Contacts of the helix formed by residues 113 - 136 (chain B) in PDB entry 1DUG
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 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B SER* 3.1 12.0 + - - +
112B LYS* 1.3 95.1 - - - +
114B PHE* 1.3 59.2 + - - +
115B GLU* 3.4 2.7 - - - +
116B THR* 3.1 29.4 + - + +
117B LEU* 3.1 19.9 - - + +
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ILE* 3.3 37.2 - - + +
109B ALA* 4.5 1.8 - - - -
111B SER 3.3 15.9 + - - +
112B LYS 3.3 2.6 + - - -
113B ASP* 1.3 71.5 - - - +
115B GLU* 1.3 82.0 + - - +
116B THR 3.0 2.2 + - - -
117B LEU* 3.0 3.5 + - - +
118B LYS* 2.9 58.1 + - + +
164B MET* 3.8 27.8 - - + -
208B THR* 3.8 19.3 - - + -
209B PHE* 3.5 47.3 - + + -
219B ASP* 5.3 3.1 - - - -
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LYS 6.1 0.2 - - - +
113B ASP* 3.4 1.3 - - - -
114B PHE* 1.3 100.1 - - + +
116B THR* 1.3 61.5 + - + +
118B LYS* 3.1 48.9 + - - +
119B VAL* 3.4 11.1 - - - +
208B THR* 5.4 4.0 - - + +
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Residues in contact with THR 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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113B ASP* 3.1 27.5 + - + +
115B GLU* 1.3 81.5 - - + +
117B LEU* 1.3 68.1 + - - +
118B LYS 3.2 2.0 - - - -
119B VAL* 3.6 19.5 + - - +
120B ASP* 4.2 4.0 + - - +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ILE* 3.6 40.6 - - + +
111B SER* 3.3 35.7 - - - +
113B ASP* 3.1 20.4 - - + +
114B PHE* 3.0 3.5 + - - +
116B THR* 1.3 79.5 + - - +
118B LYS* 1.3 64.2 + - - +
120B ASP* 3.4 8.9 + - - +
121B PHE* 3.3 14.2 + - - +
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ILE* 3.9 9.8 - - - +
114B PHE* 2.9 44.6 + - + +
115B GLU* 3.1 46.2 + - - +
117B LEU* 1.3 74.8 - - - +
119B VAL* 1.3 66.1 + - - +
120B ASP 3.0 2.5 - - - -
121B PHE* 2.9 2.7 + - - -
122B LEU* 2.7 50.7 + - + +
164B MET* 4.2 21.5 + - + +
218B SER* 5.4 7.1 + - - -
219B ASP* 5.7 3.0 + - - -
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU 3.4 20.6 - - - +
116B THR* 3.8 11.7 - - - +
117B LEU 3.4 0.4 - - - -
118B LYS* 1.3 82.9 - - + +
120B ASP* 1.3 59.7 + - - +
122B LEU* 4.1 8.3 - - - +
123B SER* 3.4 19.4 + - - -
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Residues in contact with ASP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B THR 4.2 3.3 + - - +
117B LEU* 3.4 11.0 + - - +
118B LYS 3.0 0.6 - - - -
119B VAL* 1.3 78.1 - - - +
121B PHE* 1.3 68.0 + - - +
122B LEU 3.2 0.2 - - - -
123B SER* 2.4 27.7 + - - -
124B LYS* 3.2 26.8 + - - +
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Residues in contact with PHE 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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101B ILE 3.9 7.0 - - - -
104B GLY* 3.7 31.4 - - - -
105B VAL* 3.6 30.7 - - + -
108B ILE* 3.7 23.6 - - + -
117B LEU 3.3 2.4 + - - +
118B LYS 2.9 5.5 + - - +
120B ASP* 1.3 79.9 + - - +
122B LEU* 1.3 68.2 + - + +
124B LYS* 3.2 7.2 + - + +
125B LEU* 3.0 42.2 + - + +
128B MET* 4.0 18.2 - - + -
161B VAL* 4.3 9.6 - - + -
164B MET* 3.6 28.7 - - + -
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LYS* 2.7 38.5 + - + +
119B VAL* 4.1 7.2 - - - +
121B PHE* 1.3 74.8 - - + +
123B SER* 1.3 56.8 + - - +
