Contacts of the helix formed by residues 118 - 131 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A TYR* 1.3 78.6 - - + +
119A ASN* 1.3 62.1 + - - +
120A ASP* 4.2 18.4 - - - +
121A VAL* 3.3 19.0 + - + +
122A LEU* 3.0 26.5 + - - +
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Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLU* 1.3 74.6 - - - +
120A ASP* 1.3 66.7 + - - +
122A LEU* 3.1 12.8 + - - +
123A GLU* 2.9 39.7 + - + +
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Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLU* 3.5 18.2 + - - +
119A ASN* 1.3 78.1 - - - +
121A VAL* 1.3 63.8 + - + +
123A GLU* 3.7 4.5 + - - +
124A GLN* 3.1 50.1 + - - +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA* 5.4 12.3 - - + +
85A ILE* 4.5 11.9 - - + -
86A VAL* 4.6 6.3 - - + -
117A TYR* 3.8 35.0 - - + -
118A GLU* 3.3 20.7 + - + +
119A ASN 3.2 0.6 - - - -
120A ASP* 1.3 79.3 - - + +
122A LEU* 1.3 60.3 + - - +
124A GLN* 3.2 12.4 + - - +
125A LEU* 2.9 43.1 + - + +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 4.1 23.0 - - + +
111A TRP* 4.3 11.7 - - + +
112A GLU* 3.9 43.1 - - + +
115A SER* 5.6 2.0 - - - -
117A TYR* 3.2 30.1 - - + +
118A GLU 3.0 20.3 + - - +
119A ASN* 3.1 12.8 + - - +
121A VAL* 1.3 76.7 - - - +
123A GLU* 1.3 64.4 + - - +
125A LEU* 3.4 13.5 + - + +
126A LYS* 3.0 33.3 + - - +
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU* 4.8 1.7 - - - +
119A ASN* 2.9 31.9 + - + +
120A ASP* 4.1 4.3 - - - +
122A LEU* 1.3 78.3 - - - +
124A GLN* 1.3 66.8 + - - +
126A LYS* 3.1 40.5 + - - +
127A GLN* 2.9 27.7 + - - +
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Residues in contact with GLN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A VAL* 3.6 33.4 - - + +
120A ASP* 3.1 40.1 + - - +
121A VAL* 3.5 11.8 - - - +
123A GLU* 1.3 79.0 - - + +
125A LEU* 1.3 56.0 + - - +
127A GLN* 3.3 8.8 + - - +
128A ALA* 2.9 28.6 + - - +
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Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ILE* 3.8 15.9 - - + +
86A VAL* 3.8 14.6 - - + +
89A PHE* 3.6 37.5 - - + -
108A LEU* 3.8 23.2 - - + +
111A TRP* 3.8 30.1 - - + -
117A TYR* 4.9 0.4 - - + -
121A VAL* 2.9 34.9 + - + +
122A LEU* 3.5 13.2 - - + +
123A GLU 3.2 0.2 - - - -
124A GLN* 1.3 74.5 - - - +
126A LYS* 1.3 64.3 + - - +
128A ALA* 3.2 5.3 + - - +
129A LEU* 3.0 24.8 + - - +
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Residues in contact with LYS 126 (chain A).
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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108A LEU* 3.8 19.0 - - + +
112A GLU* 3.1 40.8 + - - -
122A LEU* 3.0 19.6 + - - +
123A GLU* 3.1 42.8 + - - +
125A LEU* 1.3 75.5 - - - +
127A GLN* 1.3 62.1 + - + +
129A LEU 3.4 0.3 + - - -
130A TYR* 2.9 43.6 + - + +
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Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LYS* 6.0 0.3 - - - -
123A GLU* 2.9 16.5 + - + +
124A GLN* 3.6 10.5 - - - +
125A LEU 3.3 0.2 - - - -
126A LYS* 1.3 78.0 - - - +
128A ALA* 1.3 62.2 + - - +
131A GLY* 2.8 45.5 + - - +
132A LEU 4.6 2.4 + - - -
133A GLU* 6.1 0.7 - - - +
134A HIS* 4.6 1.9 - - - -
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A VAL* 3.7 29.2 - - + +
89A PHE* 4.2 4.3 - - + -
90A LYS* 3.8 32.4 - - + +
93A SER* 3.9 0.7 - - - -
124A GLN 2.9 18.1 + - - +
125A LEU* 3.2 8.5 + - - +
127A GLN* 1.3 76.4 - - - +
129A LEU* 1.3 53.0 + - - +
134A HIS* 2.6 30.8 + - - -
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 4.6 9.9 - - + -
93A SER* 3.3 15.4 + - - +
101A LYS* 2.9 39.7 + - + -
104A LEU* 3.5 39.9 - - + +
105A GLY* 3.6 33.0 - - - +
108A LEU* 4.1 11.4 - - + -
125A LEU 3.0 14.8 + - - +
126A LYS 3.9 2.0 - - - +
128A ALA* 1.3 79.5 - - - +
130A TYR* 1.3 83.5 + - + +
131A GLY 3.6 0.4 - - - -
134A HIS* 3.6 5.1 - - - -
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Residues in contact with TYR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LYS* 4.1 29.7 + - + +
105A GLY* 3.4 24.8 - - - -
108A LEU* 4.8 7.9 - - + -
126A LYS* 2.9 25.2 + - + +
129A LEU* 1.3 99.6 - - + +
131A GLY* 1.3 68.1 + - - +
132A LEU* 5.6 1.6 - - - +
134A HIS* 4.6 0.7 - - - -
135A HIS* 4.5 9.3 + - - -
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Residues in contact with GLY 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LYS 3.9 0.6 + - - -
127A GLN* 2.8 41.2 + - - +
129A LEU 3.6 1.2 - - - -
130A TYR* 1.3 82.6 - - - +
132A LEU* 1.3 64.9 + - - -
133A GLU* 3.1 6.4 + - - -
134A HIS* 3.3 17.0 + - - -
135A HIS* 3.7 6.8 - - - -
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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