Contacts of the helix formed by residues 110 - 130 (chain B) in PDB entry 3D0G
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 GLU 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B SER* 1.3 79.7 - - - +
111B ASP* 1.3 75.1 + - - +
113B SER* 3.4 9.2 + - - -
114B LYS* 3.4 14.1 + - - +
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Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B SER* 4.1 2.8 + - - +
110B GLU* 1.3 86.0 - - - +
112B LYS* 1.3 60.4 + - + +
113B SER 2.9 5.2 + - - -
114B LYS* 3.2 5.8 + - - +
115B ARG* 2.9 34.1 + - + +
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Residues in contact with LYS 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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108B LEU* 3.6 29.2 - - + +
109B SER* 3.3 25.7 + - - +
110B GLU 3.4 0.4 - - - -
111B ASP* 1.3 77.1 - - + +
113B SER* 1.3 57.6 + - - +
115B ARG* 4.7 3.4 - - - -
116B LEU* 3.5 22.0 + - - +
186B LEU* 4.0 21.7 - - + +
189B GLU* 3.3 35.0 + - - +
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B SER* 3.7 11.3 + - - -
106B SER* 4.7 4.8 - - - -
108B LEU* 3.6 18.4 + - - +
109B SER 2.8 22.3 + - - -
110B GLU* 3.7 4.7 - - - -
111B ASP 2.9 0.8 - - - -
112B LYS* 1.3 77.7 - - - +
114B LYS* 1.3 64.0 + - - +
115B ARG 3.3 1.3 - - - -
116B LEU* 4.0 2.5 - - - +
117B ASN* 3.2 30.2 + - - +
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Residues in contact with LYS 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 GLU 3.4 10.5 + - - +
111B ASP* 3.2 7.4 + - - +
113B SER* 1.3 78.1 - - - +
115B ARG* 1.3 54.4 + - - +
117B ASN* 3.4 13.0 + - - +
118B THR* 2.7 63.0 + - - +
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Residues in contact with ARG 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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111B ASP* 2.9 19.2 + - + +
112B LYS* 4.7 1.1 - - - -
114B LYS* 1.3 75.0 - - - +
116B LEU* 1.3 67.0 + - - +
118B THR* 2.9 27.0 + - - +
119B ILE* 2.9 41.1 + - + +
179B LEU* 5.3 5.7 - - - +
182B GLU* 2.9 41.2 + - - +
186B LEU* 4.0 12.6 - - + -
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Residues in contact with LEU 116 (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 SER* 5.2 11.0 - - - -
108B LEU* 4.2 21.3 - - + -
112B LYS 3.5 15.7 + - - +
113B SER* 3.8 4.9 + - - +
114B LYS 3.5 0.4 - - - -
115B ARG* 1.3 78.4 - - - +
117B ASN* 1.3 61.8 + - - +
118B THR 3.1 0.3 + - - -
119B ILE* 3.2 6.6 + - + +
120B LEU* 3.0 40.1 + - + +
183B TYR* 4.4 19.3 - - + +
186B LEU* 3.7 32.6 - - + +
187B LYS* 3.8 37.9 - - + +
190B MET* 5.3 2.2 - - + -
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Residues in contact with ASN 117 (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 SER* 4.9 8.3 + - - -
113B SER* 3.2 21.9 + - - +
114B LYS* 3.6 15.7 - - - +
116B LEU* 1.3 81.3 - - - +
118B THR* 1.3 60.0 + - - +
120B LEU* 4.0 19.0 - - - +
121B ASN* 3.4 34.0 + - - +
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Residues in contact with THR 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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114B LYS* 2.7 35.9 + - - +
115B ARG* 2.9 30.9 + - - +
117B ASN* 1.3 76.1 - - - +
119B ILE* 1.3 62.2 + - - +
121B ASN* 3.2 4.7 + - + +
122B THR* 2.6 41.6 + - - +
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Residues in contact with ILE 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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115B ARG* 2.9 47.0 + - + +
116B LEU* 3.4 13.9 - - + +
118B THR* 1.3 76.1 - - - +
120B LEU* 1.3 57.5 + - - +
122B THR* 3.7 3.6 - - - -
123B MET* 2.9 40.0 + - + +
179B LEU* 3.5 43.1 - - + +
182B GLU* 3.3 35.0 - - + +
183B TYR* 3.7 20.2 - - + +
186B LEU* 4.9 3.8 - - + -
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Residues in contact with LEU 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 LEU* 3.0 26.9 + - + +
117B ASN* 4.0 22.0 - - - +
118B THR 3.2 0.2 - - - -
119B ILE* 1.3 75.5 - - - +
121B ASN* 1.3 64.3 + - - +
123B MET* 3.7 8.7 + - + +
124B SER* 3.2 23.2 + - - -
183B TYR* 3.5 38.6 - - + -
187B LYS* 4.3 11.9 - - - +
507B SER 4.6 2.9 - - - +
508B ASN* 5.8 0.7 - - - -
509B ASP* 4.2 22.9 - - + +
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Residues in contact with ASN 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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117B ASN* 3.4 24.6 + - - +
