Contacts of the helix formed by residues 104 - 115 (chain B) in PDB entry 1DSB
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 SER 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A SER 4.1 8.3 - - - -
170A ASN* 3.8 19.4 + - - -
68B LEU* 3.9 14.6 - - - +
102B ILE* 3.7 2.3 - - - +
103B ARG* 1.3 82.8 - - - +
105B ALA* 1.3 64.7 + - - +
106B SER* 3.0 20.4 + - - -
107B ASP* 3.0 25.2 + - - +
108B ILE* 3.6 6.6 + - - +
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Residues in contact with ALA 105 (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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169A SER 5.2 0.6 + - - -
68B LEU* 3.9 4.6 - - - +
71B ASP* 3.9 27.3 + - + +
104B SER* 1.3 73.7 - - - +
106B SER* 1.3 61.7 + - - +
108B ILE* 3.1 30.5 + - + +
109B ARG* 3.4 6.4 + - - +
122B TYR* 4.8 2.4 + - - -
126B TRP* 5.1 11.3 - - + -
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Residues in contact with SER 106 (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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104B SER* 3.0 19.1 + - - -
105B ALA* 1.3 76.1 - - - +
107B ASP* 1.3 64.6 + - - +
109B ARG* 3.3 19.5 + - - +
110B ASP* 3.2 19.3 + - - +
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Residues in contact with ASP 107 (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 THR 3.3 24.5 - - - +
102B ILE* 3.6 12.3 - - + +
103B ARG* 3.0 24.4 + - - +
104B SER* 3.0 23.5 + - - +
106B SER* 1.3 80.4 + - - +
108B ILE* 1.3 62.7 + - - +
110B ASP* 3.4 20.6 + - - +
111B VAL* 3.5 15.6 + - - +
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Residues in contact with ILE 108 (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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68B LEU* 4.0 15.7 - - + -
71B ASP* 4.1 17.7 - - + +
72B LEU* 4.0 20.0 - - + -
75B ALA* 3.4 26.9 - - + -
92B LEU* 4.0 13.2 - - + -
102B ILE* 3.8 19.7 - - + -
104B SER 3.9 1.6 - - - +
105B ALA* 3.1 26.9 + - + +
107B ASP* 1.3 75.6 - - - +
109B ARG* 1.3 65.5 + - - +
111B VAL* 3.1 16.1 + - - +
112B PHE* 3.2 21.3 - - + -
122B TYR* 3.7 9.2 - - - +
126B TRP* 5.3 2.2 - - + -
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Residues in contact with ARG 109 (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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105B ALA 3.4 4.7 + - - +
106B SER* 3.3 16.6 + - - +
108B ILE* 1.3 78.6 - - - +
110B ASP* 1.3 68.8 + - - +
112B PHE* 3.0 15.4 + - - +
113B ILE* 3.1 34.6 + - + +
119B GLY* 3.4 20.4 + - - -
122B TYR* 3.7 32.1 + - + -
123B ASP* 2.8 42.2 + - - -
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Residues in contact with ASP 110 (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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106B SER* 3.2 16.4 + - - +
107B ASP* 3.6 17.5 - - - +
108B ILE 3.2 0.8 - - - -
109B ARG* 1.3 82.1 + - - +
111B VAL* 1.3 61.0 + - - +
113B ILE* 3.9 14.7 - - - +
114B ASN* 3.0 37.1 + - - +
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Residues in contact with VAL 111 (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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88B VAL* 4.4 11.9 - - + -
91B PRO* 3.8 33.4 - - + +
92B LEU* 4.1 19.3 - - + -
95B GLY* 5.9 0.4 - - - -
101B THR* 6.1 0.7 - - - +
102B ILE* 4.0 24.7 - - + -
107B ASP 3.5 11.6 + - - +
108B ILE 3.1 10.4 + - - +
110B ASP* 1.3 77.0 - - + +
112B PHE* 1.3 64.9 + - + +
114B ASN* 3.4 9.3 + - - +
115B ALA* 3.2 19.4 + - - +
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Residues in contact with PHE 112 (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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75B ALA* 3.5 25.6 - - + -
78B VAL* 4.0 16.4 - - + -
79B ALA* 4.0 20.4 - - + -
82B LEU* 4.6 6.1 - - + -
84B VAL* 4.1 14.4 - - + -
88B VAL* 4.2 18.2 - - + -
92B LEU* 4.5 12.1 - - + -
108B ILE* 3.2 38.4 - - + -
109B ARG 3.0 8.1 + - - +
111B VAL* 1.3 77.6 - - + +
113B ILE* 1.3 64.3 + - + +
115B ALA* 3.0 17.7 + - - +
116B GLY 3.4 0.3 + - - -
117B ILE* 3.1 30.2 + - + +
122B TYR* 3.4 36.3 - + + -
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Residues in contact with ILE 113 (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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109B ARG* 3.1 55.8 + - + +
110B ASP* 3.9 13.0 - - - +
112B PHE* 1.3 75.8 - - + +
114B ASN* 1.3 66.3 + - - +
116B GLY* 3.1 14.6 + - - -
117B ILE 3.2 19.6 + - - +
119B GLY* 3.9 16.4 - - - +
122B TYR* 5.6 1.8 - - + -
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Residues in contact with ASN 114 (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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110B ASP* 3.0 31.9 + - - +
111B VAL* 3.4 10.1 - - - +
113B ILE* 1.3 83.6 - - - +
115B ALA* 1.3 57.0 + - - +
116B GLY 3.2 1.5 + - - -
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Residues in contact with ALA 115 (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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84B VAL* 6.2 0.4 - - + -
87B LYS* 4.4 30.9 - - + +
88B VAL* 4.4 11.0 - - + -
111B VAL 3.2 9.1 + - - +
112B PHE 3.0 11.6 + - - +
114B ASN* 1.3 77.8 - - - +
116B GLY* 1.3 60.0 + - - +
117B ILE* 3.6 7.4 - - + +
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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