124B LYS 3.4 0.2 - - - -
125B LEU* 3.9 28.2 - - + +
126B PRO* 3.2 22.0 - - - +
161B VAL* 5.5 0.7 - - + +
164B MET* 3.8 35.7 - - + +
165B ASP* 4.1 36.1 - - + +
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Residues in contact with SER 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 VAL 3.4 12.6 + - - -
120B ASP* 2.4 28.6 + - - -
122B LEU* 1.3 79.4 - - - +
124B LYS* 1.3 71.2 + - - +
125B LEU 3.4 0.2 - - - -
126B PRO* 3.4 13.1 - - - +
127B GLU* 5.1 1.2 + - - +
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Residues in contact with LYS 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 ASP* 3.2 29.5 + - - +
121B PHE* 3.2 8.5 + - + +
123B SER* 1.3 88.2 - - - +
125B LEU* 1.3 62.2 + - - +
126B PRO* 3.4 1.6 - - - -
127B GLU* 3.4 26.5 + - - +
128B MET* 3.5 22.6 + - + +
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Residues in contact with LEU 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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101B ILE* 4.1 18.6 - - + -
121B PHE* 3.0 22.4 + - + +
122B LEU* 3.9 26.7 - - + +
124B LYS* 1.3 74.7 - - - +
126B PRO* 1.3 71.4 - - + +
128B MET* 2.9 27.0 + - + +
129B LEU* 2.8 51.3 + - + +
161B VAL* 4.2 17.9 - - + -
168B CYS* 4.1 16.4 - - + -
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Residues in contact with PRO 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 LEU 3.2 19.5 - - - +
123B SER* 3.4 14.6 - - - +
124B LYS 3.4 0.9 - - - -
125B LEU* 1.3 91.2 - - + +
127B GLU* 1.3 55.6 + - - +
129B LEU* 3.3 1.1 + - + -
130B LYS* 2.8 34.1 + - - +
168B CYS 6.2 0.2 - - - +
172B PHE* 3.5 24.6 - - + -
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Residues in contact with GLU 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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44A LYS* 2.9 30.7 + - - -
45A PHE* 3.5 25.7 - - + -
123B SER 5.1 1.3 + - - +
124B LYS* 3.4 22.8 + - - +
125B LEU 3.2 0.4 - - - -
126B PRO* 1.3 80.1 - - - +
128B MET* 1.3 63.1 + - + +
130B LYS* 3.6 12.3 + - + +
131B MET* 3.4 22.4 + - + +
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Residues in contact with MET 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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51A PHE* 5.6 0.2 - - - -
97B ALA 5.9 0.2 - - - +
100B ASP* 4.4 21.5 - - - +
101B ILE* 3.7 28.3 - - + -
121B PHE* 4.0 21.1 - - + +
124B LYS* 3.5 14.8 + - + +
125B LEU* 2.9 39.5 + - + +
127B GLU* 1.3 78.1 - - + +
129B LEU* 1.3 63.8 + - - +
131B MET* 3.4 15.7 + - - +
132B PHE* 3.5 18.2 - - + -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ILE* 3.9 22.0 - - + -
125B LEU* 2.8 44.8 + - + +
126B PRO* 4.9 0.7 - - + -
128B MET* 1.3 74.6 - - - +
130B LYS* 1.3 65.4 + - - +
132B PHE* 3.0 11.4 + - + +
133B GLU* 2.9 18.9 + - - +
154B LEU* 5.4 0.9 - - + -
158B LEU* 4.1 24.9 - - + -
161B VAL* 5.2 2.7 - - + -
168B CYS* 3.6 26.0 - - - +
169B LEU* 3.8 12.6 - - + -
172B PHE* 3.8 16.6 - - + -
175B LEU* 3.6 14.5 - - + +
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Residues in contact with LYS 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 PRO 2.8 19.2 + - - +
127B GLU* 3.7 10.3 - - + +
128B MET 3.3 0.4 - - - -
129B LEU* 1.3 77.4 - - - +
