Contacts of the helix formed by residues 117 - 132 (chain B) in PDB entry 1DCT
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 GLN 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B MET 3.5 6.5 + - - -
116B ALA* 1.3 71.0 - - - +
118B ARG* 1.3 54.5 + - - +
119B HIS 2.6 13.2 + - - -
120B ASN* 2.7 31.8 + - - +
14N G 3.1 20.4 + - - +
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Residues in contact with ARG 118 (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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80B LEU* 2.8 65.5 + - - +
116B ALA* 4.2 11.2 - - + -
117B GLN* 1.3 77.4 - - - +
119B HIS* 1.3 70.5 + - + +
120B ASN 3.7 0.4 + - - -
121B LYS* 5.6 4.0 + - - +
12N C 4.6 17.4 + - - -
13N T 3.8 24.9 + - - +
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Residues in contact with HIS 119 (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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73B SER 4.2 0.4 + - - -
74B TRP* 3.4 47.3 - + + -
80B LEU* 3.4 44.6 + - + +
82B GLY* 3.5 14.7 - - - -
113B GLY 3.4 24.7 + - - -
114B MET 3.8 13.7 + - - +
116B ALA* 3.1 9.6 + - + +
117B GLN 2.6 5.3 + - - -
118B ARG* 1.3 85.5 - - + +
120B ASN* 1.3 63.6 + - - +
121B LYS 3.2 2.5 - - - -
122B ALA* 3.1 7.9 + - + +
123B VAL* 3.0 22.4 + - + +
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Residues in contact with ASN 120 (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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116B ALA 3.7 4.0 + - - +
117B GLN* 2.7 34.9 + - - +
118B ARG 3.7 0.4 - - - -
119B HIS* 1.3 70.3 - - - +
121B LYS* 1.3 67.3 + - - +
123B VAL* 3.2 9.2 + - - +
124B GLN* 2.7 44.2 + - - +
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Residues in contact with LYS 121 (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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118B ARG 5.6 3.8 + - - -
119B HIS 3.2 0.6 - - - -
120B ASN* 1.3 82.0 - - - +
122B ALA* 1.3 66.3 + - - +
124B GLN* 3.0 6.8 + - - +
125B GLU* 2.9 40.9 + - + +
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Residues in contact with ALA 122 (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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74B TRP* 3.8 29.4 - - + -
83B ILE* 4.2 23.8 - - + -
119B HIS* 3.1 9.2 + - + +
121B LYS* 1.3 79.1 - - - +
123B VAL* 1.3 65.9 + - - +
125B GLU* 2.9 25.5 + - - +
126B PHE* 2.9 20.6 + - + -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TRP* 5.7 0.2 - - + -
114B MET* 3.5 44.9 - - + +
115B MET* 4.8 12.8 - - + -
119B HIS* 3.0 15.9 + - + +
120B ASN* 3.7 11.4 - - - +
122B ALA* 1.3 78.9 - - + +
124B GLN* 1.3 63.5 + - - +
126B PHE* 3.2 10.9 + - - +
127B ILE* 3.0 38.4 + - + +
139B ILE* 5.4 2.2 - - + -
158B TYR* 3.5 18.2 - - + +
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Residues in contact with GLN 124 (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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120B ASN* 2.7 36.6 + - - +
121B LYS* 3.1 13.2 - - - +
123B VAL* 1.3 72.8 - - - +
125B GLU* 1.3 66.3 + - + +
127B ILE* 3.0 23.1 + - - +
128B GLN* 2.9 33.4 + - + +
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Residues in contact with GLU 125 (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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83B ILE* 4.7 2.9 - - - +
92B TYR* 3.7 22.4 + - + +
121B LYS* 2.9 29.0 + - + +
122B ALA* 2.9 13.9 + - - +
124B GLN* 1.3 76.1 - - + +
126B PHE* 1.3 65.0 + - + +
128B GLN* 3.1 9.3 + - - +
129B GLU* 2.9 31.8 + - + +
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Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TRP* 3.8 22.9 - + - -
83B ILE* 4.3 9.9 - - + -
88B GLY 4.4 4.0 - - - -
91B PHE* 3.1 46.4 - + + -
92B TYR* 3.5 43.5 - + - -
95B ILE* 4.1 7.6 - - + -
114B MET* 3.6 26.7 - - + -
122B ALA* 2.9 21.7 + - + -
123B VAL* 3.3 10.3 - - - +
125B GLU* 1.3 75.9 - - - +
127B ILE* 1.3 67.5 + - + +
129B GLU* 3.0 10.5 + - - +
130B PHE* 2.9 32.2 + - + -
158B TYR* 4.6 2.9 - - + -
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Residues in contact with ILE 127 (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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123B VAL* 3.2 25.1 - - + +
124B GLN* 3.0 21.4 + - - +
126B PHE* 1.3 74.9 - - - +
128B GLN* 1.3 58.4 + - - +
130B PHE* 2.5 36.6 + - - +
131B ASP* 3.0 10.7 + - + -
137B VAL* 3.9 22.2 - - + -
139B ILE* 3.4 31.4 - - + -
158B TYR* 4.2 15.7 - - + -
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Residues in contact with GLN 128 (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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124B GLN* 2.9 26.2 + - + +
125B GLU* 3.4 13.5 - - - +
127B ILE* 1.3 72.5 - - - +
129B GLU* 1.3 55.2 + - - +
131B ASP* 2.9 17.9 + - - +
132B ASN* 2.7 67.6 + - - +
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Residues in contact with GLU 129 (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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92B TYR* 5.1 11.1 - - + -
95B ILE* 4.2 26.1 - - + +
99B LYS* 3.0 33.9 + - - -
125B GLU* 2.9 24.1 + - + +
126B PHE* 3.1 10.5 - - - +
127B ILE 2.7 3.8 + - - -
128B GLN* 1.3 77.3 - - - +
130B PHE* 1.3 63.1 + - - +
132B ASN* 2.8 21.4 + - - +
133B ALA* 2.8 23.6 + - - +
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Residues in contact with PHE 130 (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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91B PHE* 3.7 25.1 - + - -
94B TYR* 4.6 6.3 - + - -
95B ILE* 3.7 23.8 - - + -
98B LEU* 3.6 15.9 - - + -
106B PHE* 2.9 43.3 - + + -
126B PHE* 2.9 36.0 + - + -
127B ILE* 2.5 21.3 + - + +
129B GLU* 1.3 70.9 - - - +
131B ASP* 1.3 61.2 + - - +
133B ALA* 3.1 20.8 + - - +
135B TYR* 3.1 18.8 + - + +
137B VAL* 3.2 20.2 - - + -
158B TYR* 4.1 17.9 - + + -
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Residues in contact with ASP 131 (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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127B ILE* 3.0 8.1 + - + +
128B GLN* 2.9 24.2 + - - +
130B PHE* 1.3 73.9 - - - +
132B ASN* 1.3 72.7 + - - +
133B ALA 2.8 4.3 - - - -
134B GLY 2.8 18.4 + - - -
135B TYR 3.5 11.4 + - - +
137B VAL* 4.4 3.1 - - + +
163B LYS* 2.6 36.3 + - - +
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Residues in contact with ASN 132 (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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99B LYS* 5.6 6.3 - - - -
102B LYS* 5.4 1.6 + - - -
128B GLN* 2.7 41.9 + - - +
129B GLU* 2.8 27.5 + - - +
131B ASP* 1.3 86.1 + - - +
133B ALA* 1.3 58.3 + - - +
134B GLY 3.3 0.4 - - - -
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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