Contacts of the helix formed by residues 116 - 138 (chain D) in PDB entry 2B05
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 116 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D PRO* 4.5 22.6 - - - +
111D ASN 3.6 5.0 - - - +
112D CYS* 3.3 12.4 - - + -
113D SER* 2.6 52.7 + - - +
114D GLU 3.4 0.6 - - - -
115D THR* 1.3 76.7 - - - +
117D TYR* 1.3 63.5 + - - +
118D GLU* 3.3 3.4 - - - -
119D SER* 3.2 17.2 + - - +
120D LYS* 3.0 22.7 + - - +
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Residues in contact with TYR 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D GLU 4.5 4.5 + - - +
115D THR 3.0 9.7 + - - +
116D GLN* 1.3 74.7 - - - +
118D GLU* 1.3 63.7 + - - +
120D LYS* 3.3 6.7 + - - +
121D VAL* 3.0 31.4 + - + +
160D ILE* 5.4 5.8 - - + +
164D HIS* 4.1 27.1 - - + +
165D MET* 5.3 7.4 - - + -
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Residues in contact with GLU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ARG* 4.4 16.2 - - - +
116D GLN 3.3 1.0 - - - -
117D TYR* 1.3 77.6 - - + +
119D SER* 1.3 57.3 + - - +
121D VAL* 3.5 2.6 + - - +
122D PHE* 2.9 30.3 + - - +
165D MET* 3.7 31.8 - - + +
169D HIS* 4.1 14.6 - - + +
171D ILE* 4.2 9.3 - - + +
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Residues in contact with SER 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU 5.1 4.5 + - - -
42D ARG* 3.4 23.2 + - - +
112D CYS* 3.6 18.2 - - - -
116D GLN* 3.2 16.2 + - - +
117D TYR 3.2 0.4 - - - -
118D GLU* 1.3 76.8 - - - +
120D LYS* 1.3 66.1 + - - +
122D PHE* 3.2 6.1 + - - +
123D TYR* 2.9 42.3 + - - -
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Residues in contact with LYS 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ILE* 4.6 19.7 - - + -
112D CYS* 3.7 38.6 + - + -
113D SER 4.5 9.6 + - - +
114D GLU* 4.8 10.9 + - - +
116D GLN 3.0 12.6 + - - +
117D TYR* 3.8 8.7 - - - +
119D SER* 1.3 75.3 - - - +
121D VAL* 1.3 58.5 + - + +
123D TYR* 3.8 3.1 - - - +
124D LEU* 2.8 52.9 + - + +
156D GLU* 6.0 2.9 - - - +
160D ILE* 5.6 4.3 - - + -
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D TYR* 3.0 20.1 + - + +
118D GLU 3.8 3.1 - - - +
120D LYS* 1.3 73.9 - - - +
122D PHE* 1.3 58.2 + - - +
124D LEU* 3.8 0.6 - - - +
125D LYS* 2.8 30.9 + - + +
157D ALA* 3.6 32.2 - - + +
160D ILE* 3.9 12.3 - - + -
161D SER* 3.8 23.6 - - - +
165D MET* 4.2 9.4 - - + -
171D ILE* 3.6 24.7 - - + +
175D LEU* 4.3 16.6 - - + -
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Residues in contact with PHE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ARG* 3.4 49.1 - - + -
43D ASN* 3.6 24.9 - - - -
46D SER* 3.8 21.8 - - - -
118D GLU 2.9 18.3 + - - +
119D SER 3.2 4.5 + - - +
121D VAL* 1.3 75.1 - - - +
123D TYR* 1.3 67.5 + + - +
125D LYS* 3.3 11.5 + - + +
126D MET* 3.0 47.5 + - + +
171D ILE* 4.0 26.0 - - + +
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Residues in contact with TYR 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU* 3.5 27.3 + - + +
42D ARG* 3.2 33.6 - - + +
45D LEU* 5.1 1.8 - - + -
104D LEU* 3.7 21.7 - - + +
108D LEU* 3.7 49.4 - - + +
109D ILE* 3.7 19.9 - - + +
112D CYS* 3.9 6.3 - - - -
119D SER* 2.9 39.6 + - - +
120D LYS* 4.0 2.0 - - - +
122D PHE* 1.3 88.0 - + - +
124D LEU* 1.3 61.1 + - - +