131B MET* 1.3 63.4 + - - +
133B GLU* 3.4 4.0 - - + +
134B ASP* 2.9 50.3 + - - +
172B PHE* 3.7 20.5 - - + -
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Residues in contact with MET 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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45A PHE* 4.3 18.2 - - + -
49A LEU 4.6 1.6 - - - +
50A GLU* 2.8 34.6 - - - +
51A PHE* 3.5 28.4 - - + -
52A PRO* 3.3 28.0 - - + +
127B GLU* 3.4 19.3 - - + +
128B MET* 3.4 8.5 + - - +
129B LEU 3.2 1.0 - - - -
130B LYS* 1.3 85.7 - - - +
132B PHE* 1.3 58.3 + - - +
134B ASP* 3.6 16.7 + - + +
135B ARG* 3.0 25.6 + - - +
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Residues in contact with PHE 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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51A PHE* 3.9 19.1 - + - -
94B LEU* 4.3 7.0 - - + -
97B ALA* 3.5 31.2 - - + -
98B VAL* 3.5 29.8 - - + -
101B ILE* 3.7 27.4 - - + -
128B MET* 3.5 21.5 - - + -
129B LEU* 3.0 8.6 + - + +
131B MET* 1.3 75.3 - - - +
133B GLU* 1.3 60.5 + - - +
135B ARG* 3.2 4.7 + - - +
136B LEU* 3.0 34.3 + - - +
142B LEU* 3.8 26.7 - - + -
154B LEU* 3.9 14.4 - - + -
175B LEU* 3.9 17.9 - - + -
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Residues in contact with GLU 133 (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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129B LEU 2.9 11.6 + - - +
130B LYS* 3.4 11.0 - - + +
132B PHE* 1.3 78.4 - - - +
134B ASP* 1.3 65.3 + - - +
136B LEU* 3.4 8.8 + - - +
137B CYS* 3.6 0.9 + - - +
171B ALA 5.0 0.9 - - - +
172B PHE* 3.2 33.1 - - + +
173B PRO* 3.6 9.0 - - - +
174B LYS* 3.0 59.1 + - + +
175B LEU* 3.0 37.5 + - + +
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Residues in contact with ASP 134 (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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130B LYS* 2.9 49.9 + - - +
131B MET* 3.9 17.4 - - + +
133B GLU* 1.3 78.1 - - - +
135B ARG* 1.3 66.3 + - - +
137B CYS* 3.1 22.8 + - - +
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Residues in contact with ARG 135 (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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50A GLU* 2.6 35.9 + - + -
51A PHE* 4.1 16.6 - - + -
90B GLU* 2.8 36.2 + - - +
94B LEU* 4.0 9.6 - - + +
131B MET 3.0 18.8 + - - +
132B PHE* 3.2 11.0 + - - +
134B ASP* 1.3 75.5 - - - +
136B LEU* 1.3 59.4 + - - +
137B CYS 3.2 3.0 + - - +
139B LYS* 3.3 47.1 + - + +
142B LEU* 4.1 21.8 - - + -
143B ASN* 3.5 33.5 - - - +
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Residues in contact with LEU 136 (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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132B PHE 3.0 13.3 + - - +
133B GLU 3.8 7.0 - - - +
134B ASP 3.1 0.8 - - - -
135B ARG* 1.3 76.6 - - - +
137B CYS* 1.3 58.2 + - - +
138B HIS 3.0 8.8 + - - -
139B LYS 3.1 28.9 + - - +
140B THR 4.2 6.5 - - - +
141B TYR 3.9 26.5 - - - +
142B LEU* 4.1 16.8 - - + +
174B LYS* 3.9 23.0 - - + +
175B LEU* 3.6 30.7 - - + -
178B PHE* 3.8 27.6 - - + -
181B ARG* 4.9 2.7 - - - +
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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