Contacts of the helix formed by residues 106 - 120 (chain A) in PDB entry 2UXG
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 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A PRO* 5.1 10.3 - - + +
83A PHE* 4.1 26.2 - - + -
105A ASN* 1.4 94.3 - - + +
107A LYS* 1.3 67.2 + - - +
108A LYS 4.4 0.2 - - - +
109A ALA* 3.0 12.8 + - + -
110A GLN 2.8 19.8 + - - -
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Residues in contact with LYS 107 (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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105A ASN 3.4 4.6 + - - +
106A PRO* 1.3 70.6 - - - +
108A LYS* 1.3 59.4 + - - +
110A GLN* 3.2 5.1 + - - +
111A GLU* 2.8 40.8 + - - +
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Residues in contact with LYS 108 (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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13A ASP* 3.6 31.9 + - - -
14A GLY* 5.6 0.2 - - - -
83A PHE* 3.3 50.4 - - + -
106A PRO* 3.1 2.2 + - - +
107A LYS* 1.3 78.4 - - - +
109A ALA* 1.3 63.2 + - - +
111A GLU* 3.2 33.9 + - - +
112A ARG* 3.1 61.4 + - - +
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Residues in contact with ALA 109 (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 PRO 3.8 22.2 - - - +
83A PHE* 4.1 8.4 - - - +
85A VAL* 3.5 26.5 - - + +
105A ASN* 4.2 7.6 - - + +
106A PRO* 3.0 25.5 + - + +
108A LYS* 1.3 77.6 - - - +
110A GLN* 1.3 63.7 + - - +
112A ARG 3.3 1.7 + - - -
113A LEU* 3.0 23.7 + - + +
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Residues in contact with GLN 110 (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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100A VAL 2.9 24.4 + - - -
101A LYS 3.7 7.5 + - - +
103A ALA* 3.4 23.4 - - - +
105A ASN* 2.8 42.2 + - + +
106A PRO 2.8 18.7 + - - +
107A LYS* 3.7 6.1 - - - +
109A ALA* 1.3 73.7 - - - +
111A GLU* 1.3 57.7 + - - +
113A LEU* 3.3 8.9 + - - +
114A ASP* 2.9 64.9 + - - +
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Residues in contact with GLU 111 (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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107A LYS* 2.8 25.9 + - - +
108A LYS* 3.2 47.6 + - + +
110A GLN* 1.3 71.6 - - - +
112A ARG* 1.3 56.1 + - + +
114A ASP* 3.8 6.9 - - - +
115A ALA* 2.8 31.9 + - - +
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Residues in contact with ARG 112 (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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13A ASP* 3.2 55.7 + - - +
14A GLY* 3.8 1.8 - - - -
15A ALA 3.0 20.4 + - - +
16A MET 2.7 27.2 + - - -
17A VAL* 3.7 6.3 - - - +
21A ALA* 5.6 3.3 - - - +
83A PHE* 2.8 44.9 + - - +
84A MET* 4.0 0.8 - - - +
85A VAL* 3.5 23.3 - - + +
86A GLY* 5.8 0.2 - - - -
108A LYS* 3.1 37.4 + - - +
109A ALA 3.3 2.7 + - - +
111A GLU* 1.3 75.7 - - + +
113A LEU* 1.3 58.0 + - - +
115A ALA* 3.6 6.1 + - - +
116A ALA* 3.0 28.9 + - - +
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Residues in contact with LEU 113 (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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45A ILE* 4.2 10.5 - - + -
48A MET* 3.6 30.5 - - + -
85A VAL* 3.8 21.5 - - + -
86A GLY 3.6 24.7 - - - +
87A VAL* 3.8 11.4 - - + +
100A VAL* 3.9 10.5 - - + -
105A ASN* 4.0 22.4 - - - +
109A ALA 3.0 18.7 + - - +
110A GLN* 3.6 16.8 - - - +
112A ARG* 1.3 75.7 - - - +
114A ASP* 1.3 57.6 + - - +
116A ALA* 3.2 7.5 + - - +
117A LEU* 3.0 32.7 + - - +
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Residues in contact with ASP 114 (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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100A VAL 4.3 0.2 - - - +
101A LYS* 3.9 24.0 + - + +
110A GLN* 2.9 51.5 + - - +
111A GLU* 3.8 6.5 - - - +
113A LEU* 1.3 76.1 - - - +
115A ALA* 1.3 56.8 + - - +
117A LEU* 3.3 10.3 + - - +
118A ALA* 3.0 28.9 + - - +
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Residues in contact with ALA 115 (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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111A GLU 2.8 21.7 + - - +
112A ARG* 3.8 6.5 - - - +
114A ASP* 1.3 70.5 - - - +
116A ALA* 1.3 59.7 + - - +
118A ALA* 3.3 7.0 + - - +
119A ALA* 2.9 31.4 + - - +
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Residues in contact with ALA 116 (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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21A ALA* 3.7 12.8 - - + +
22A SER* 3.6 24.0 - - - -
86A GLY* 4.9 1.3 - - - -
87A VAL* 3.7 19.1 - - + +
112A ARG 3.0 15.5 + - - +
113A LEU* 3.2 9.2 + - - +
115A ALA* 1.3 75.0 - - - +
117A LEU* 1.3 64.3 + - - +
119A ALA* 3.2 4.2 + - - +
120A LEU* 3.0 30.0 + - - +
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Residues in contact with LEU 117 (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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73A VAL* 3.8 25.1 - - + -
87A VAL* 4.0 14.1 - - + -
97A LEU* 3.8 24.0 - - + -
100A VAL* 3.7 25.4 - - + -
101A LYS* 3.5 39.7 - - + +
113A LEU 3.0 16.4 + - - +
114A ASP* 3.3 10.7 + - - +
116A ALA* 1.3 77.5 - - - +
118A ALA* 1.3 62.6 + - - +
120A LEU* 3.3 5.3 + - + -
122A ASN* 3.0 39.5 + - + +
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Residues in contact with ALA 118 (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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114A ASP 3.0 16.8 + - - +
115A ALA* 3.7 7.2 - - - +
117A LEU* 1.3 75.3 - - - +
119A ALA* 1.3 60.8 + - - +
121A GLY* 3.0 19.1 + - - -
122A ASN* 4.0 14.0 + - - +
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Residues in contact with ALA 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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22A SER* 3.8 15.0 - - - +
115A ALA 2.9 17.6 + - - +
116A ALA* 3.2 5.6 + - - +
118A ALA* 1.3 76.1 - - - +
120A LEU* 1.3 58.9 + - - +
121A GLY* 3.1 4.3 + - - -
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Residues in contact with LEU 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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22A SER* 3.9 7.2 - - - +
23A LEU* 3.4 13.2 - - - +
24A LYS* 3.2 66.1 + - + +
87A VAL* 3.6 39.0 - - + +
89A GLN* 3.4 29.3 + - + +
116A ALA 3.0 20.3 + - - +
117A LEU* 3.6 3.8 - - - +
118A ALA 3.1 0.6 - - - -
119A ALA* 1.3 75.9 - - - +
121A GLY* 1.3 59.9 + - - +
122A ASN* 3.3 11.4 + - - +
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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