126D MET* 3.1 9.8 + - - +
127D LYS* 2.9 27.0 + - - +
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Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ILE* 4.0 28.3 - - + -
120D LYS* 2.8 43.6 + - + +
123D TYR* 1.3 72.0 - - - +
125D LYS* 1.3 57.9 + - - +
127D LYS* 3.3 16.7 + - + +
128D GLY* 2.9 23.0 + - - -
153D ALA* 3.5 21.7 - - - +
156D GLU* 3.6 41.1 - - + +
157D ALA* 3.7 22.9 - - + +
160D ILE* 5.7 3.4 - - + -
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Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D VAL 2.8 19.4 + - - +
122D PHE* 3.5 13.4 + - + +
124D LEU* 1.3 74.3 - - - +
126D MET* 1.3 70.1 + - - +
128D GLY* 3.1 2.6 + - - +
129D ASP* 2.8 53.4 + - - +
154D TYR* 3.9 6.5 - - + -
157D ALA* 4.1 1.0 - - - +
171D ILE* 4.7 8.1 - - + +
174D GLY* 3.7 17.0 - - - -
175D LEU* 3.9 44.4 - - + +
178D ASN* 3.4 17.9 - - - +
506J LEU* 4.1 21.1 - - - +
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Residues in contact with MET 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LEU* 4.5 19.7 - - + +
46D SER* 4.4 26.2 - - - +
49D TYR* 5.2 1.3 - - + -
100D VAL* 3.7 27.8 - - + -
104D LEU* 3.8 19.1 - - + -
122D PHE* 3.0 43.5 + - + +
123D TYR* 3.1 12.3 + - - +
125D LYS* 1.3 78.8 - - - +
127D LYS* 1.3 58.9 + - - +
129D ASP* 3.0 10.4 + - - +
130D TYR* 2.8 51.9 + - + +
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Residues in contact with LYS 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LEU* 3.9 9.1 - - + +
104D LEU* 3.8 14.5 - - + +
105D ASP* 2.8 42.0 + - - +
109D ILE* 4.0 13.6 - - + +
123D TYR 2.9 12.8 + - - +
124D LEU* 3.5 16.8 - - + +
126D MET* 1.3 78.3 - - - +
128D GLY* 1.3 61.8 + - - +
130D TYR 3.5 0.3 + - - -
131D TYR* 3.2 50.0 + - + -
149D SER* 5.4 1.8 - - - -
153D ALA* 3.6 17.9 - - + -
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Residues in contact with GLY 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D LEU 2.9 11.4 + - - -
125D LYS 3.1 3.7 + - - -
127D LYS* 1.3 76.7 - - - +
129D ASP* 1.3 55.5 + - - +
131D TYR 3.6 0.2 + - - -
132D ARG* 2.9 26.2 + - - +
150D SER* 3.0 17.4 + - - -
153D ALA* 3.5 15.3 - - - +
154D TYR* 3.3 23.6 - - - -
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Residues in contact with ASP 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LYS* 2.8 49.8 + - - +
126D MET* 3.0 11.7 + - - +
128D GLY* 1.3 72.0 - - - +
130D TYR* 1.3 62.8 + - + +
132D ARG* 2.8 11.2 + - - +
133D TYR* 2.9 50.8 + - + +
154D TYR* 2.6 25.7 + - - -
178D ASN* 2.8 24.6 + - - +
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Residues in contact with TYR 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D SER* 4.2 3.0 + - - -
49D TYR* 3.1 36.0 + - + +
50D LYS* 3.1 13.2 + - + +
53D VAL* 3.7 24.0 - - + -
96D VAL* 5.1 0.2 - - + -
97D CYS* 3.7 18.3 - - + +
100D VAL* 3.9 29.6 - - + -
101D LEU* 4.2 23.6 - - + -
126D MET* 2.8 57.5 + - + +
129D ASP* 1.3 77.7 - - + +
131D TYR* 1.3 60.3 + - - +
133D TYR* 3.4 23.4 + + - +
134D LEU* 3.1 31.1 + - - +
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Residues in contact with TYR 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LEU* 3.6 32.4 - - + +
105D ASP* 4.7 7.1 + - - -
127D LYS* 3.2 48.9 + - + +
130D TYR* 1.3 75.2 - - - +
