Contacts of the helix formed by residues 105 - 120 (chain A) in PDB entry 1DRK
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 ASN 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ASP* 4.3 13.1 + - - -
102A ALA* 4.9 1.6 - - - +
103A SER* 3.1 27.8 + - - +
104A ASP* 1.3 69.8 + - - +
106A VAL* 1.3 65.2 + - - +
108A GLY* 3.7 3.1 - - - +
109A GLY 3.1 17.7 + - - -
136A SER* 5.8 0.4 + - - -
137A ALA* 4.0 16.8 - - - +
140A GLU* 3.5 33.3 + - + +
141A ARG* 2.8 54.8 + - + +
214A PHE* 3.8 7.6 - - - -
235A GLN* 4.4 1.0 + - - +
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Residues in contact with VAL 106 (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 ASP* 3.3 8.9 - - - +
105A ASN* 1.3 78.1 - - - +
107A LEU* 1.3 61.8 + - - +
110A LYS* 3.2 7.3 + - + +
140A GLU* 3.3 35.0 - - + +
143A GLU* 3.8 22.4 - - - +
144A GLY* 3.1 31.4 - - - +
147A GLN* 3.7 26.5 - - - +
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Residues in contact with LEU 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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104A ASP* 3.3 29.0 + - + +
106A VAL* 1.3 75.9 - - - +
108A GLY* 1.3 65.9 + - - +
110A LYS* 3.1 20.8 + - + +
111A ILE* 3.0 49.0 + - + +
265A LEU* 4.4 13.2 - - + -
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Residues in contact with GLY 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 ASP 3.0 11.6 + - - -
105A ASN 3.4 2.2 + - - -
106A VAL 3.3 0.4 - - - -
107A LEU* 1.3 77.0 - - - +
109A GLY* 1.3 60.8 + - - +
111A ILE* 3.5 4.6 + - - +
112A ALA* 3.1 22.5 + - - +
214A PHE* 3.6 22.7 - - - -
233A ILE* 3.9 6.6 - - - +
265A LEU* 3.5 21.9 - - - +
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Residues in contact with GLY 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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105A ASN 3.1 11.4 + - - -
106A VAL 3.4 2.7 + - - -
107A LEU 3.3 0.2 - - - -
108A GLY* 1.3 75.5 - - - +
110A LYS* 1.3 56.3 + - - +
112A ALA* 3.5 3.6 + - - +
113A GLY 3.1 21.3 + - - -
141A ARG* 3.7 22.4 - - - -
144A GLY 3.6 6.7 - - - -
145A PHE* 3.6 11.8 - - - +
187A PHE* 4.2 14.6 - - - -
214A PHE* 4.0 1.6 - - - -
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Residues in contact with LYS 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 VAL 3.2 11.1 + - - +
107A LEU* 3.1 23.8 + - + +
109A GLY* 1.3 74.4 - - - +
111A ILE* 1.3 57.4 + - + +
113A GLY* 3.1 2.8 + - - -
114A ASP* 2.8 67.6 + - - +
144A GLY* 3.2 18.1 + - - +
147A GLN* 3.8 26.7 - - + +
148A ALA* 4.0 5.9 - - + +
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Residues in contact with ILE 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 LEU* 3.0 48.8 + - + +
108A GLY* 3.7 7.0 - - - +
110A LYS* 1.3 76.0 - - + +
112A ALA* 1.3 65.2 + - - +
114A ASP* 3.4 10.9 + - - +
115A TYR* 2.9 24.1 + - - +
233A ILE* 3.8 21.5 - - + -
265A LEU* 5.0 9.6 - - + -
266A LYS* 6.5 0.2 - - - -
267A LEU* 4.4 23.6 - - + +
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Residues in contact with ALA 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 GLY 3.1 12.7 + - - +
109A GLY 3.5 9.2 - - - +
110A LYS 3.2 0.2 - - - -
111A ILE* 1.3 76.5 - - - +
113A GLY* 1.3 63.7 + - - +
115A TYR* 3.3 3.8 + - - +
116A ILE* 3.2 27.7 + - - +
187A PHE* 3.3 39.9 - - + -
212A VAL* 4.2 12.8 - - + +
233A ILE* 4.2 11.9 - - + +
