Contacts of the helix formed by residues 106 - 120 (chain A) in PDB entry 3D9O
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 ASP 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PRO 4.6 3.3 - - - +
57A GLU* 4.7 7.8 - - - +
60A VAL* 3.7 25.8 - - + +
61A PRO* 5.5 0.2 - - - +
102A CYS* 3.8 15.3 - - + +
103A PRO* 2.8 31.6 + - + +
105A ASP* 1.3 88.2 + - - +
107A LYS* 1.3 63.2 + - - +
108A SER 3.2 2.9 - - - -
109A LYS* 3.2 44.1 + - - +
110A ILE* 3.6 5.4 + - - +
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Residues in contact with LYS 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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100A TYR* 4.6 9.0 - - + -
102A CYS* 3.9 13.2 - - - -
103A PRO 3.7 2.6 + - - -
104A GLY* 3.3 17.1 + - - +
106A ASP* 1.3 79.0 - - - +
108A SER* 1.3 61.9 + - - +
110A ILE* 3.3 14.8 + - - +
111A VAL* 3.3 18.4 + - + +
135A ALA* 2.9 36.3 + - - +
136A ALA* 5.1 2.0 + - - +
138A LEU* 3.7 38.1 + - + +
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Residues in contact with SER 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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104A GLY 4.7 0.2 + - - -
105A ASP 3.3 16.3 + - - -
107A LYS* 1.3 78.4 - - - +
109A LYS* 1.3 61.8 + - - +
111A VAL* 3.5 7.2 + - - +
112A ARG* 3.0 62.0 + - - +
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Residues in contact with LYS 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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60A VAL* 3.9 25.1 - - + -
63A LEU* 5.1 0.4 - - - -
64A TYR* 3.9 19.3 + - + +
105A ASP* 4.7 3.8 - - - +
106A ASP* 3.2 38.1 + - - +
108A SER* 1.3 78.9 + - - +
110A ILE* 1.3 61.4 + - - +
112A ARG* 3.6 19.0 + - - +
113A VAL* 3.3 27.1 + - - +
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Residues in contact with ILE 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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60A VAL* 4.0 12.3 - - + -
63A LEU* 3.8 19.1 - - + -
96A PHE* 3.6 30.3 - - + -
99A LEU* 3.6 32.3 - - + +
100A TYR* 3.6 32.8 - - + +
102A CYS* 3.7 18.8 - - - -
106A ASP 3.6 7.2 + - - +
107A LYS* 3.3 8.0 + - - +
108A SER 3.3 0.6 - - - -
109A LYS* 1.3 75.8 - - - +
111A VAL* 1.3 60.8 + - - +
113A VAL* 3.1 5.0 + - - +
114A LEU* 2.9 26.5 + - + +
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Residues in contact with VAL 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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100A TYR* 4.8 2.5 - - - +
107A LYS* 3.3 18.4 + - + +
108A SER* 4.0 8.3 - - - +
109A LYS 3.5 0.2 - - - -
110A ILE* 1.3 76.7 - - + +
112A ARG* 1.3 52.9 + - + +
114A LEU* 3.2 9.0 + - + +
115A ASN* 2.7 51.0 + - - +
132A LEU* 4.4 12.8 - - + -
135A ALA* 3.6 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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108A SER* 3.0 57.8 + - - +
109A LYS* 3.5 17.7 - - - +
110A ILE 3.2 0.2 - - - -
111A VAL* 1.3 76.2 - - + +
113A VAL* 1.3 62.4 + - + +
115A ASN* 3.2 12.3 + - - +
116A LEU* 3.0 33.9 + - + +
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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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63A LEU* 3.8 23.6 - - + -
64A TYR* 3.7 29.4 - - + -
67A ASP* 4.2 13.9 - - - +
109A LYS 3.3 13.4 + - - +
110A ILE 3.1 8.6 + - - +
112A ARG* 1.3 76.9 - - + +