132D ARG* 1.3 57.4 + - - +
134D LEU* 3.2 22.7 + - + +
135D ALA* 2.8 27.2 + - - +
145D THR* 6.4 0.2 - - + -
146D VAL* 3.6 30.9 - - + +
149D SER* 3.7 36.5 + - - -
150D SER* 3.7 12.6 - - - -
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Residues in contact with ARG 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ARG* 4.1 2.8 - - - +
128D GLY 2.9 18.1 + - - +
129D ASP* 2.8 30.9 + - - +
131D TYR* 1.3 71.8 - - - +
133D TYR* 1.3 71.4 + - + +
135D ALA* 3.0 9.4 + - - +
136D GLU* 3.0 34.4 + - - +
150D SER* 3.7 10.2 + - - +
154D TYR* 2.9 16.2 + - - +
178D ASN* 3.4 20.2 + - - +
181D VAL* 4.1 16.1 - - - +
182D PHE* 4.0 19.1 - - + +
185D GLU* 6.2 0.2 - - - -
186D ILE* 4.0 25.3 - - + +
505J SEP 2.8 44.2 + - - -
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Residues in contact with TYR 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LYS* 3.1 19.3 - - - +
53D VAL* 3.8 23.1 - - + -
57D ARG* 3.2 45.5 - - - -
93D LEU* 3.9 15.9 - - + +
97D CYS* 3.9 9.6 - - - -
129D ASP* 2.9 31.8 + - + +
130D TYR* 3.6 37.2 - + - +
131D TYR 3.3 0.2 - - - -
132D ARG* 1.3 84.1 - - - +
134D LEU* 1.3 65.0 + - - +
136D GLU* 3.3 23.4 + - - +
137D VAL* 3.9 4.3 + - - +
505J SEP 2.6 26.6 + - - -
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D LEU* 4.8 0.9 - - + -
94D GLU* 3.8 33.4 - - + +
97D CYS* 3.5 24.0 - - + -
98D GLN* 5.4 1.8 - - + +
101D LEU* 3.9 18.6 - - + -
130D TYR 3.1 14.9 + - - +
131D TYR* 3.2 34.7 + - + +
133D TYR* 1.3 77.0 - - - +
135D ALA* 1.3 61.5 + - - +
137D VAL* 3.3 9.3 + - - +
138D ALA* 3.1 23.1 + - + +
146D VAL* 4.0 18.6 - - + -
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D TYR 2.8 13.8 + - - +
132D ARG* 3.0 14.5 + - - +
134D LEU* 1.3 75.9 - - - +
136D GLU* 1.3 63.4 + - - +
137D VAL 3.1 1.6 + - - -
138D ALA* 3.4 15.8 + - - +
143D ARG* 4.0 13.3 + - - +
146D VAL* 3.7 11.6 - - + +
147D VAL* 3.7 30.3 - - + +
182D PHE* 5.7 0.7 - - + -
186D ILE* 4.2 15.0 - - + -
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Residues in contact with GLU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ARG* 2.9 50.4 + - - +
60D TRP* 3.7 20.9 - - + -
61D ARG* 4.7 6.0 + - - -
132D ARG* 3.0 29.3 + - + +
133D TYR* 3.5 13.5 - - - +
134D LEU 3.2 0.4 - - - -
135D ALA* 1.3 75.5 - - - +
137D VAL* 1.3 63.9 + - + +
138D ALA 5.0 0.6 - - - +
186D ILE* 4.2 17.3 - - + +
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Residues in contact with VAL 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D TRP* 3.3 51.4 - - + +
90D GLU* 4.0 22.1 - - + +
93D LEU* 4.1 18.8 - - + -
94D GLU* 3.8 28.8 - - + +
133D TYR 4.2 6.3 - - - +
134D LEU 3.7 9.4 - - - +
135D ALA 3.1 0.2 - - - -
136D GLU* 1.3 85.1 - - + +
138D ALA* 1.3 67.7 + - - +
139D THR* 4.5 6.5 + - - +
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D GLU* 5.4 4.9 - - - +
134D LEU* 3.1 16.7 + - + +
135D ALA 3.4 5.9 + - - +
136D GLU 5.0 0.9 - - - +
137D VAL* 1.3 82.1 - - + +
139D THR* 1.3 64.3 + - - +
142D LYS* 4.2 9.0 - - + -
143D ARG* 3.6 44.1 + - + +
146D VAL* 4.2 6.3 - - + -
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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
------------------------------------------------------------
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