Contacts of the helix formed by residues 118 - 131 (chain B) in PDB entry 4NAC
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 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B THR* 5.9 0.3 - - - +
82B ALA* 6.1 0.7 - - - +
117B TYR* 1.3 88.5 - - - +
119B ASN* 1.3 67.6 + - - +
120B ASP* 4.1 12.1 - - + +
121B VAL* 3.0 34.0 + - + +
122B LEU* 2.9 18.4 + - - +
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Residues in contact with ASN 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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112B GLU* 5.7 3.2 + - - +
117B TYR 5.2 0.2 + - - -
118B GLU* 1.3 73.7 - - - +
120B ASP* 1.3 54.5 + - - +
122B LEU* 4.1 19.1 - - - +
123B GLU* 2.8 43.6 + - - +
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Residues in contact with ASP 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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118B GLU* 3.1 13.1 - - + +
119B ASN* 1.3 79.1 - - - +
121B VAL* 1.3 65.6 + - - +
123B GLU* 3.5 6.2 + - - +
124B GLN* 3.2 45.4 + - - +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ALA* 5.4 9.2 - - + +
85B ILE* 4.6 7.4 - - + -
86B VAL* 4.5 11.4 - - + -
117B TYR* 3.9 26.9 - - + -
118B GLU* 3.0 33.8 + - + +
120B ASP* 1.3 79.1 - - - +
122B LEU* 1.3 67.7 + - - +
123B GLU 3.1 1.3 - - - -
124B GLN* 2.9 13.9 + - - +
125B LEU* 2.9 39.3 + - + +
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Residues in contact with LEU 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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108B LEU* 4.7 6.0 - - + +
111B TRP* 4.0 28.7 - - + +
112B GLU* 3.8 41.1 - - + +
115B SER* 5.3 1.1 - - - -
117B TYR* 3.3 32.3 - - + +
118B GLU 2.9 14.7 + - - +
119B ASN* 3.6 22.7 - - - +
121B VAL* 1.3 74.8 - - - +
123B GLU* 1.3 66.8 + - - +
125B LEU* 3.2 14.6 + - + +
126B LYS* 3.1 28.7 + - - +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ASN* 2.8 28.5 + - - +
120B ASP* 3.6 6.5 - - - +
122B LEU* 1.3 74.1 - - - +
124B GLN* 1.3 65.4 + - + +
125B LEU 3.3 0.2 + - - -
126B LYS* 3.4 35.9 + - + +
127B GLN* 3.1 34.6 + - + +
132B LEU* 5.7 3.8 - - + +
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Residues in contact with GLN 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL* 3.7 32.2 - - + +
120B ASP* 3.2 35.6 + - - +
121B VAL* 2.9 17.7 + - - +
123B GLU* 1.3 77.7 - - - +
125B LEU* 1.3 57.3 + - - +
127B GLN* 3.3 14.8 + - - +
128B ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 125 (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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85B ILE* 3.8 5.2 - - + +
86B VAL* 3.8 26.9 - - + +
89B PHE* 3.4 37.7 - - + +
108B LEU* 3.8 18.0 - - + +
111B TRP* 3.8 30.3 - - + -
117B TYR* 4.7 1.3 - - + -
121B VAL* 2.9 31.0 + - + +
122B LEU* 3.5 17.7 - - + +
124B GLN* 1.3 74.2 - - - +
126B LYS* 1.3 58.9 + - - +
128B ALA* 3.2 5.4 + - - +
129B LEU* 2.9 31.5 + - - +
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Residues in contact with LYS 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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108B LEU* 4.1 11.1 - - + +
112B GLU* 3.3 38.0 + - - -
122B LEU* 3.1 20.6 + - - +
123B GLU* 3.6 39.3 + - - +
125B LEU* 1.3 75.3 - - - +
127B GLN* 1.3 57.3 + - - +
129B LEU 3.2 0.2 + - - -
130B TYR* 2.8 60.1 + - + +
132B LEU* 4.4 15.0 - - + -
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Residues in contact with GLN 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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123B GLU* 3.1 22.5 + - + +
124B GLN* 3.6 16.9 - - - +
126B LYS* 1.3 75.6 - - - +
128B ALA* 1.3 58.2 + - - +
131B GLY* 2.8 29.6 + - - -
132B LEU* 3.2 49.8 + - + +
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Residues in contact with ALA 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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86B VAL* 3.6 32.1 - - + +
89B PHE* 4.3 2.9 - - + -
90B LYS* 3.8 37.2 - - + +
93B SER* 4.1 4.7 - - - -
124B GLN 2.9 14.7 + - - +
125B LEU* 3.2 8.9 + - - +
127B GLN* 1.3 77.6 - - - +
129B LEU* 1.3 61.6 - - - +
131B GLY* 4.4 2.1 + - - -
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Residues in contact with LEU 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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89B PHE* 4.6 7.4 - - + +
93B SER* 3.0 29.6 + - - +
101B LYS* 3.5 25.5 - - + +
104B LEU* 3.7 33.9 - - + -
105B GLY* 3.6 21.8 - - - +
108B LEU* 3.4 26.2 - - + -
125B LEU 2.9 16.2 + - - +
126B LYS 3.9 2.2 - - - +
128B ALA* 1.3 79.3 - - - +
130B TYR* 1.3 89.8 + - + +
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Residues in contact with TYR 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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101B LYS* 5.0 21.3 - - + +
105B GLY* 3.8 13.9 + - - -
108B LEU* 4.9 2.5 - - + +
126B LYS* 2.8 48.7 + - + +
129B LEU* 1.3 103.3 - - + +
131B GLY* 1.3 60.1 + - - +
132B LEU* 4.6 13.7 - - + +
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Residues in contact with GLY 131 (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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127B GLN 2.8 19.7 + - - -
128B ALA 4.3 2.2 + - - -
129B LEU 3.6 1.2 - - - -
130B TYR* 1.3 74.2 - - - +
132B LEU* 1.3 65.4 + - - +
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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