Contacts of the helix formed by residues 106 - 120 (chain A) in PDB entry 2D9W
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 ALA 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ASP 4.7 5.9 + - - +
88A THR* 3.9 8.9 - - - +
89A SER* 3.0 34.7 - - - +
104A ALA 3.4 4.0 + - - -
105A PRO* 1.3 69.4 - - - +
107A ALA* 1.3 60.0 + - - +
109A ARG* 4.1 5.3 + - - +
110A GLY* 3.8 13.0 + - - -
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Residues in contact with ALA 107 (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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105A PRO* 2.5 13.0 + - + +
106A ALA* 1.3 78.8 - - - +
108A GLU* 1.3 67.6 + - + +
110A GLY* 4.2 3.6 + - - -
111A ASP* 4.6 8.5 + - - +
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Residues in contact with GLU 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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14A LYS* 3.5 9.8 + - - +
15A GLN 3.6 20.1 - - - +
16A GLY* 4.0 9.9 - - - -
17A PHE 6.2 0.4 - - - +
105A PRO* 2.6 31.8 + - + -
107A ALA* 1.3 76.0 - - + +
109A ARG* 1.3 67.4 + - - +
110A GLY 3.1 2.0 - - - -
111A ASP* 2.7 17.8 + - - -
112A TRP* 2.8 34.7 + - + +
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Residues in contact with ARG 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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77A GLU* 3.5 34.3 + - - +
78A ALA 5.1 1.2 + - - -
89A SER* 3.1 45.4 + - - +
90A ALA 4.6 3.8 - - - +
91A PHE* 4.7 5.8 - - + -
104A ALA* 4.3 7.3 - - + +
105A PRO 2.7 19.9 + - - +
106A ALA* 4.1 5.4 + - - +
108A GLU* 1.3 70.0 - - - +
110A GLY* 1.3 87.4 + - - +
112A TRP* 2.8 23.4 + - - -
113A VAL* 2.9 44.8 + - + +
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Residues in contact with GLY 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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106A ALA 3.8 10.5 + - - -
107A ALA 4.7 2.2 - - - -
108A GLU 2.9 1.6 + - - -
109A ARG* 1.3 104.1 + - - +
111A ASP* 1.3 61.8 + - - +
113A VAL* 4.5 0.2 - - - +
114A GLN* 3.6 22.6 + - - +
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Residues in contact with ASP 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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14A LYS* 3.7 20.8 - - + +
107A ALA 4.6 6.5 + - - +
108A GLU* 2.7 14.3 + - - +
110A GLY* 1.3 72.0 - - - -
112A TRP* 1.3 68.6 + - - +
114A GLN* 3.0 11.3 + - - +
115A ALA* 2.8 22.8 + - - +
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Residues in contact with TRP 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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14A LYS* 3.0 50.6 - - + +
16A GLY* 3.7 34.4 - - - -
17A PHE 5.3 1.0 + - - -
18A LEU* 4.2 22.7 - - + +
35A ALA* 4.8 7.9 - - + -
37A LEU* 3.9 35.9 - - + -
48A LEU* 4.5 5.8 - - + -
91A PHE* 5.8 3.4 - + + -
104A ALA* 4.3 13.4 - - + +
105A PRO* 5.2 1.2 - - - +
108A GLU* 2.8 40.6 + - + +
109A ARG* 2.8 13.8 + - + +
111A ASP* 1.3 72.5 - - - +
113A VAL* 1.3 67.7 + - + +
115A ALA* 2.9 1.4 + - - +
116A ILE* 2.7 50.8 + - + +
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Residues in contact with VAL 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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75A VAL* 5.1 10.7 - - + +
76A ALA 4.6 1.3 - - - +
77A GLU* 3.3 37.5 - - + +
91A PHE* 4.2 17.7 - - + -
109A ARG* 2.9 47.2 + - + +
110A GLY 4.5 0.4 - - - +
112A TRP* 1.3 76.6 - - + +
114A GLN* 1.3 55.9 + - - +
116A ILE* 3.8 8.6 - - - +
117A CYS* 2.7 45.9 + - + +
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Residues in contact with GLN 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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110A GLY 3.6 15.9 + - - +
111A ASP* 3.0 13.9 + - - +
113A VAL* 1.3 79.6 - - - +
115A ALA* 1.3 58.6 + - - +
117A CYS* 3.7 4.1 - - - +
118A LEU* 2.8 49.0 + - + +
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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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13A VAL* 5.6 4.9 - - + -
14A LYS* 5.0 8.5 - - + -
37A LEU* 3.7 24.5 - - + -
111A ASP 2.8 16.3 + - - +
112A TRP* 3.6 7.4 - - - +
114A GLN* 1.3 72.2 - - - +
116A ILE* 1.3 56.1 + - - +
118A LEU* 2.7 34.0 + - - +
119A LEU* 2.8 19.2 + - + +
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Residues in contact with ILE 116 (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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18A LEU* 5.8 0.9 - - + -
37A LEU* 4.3 13.5 - - + -
48A LEU* 5.4 8.1 - - + -
69A LEU* 3.9 27.6 - - + -
72A CYS* 5.0 1.6 - - - -
75A VAL* 4.5 20.2 - - + -
91A PHE* 4.4 26.5 - - + -
93A LEU* 6.0 3.8 - - + -
112A TRP* 2.7 53.1 + - + +
113A VAL* 3.8 6.5 - - - +
115A ALA* 1.3 71.8 - - - +
117A CYS* 1.3 57.5 + - - +
119A LEU 3.1 0.4 + - - +
120A ALA* 2.6 45.4 + - + +
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Residues in contact with CYS 117 (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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75A VAL* 4.3 15.5 - - + -
113A VAL* 2.7 28.5 + - + +
114A GLN* 3.7 4.0 - - - +
116A ILE* 1.3 75.6 - - - +
118A LEU* 1.3 58.9 + - + +
121A PHE* 3.2 53.7 - - - +
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Residues in contact with LEU 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 GLN* 2.8 42.6 + - + +
115A ALA* 2.7 15.5 + - - +
117A CYS* 1.3 80.2 - - - +
119A LEU* 1.3 57.7 + - + +
121A PHE 4.1 0.5 - - - +
122A SER* 3.3 22.2 - - - -
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Residues in contact with LEU 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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13A VAL* 4.8 13.9 - - + -
37A LEU* 4.2 27.4 - - + -
38A TYR 4.1 9.0 - - - +
40A GLY* 4.2 19.1 - - - +
46A ALA* 3.7 32.5 - - + -
69A LEU* 4.0 6.3 - - + -
70A SER* 5.5 0.5 - - - -
115A ALA* 2.8 13.1 + - + +
116A ILE 3.9 1.1 - - - +
118A LEU* 1.3 78.6 - - + +
120A ALA* 1.3 61.2 + - - +
121A PHE 3.0 1.6 - - - -
122A SER* 2.7 35.1 + - - +
123A GLY 4.6 0.3 + - - -
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Residues in contact with ALA 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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69A LEU* 3.3 40.1 - - + +
70A SER* 3.9 20.2 + - - +
72A CYS* 3.9 9.8 - - + +
116A ILE* 2.6 28.1 + - + +
119A LEU* 1.3 74.2 - - - +
121A PHE* 1.3 75.1 + - + +
122A SER 3.7 1.2 + - - -
123A GLY 5.3 0.9 + - - -
124A PRO* 5.8 2.8 - - - +
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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