +
137E PHE* 3.6 27.3 + - + -
156E MET* 4.6 9.4 - - + -
158E PRO* 4.8 3.5 - - + +
160E GLY* 3.5 26.0 - - - +
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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