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Residues in contact with GLY 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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109A GLY 3.1 9.7 + - - -
110A LYS 3.1 3.8 + - - -
112A ALA* 1.3 80.4 - - - +
114A ASP* 1.3 61.2 + - - +
116A ILE* 3.2 3.4 + - - +
117A ALA* 3.1 18.2 + - - +
145A PHE* 4.0 18.1 - - - -
148A ALA* 3.5 22.2 - - - -
152A HIS* 4.4 0.2 - - - -
154A PHE* 3.5 12.9 - - - -
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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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110A LYS* 2.8 54.5 + - - +
111A ILE* 3.8 9.7 - - - +
112A ALA 3.4 0.2 - - - -
113A GLY* 1.3 72.3 - - - +
115A TYR* 1.3 63.6 + - - +
117A ALA* 3.2 4.0 + - - +
118A LYS* 3.0 22.2 + - - +
148A ALA* 4.2 5.2 - - - +
151A ALA* 5.5 1.7 - - - +
152A HIS* 2.9 30.3 + - + +
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Residues in contact with TYR 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 ILE 2.9 18.1 + - - +
112A ALA* 3.7 5.2 - - - +
113A GLY 3.2 0.2 - - - -
114A ASP* 1.3 73.1 - - - +
116A ILE* 1.3 66.4 + - - +
118A LYS* 3.3 27.2 + - + +
119A LYS* 3.2 47.0 + - + +
210A MET* 3.4 22.7 - - + -
212A VAL* 4.1 7.2 - - + -
230A ALA* 3.5 16.7 + - + +
231A ALA* 3.4 27.4 - - + -
267A LEU* 4.0 26.2 - - + -
269A VAL* 3.7 23.7 - - + +
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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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112A ALA 3.2 14.2 + - - +
113A GLY* 3.5 7.0 - - - +
115A TYR* 1.3 78.6 - - - +
117A ALA* 1.4 55.9 + - - +
119A LYS 3.1 0.7 + - - -
120A ALA* 2.7 38.5 + - + +
124A ALA* 4.8 0.2 - - + -
126A VAL* 4.3 11.4 - - + -
145A PHE* 4.3 13.9 - - + -
154A PHE* 3.9 15.7 - - + -
185A ALA* 3.8 26.2 - - + -
186A VAL 4.3 8.1 - - - +
187A PHE* 4.0 26.2 - - + +
210A MET* 3.7 9.4 - - + -
212A VAL* 3.7 26.0 - - + -
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Residues in contact with ALA 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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113A GLY 3.1 5.7 + - - -
114A ASP 3.2 5.4 + - - +
116A ILE* 1.4 77.1 - - - +
118A LYS* 1.3 58.8 + - - +
121A GLY* 3.0 32.8 + - - +
122A GLU* 3.7 10.3 + - - +
152A HIS* 3.3 45.8 - - + +
154A PHE* 3.3 14.6 - - + -
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Residues in contact with LYS 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 12.6 + - - +
115A TYR* 3.4 33.2 - - + +
117A ALA* 1.3 79.1 - - - +
119A LYS* 1.3 87.0 + - + +
121A GLY* 4.6 0.9 + - - -
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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 TYR* 3.2 31.1 + - + +
116A ILE 3.1 2.0 + - - -
118A LYS* 1.3 113.2 + - + +
120A ALA* 1.3 64.1 + - - +
121A GLY 3.3 1.9 + - - -
210A MET* 3.5 29.8 - - + -
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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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116A ILE* 2.7 20.2 + - + +
119A LYS* 1.3 74.5 - - - +
121A GLY* 1.3 62.0 + - - +
122A GLU 5.1 0.5 - - - +
124A ALA* 3.9 19.9 - - + +
184A GLN* 3.8 26.7 + - + +
185A ALA* 4.5 7.9 - - + -
210A MET* 4.1 13.4 - - + -
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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