114A LEU* 1.3 56.6 + - + +
116A LEU* 3.2 12.8 + - + +
117A TRP* 2.9 63.5 + - + +
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Residues in contact with LEU 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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96A PHE* 3.6 27.8 - - + -
100A TYR* 3.5 24.5 - - - +
110A ILE* 2.9 16.4 + - + +
111A VAL* 3.6 11.0 - - + +
113A VAL* 1.3 75.4 - - - +
115A ASN* 1.3 58.4 + - - +
117A TRP* 3.3 16.6 + - + +
118A GLN* 2.9 29.6 + - - +
128A ILE* 4.1 11.8 - - + +
131A LEU* 3.6 43.5 - - + -
132A LEU* 3.8 22.2 - - + +
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Residues in contact with ASN 115 (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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111A VAL* 2.7 37.9 + - - +
112A ARG* 3.4 11.1 - - - +
114A LEU* 1.3 71.7 - - - +
116A LEU* 1.3 59.6 + - + +
118A GLN* 3.4 16.6 + - - +
119A LYS* 3.0 28.4 + - - +
132A LEU* 4.3 13.5 - - - +
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Residues in contact with LEU 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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67A ASP* 5.9 3.6 - - - +
71A ARG* 6.5 0.9 - - - -
112A ARG* 3.0 24.5 + - + +
113A VAL* 3.2 12.1 + - + +
115A ASN* 1.3 74.9 - - + +
117A TRP* 1.3 69.5 + - + +
119A LYS* 3.3 7.4 + - + +
120A ASN* 3.0 32.9 + - - +
122A VAL* 5.0 0.4 - - - -
502A SO4 3.5 33.9 - - - +
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Residues in contact with TRP 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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63A LEU* 3.6 22.7 - - + -
66A ILE* 4.0 22.4 - - + -
67A ASP* 2.8 33.9 + - - +
70A VAL* 5.8 1.1 - - + +
71A ARG* 5.2 2.2 - - - +
92A ILE* 4.1 6.7 - - + -
96A PHE* 3.6 27.8 - + - -
113A VAL* 2.9 28.3 + - + +
114A LEU* 3.4 25.1 - - + +
116A LEU* 1.3 78.9 - - + +
118A GLN* 1.3 56.7 + - - +
120A ASN 3.4 0.3 + - - -
121A ASN* 2.9 10.0 + - - -
122A VAL* 2.9 54.4 + - + +
123A PHE* 3.5 35.2 - + - -
128A ILE* 3.7 12.2 - - + +
131A LEU* 4.6 2.0 - - + -
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Residues in contact with GLN 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 LEU 2.9 16.3 + - - +
115A ASN* 3.7 15.4 + - - +
116A LEU 3.3 0.2 - - - -
117A TRP* 1.3 73.2 - - - +
119A LYS* 1.3 65.5 + - - +
121A ASN* 3.3 20.1 + - - +
125A SER* 4.8 13.7 + - - -
128A ILE* 3.5 23.5 - - + +
129A GLN* 4.3 12.3 - - - +
132A LEU* 4.2 18.7 - - - +
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Residues in contact with LYS 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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115A ASN 3.0 17.8 + - - +
116A LEU* 3.3 9.8 + - + +
118A GLN* 1.3 76.3 - - - +
120A ASN* 1.3 83.4 + - - +
121A ASN* 3.6 8.7 + - - -
502A SO4 4.1 8.7 + - - +
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Residues in contact with ASN 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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71A ARG* 6.3 1.4 - - - +
74A ARG* 3.4 14.6 + - - +
79A GLN* 4.7 4.5 + - - -
116A LEU* 3.0 29.4 + - - +
119A LYS* 1.3 96.4 + - - +
121A ASN* 1.3 70.3 + - - +
122A VAL* 3.2 14.6 + - + +
502A SO4 2.8 42.1 + - - -
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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