Contacts of the helix formed by residues 116 - 130 (chain B) in PDB entry 2C8U
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 PRO 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B MET 4.7 0.9 - - - +
115B LYS* 1.3 92.1 - - + +
117B GLU* 1.3 63.8 + - + +
118B GLU 2.6 39.5 + - - +
119B GLU* 4.0 6.7 - - + +
120B LYS* 3.1 14.0 + - - +
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B PRO* 1.3 72.1 - - + +
118B GLU* 1.3 75.8 + - + +
120B LYS* 3.4 8.9 - - - +
121B GLN* 2.9 45.4 + - - +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B PRO* 2.6 21.3 + - - +
117B GLU* 1.3 84.9 - - + +
119B GLU* 1.3 59.9 + - - +
120B LYS 3.2 2.5 - - - +
121B GLN* 4.2 15.9 - - + +
122B LYS* 3.5 38.4 - - + +
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LYS* 3.4 34.5 + - + +
116B PRO* 3.4 10.6 + - + +
118B GLU* 1.3 69.6 + - - +
120B LYS* 1.3 65.8 + - - +
122B LYS* 2.9 13.9 + - + +
123B ILE* 2.8 45.5 + - + +
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Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B TYR* 5.9 0.6 - - - -
112B THR* 3.8 32.3 + - - +
113B LEU* 4.9 7.9 - - - +
115B LYS* 3.6 20.1 - - + +
116B PRO 3.1 20.2 + - - +
117B GLU* 3.4 7.9 - - - +
118B GLU* 3.2 0.2 - - - +
119B GLU* 1.3 74.8 - - - +
121B GLN* 1.3 56.0 + - + +
123B ILE* 3.0 5.8 + - - +
124B ILE* 2.8 57.5 + - + +
173B LEU* 4.5 7.4 - - - +
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Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLU* 2.9 45.0 + - - +
118B GLU* 4.2 12.7 - - + +
119B GLU 3.4 0.4 - - - -
120B LYS* 1.3 74.5 - - + +
122B LYS* 1.3 58.4 + - + +
124B ILE* 3.9 8.6 - - + +
125B LYS* 3.2 31.1 + - - +
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B GLU* 3.5 36.3 - - + +
119B GLU* 2.9 14.7 + - + +
121B GLN* 1.3 77.4 - - + +
123B ILE* 1.3 62.1 + - + +
125B LYS* 3.7 9.5 + - - +
126B GLU* 3.1 36.1 + - - +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LYS* 3.6 47.3 - - + +
112B THR* 4.0 7.4 - - + +
115B LYS* 4.7 3.8 - - + -
119B GLU* 2.8 55.3 + - + +
120B LYS* 3.5 6.1 - - - +
122B LYS* 1.3 72.8 - - + +
124B ILE* 1.3 67.4 + - - +
126B GLU* 2.9 10.7 + - + +
127B ILE* 2.8 33.1 + - + +
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B THR* 3.8 19.1 - - + -
120B LYS* 2.8 45.9 + - + +
121B GLN* 3.9 8.7 - - + +
123B ILE* 1.3 71.9 - - - +
125B LYS* 1.3 58.7 + - - +
127B ILE* 3.4 8.1 - - - +
128B LEU* 2.9 61.1 + - + +
173B LEU* 3.8 40.4 - - + +
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Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B GLN 3.2 16.7 + - - +
122B LYS* 3.7 9.9 - - - +
124B ILE* 1.3 81.3 - - - +
126B GLU* 1.3 62.5 + - + +
128B LEU* 4.2 4.0 - - - -
129B ASN* 3.1 38.0 + - - +
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Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B LYS* 3.1 21.5 + - - +
123B ILE* 2.9 14.5 + - + +
125B LYS* 1.3 76.2 - - + +
127B ILE* 1.3 60.2 + - + +
129B ASN* 3.5 2.6 + - - +
130B GLY* 3.0 24.8 + - - -
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B GLU* 3.4 47.3 - - - +
109B TYR 4.1 0.7 - - - +
111B LYS* 4.0 19.3 - - + +
112B THR* 3.7 19.5 - - + -
123B ILE* 2.8 28.0 + - + +
124B ILE* 3.4 10.8 - - - +
126B GLU* 1.3 75.7 - - + +
128B LEU* 1.3 63.5 + - + +
130B GLY 3.1 14.1 + - - +
131B LYS 3.4 2.7 + - - +
132B VAL* 3.2 36.6 + - + -
173B LEU* 3.7 17.9 - - + -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ILE* 2.9 42.6 + - + +
125B LYS* 4.3 3.8 - - - +
127B ILE* 1.3 76.7 - - + +
129B ASN* 1.3 62.8 + - - +
132B VAL* 4.2 20.4 - - + -
133B PRO* 3.3 10.4 - - - +
170B VAL* 4.8 5.4 - - + -
173B LEU* 4.7 14.4 - - + -
174B ASP* 3.8 29.8 - - + +
177B PHE* 3.3 50.0 - - + -
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Residues in contact with ASN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LYS* 3.1 31.1 + - - +
126B GLU* 3.8 2.7 - - - +
127B ILE 3.1 0.4 - - - -
128B LEU* 1.3 82.4 + - - +
130B GLY* 1.3 63.0 + - - +
133B PRO* 4.4 5.3 - - - +
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Residues in contact with GLY 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLU 3.0 16.6 + - - -
127B ILE 3.1 2.0 + - - -
129B ASN* 1.3 78.0 - - - +
131B LYS* 1.3 65.7 + - - -
132B VAL 3.4 1.6 - - - -
133B PRO* 3.3 16.0 - - - +
134B VAL* 3.6 13.3 - - - +
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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