118B THR* 3.2 6.9 + - + +
119B ILE 3.2 0.4 - - - -
120B LEU* 1.3 80.8 - - - +
122B THR* 1.3 58.9 + - - +
124B SER* 3.3 9.1 + - - -
125B THR* 2.6 36.7 + - - -
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Residues in contact with THR 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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118B THR* 2.6 33.1 + - - +
119B ILE* 3.7 3.3 - - - -
121B ASN* 1.3 73.3 - - - +
123B MET* 1.3 53.2 + - - +
125B THR* 2.9 8.0 + - - -
126B ILE* 2.7 58.3 + - + +
179B LEU* 3.9 17.9 - - + +
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Residues in contact with MET 123 (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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119B ILE* 2.9 28.7 + - + +
120B LEU* 4.0 11.0 - - + +
122B THR* 1.3 69.6 - - - +
124B SER* 1.3 66.7 + - - +
126B ILE* 3.4 3.0 + - - +
127B TYR* 3.1 24.4 + - - +
176B LEU* 3.6 29.5 - - + +
179B LEU* 3.9 14.8 - - + -
180B TYR* 4.0 38.6 - - + -
183B TYR* 3.7 35.0 - - + -
507B SER* 3.4 29.6 - - - +
509B ASP 5.6 0.7 - - - +
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Residues in contact with SER 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 LEU 3.2 13.1 + - - -
121B ASN* 3.3 13.9 - - - -
122B THR 3.2 0.2 - - - -
123B MET* 1.3 79.9 - - - +
125B THR* 1.3 57.5 + - - +
127B TYR* 3.5 3.5 + - - +
128B SER* 2.9 29.7 + - - -
507B SER 4.0 1.0 + - - -
508B ASN* 3.3 31.8 + - - +
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Residues in contact with THR 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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121B ASN* 2.6 27.5 + - - -
122B THR* 2.9 7.7 + - - -
124B SER* 1.3 75.5 - - - +
126B ILE* 1.3 65.3 + - - +
127B TYR 3.2 1.3 - - - -
128B SER* 3.5 7.0 - - - +
129B THR* 2.4 43.1 + - + +
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Residues in contact with ILE 126 (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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122B THR* 2.7 41.2 + - + +
123B MET* 3.9 7.4 - - - +
125B THR* 1.3 72.7 - - - +
127B TYR* 1.3 64.1 + - - +
129B THR* 5.1 0.9 - - - -
130B GLY* 3.1 22.0 + - - -
172B VAL* 3.8 16.2 - - + +
175B GLN* 3.5 50.0 - - + +
176B LEU* 4.1 12.3 - - + -
179B LEU* 3.7 29.8 - - + -
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Residues in contact with TYR 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 MET 3.1 16.5 + - - +
124B SER 3.5 4.7 - - - +
126B ILE* 1.3 80.4 - - - +
128B SER* 1.3 68.4 + - - +
129B THR 3.3 0.7 + - - -
130B GLY 3.6 1.7 + - - +
144B LEU* 3.2 33.2 - - + +
168B TRP* 3.6 32.8 - + - -
172B VAL* 5.0 3.1 - - + -
176B LEU* 5.2 4.6 - - + +
271B TRP* 3.5 13.2 - - - -
345B HIS* 5.2 7.0 - + - -
501B ALA 3.9 6.5 - - - -
502B SER* 3.1 22.2 - - - -
503B LEU 3.5 1.3 - - - -
504B PHE* 3.2 51.3 + + + +
507B SER* 3.3 21.5 - - - +
508B ASN* 4.3 4.9 - - - +
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Residues in contact with SER 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 SER* 2.9 17.7 + - - -
125B THR* 3.5 13.3 + - - +
127B TYR* 1.3 85.2 - - - +
129B THR* 1.3 60.5 + - - +
130B GLY 4.8 1.5 - - - +
143B LEU* 4.8 12.6 - - - +
345B HIS* 6.5 1.8 - - - -
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Residues in contact with THR 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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125B THR* 2.4 42.2 + - + +
126B ILE* 4.7 0.9 - - - -
128B SER* 1.3 78.7 + - - +
130B GLY* 1.3 68.3 + - - +
131B LYS* 3.3 23.6 + - - +
143B LEU* 5.2 4.8 - - - +
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Residues in contact with GLY 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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126B ILE 3.1 18.2 + - - -
127B TYR 3.6 3.8 + - - +
128B SER 3.5 2.6 - - - +
129B THR* 1.3 80.3 - - - +
131B LYS* 1.3 59.8 + - - +
143B LEU* 3.9 19.8 - - - +
144B LEU 4.3 1.0 + - - -
168B TRP* 4.2 12.2 - - - -
172B VAL* 3.7 18.8 - - - -
175B GLN* 5.8 2.0 - - - -
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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
------------------------------------------------------------
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