Contacts of the helix formed by residues 116 - 138 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PRO* 4.7 21.4 - - - +
111B ASN 3.7 4.1 + - - +
112B CYS* 3.3 10.2 - - + +
113B SER* 2.5 53.1 + - - +
114B GLU 3.4 0.4 - - - -
115B THR* 1.3 77.8 - - - +
117B TYR* 1.3 62.9 + - - +
118B GLU* 3.3 7.2 - - - -
119B SER* 3.3 17.1 + - - +
120B LYS* 3.1 22.4 + - - +
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Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU 3.1 23.3 - - - -
115B THR* 3.1 29.8 + - - +
116B GLN* 1.3 71.7 - - - +
118B GLU* 1.3 74.4 + - - +
120B LYS* 3.2 7.8 + - - +
121B VAL* 2.9 30.1 + - + +
160B ILE* 4.3 12.1 - - + -
164B HIS* 3.4 68.8 + + + +
165B MET* 4.5 5.6 - - + -
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 4.6 10.1 - - - +
115B THR 4.7 4.2 - - - +
116B GLN* 4.4 3.5 - - - -
117B TYR* 1.3 91.1 + - - +
119B SER* 1.3 57.4 + - - +
121B VAL* 3.5 2.8 + - - +
122B PHE* 2.9 30.3 + - - +
165B MET* 3.4 24.5 - - + +
169B HIS* 4.1 17.5 + - + +
171B ILE* 4.2 13.9 - - + +
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU 4.9 3.8 + - - -
42B ARG* 3.0 31.8 + - - +
112B CYS* 3.6 16.8 - - - -
116B GLN* 3.3 19.3 + - - +
118B GLU* 1.3 77.3 - - - +
120B LYS* 1.3 59.8 + - - +
122B PHE* 3.2 3.8 + - - +
123B TYR* 2.9 44.1 + - - -
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Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 5.3 10.1 - - + +
112B CYS* 3.8 23.0 - - + +
113B SER 5.4 3.1 - - - +
116B GLN 3.1 14.0 + - - +
117B TYR* 3.6 10.5 - - - +
119B SER* 1.3 74.9 - - - +
121B VAL* 1.3 57.9 + - - +
123B TYR* 3.8 2.0 - - - +
124B LEU* 2.8 44.4 + - + +
156B GLU* 6.0 0.2 - - - +
160B ILE* 4.3 23.1 - - + -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TYR* 2.9 24.6 + - + +
118B GLU 3.8 2.9 - - - +
120B LYS* 1.3 70.8 - - - +
122B PHE* 1.3 65.8 + - - +
124B LEU* 4.1 0.8 - - - +
125B LYS* 2.9 24.0 + - + +
157B ALA* 3.9 28.4 - - + +
160B ILE* 3.8 24.7 - - + -
161B SER* 3.9 17.0 - - - +
165B MET* 4.3 6.3 - - + -
171B ILE* 3.7 21.3 - - + +
175B LEU* 4.0 20.0 - - + -
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Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 3.6 59.0 - - + +
43B ASN* 3.9 21.3 - - - -
45B LEU* 6.4 0.2 - - + -
46B SER* 3.8 21.3 - - - -
118B GLU 2.9 19.6 + - - +
119B SER 3.2 4.9 + - - +
121B VAL* 1.3 77.4 - - - +
123B TYR* 1.3 65.5 + + - +
125B LYS* 3.4 12.5 + - + +
126B MET* 3.0 45.0 + - + +
171B ILE* 4.2 23.8 - - + +
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Residues in contact with TYR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.6 22.4 + - + +
42B ARG* 3.1 39.1 - - + +
45B LEU* 5.0 2.5 - - + -
104B LEU* 3.7 21.7 - - + +
108B LEU* 3.6 53.9 - - + +
109B ILE* 3.6 20.3 - - + +
112B CYS* 3.7 10.1 - - - -
119B SER* 2.9 38.8 + - - +
120B LYS* 4.0 2.0 - - - +
122B PHE* 1.3 81.5 - + - +
124B LEU* 1.3 59.2 + - - +
126B MET* 3.2 7.1 + - - +
127B LYS* 2.9 26.3 + - - +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 4.0 28.3 - - + -
120B LYS* 2.8 34.1 + - + +
123B TYR* 1.3 69.2 - - - +
125B LYS* 1.3 59.9 + - - +
127B LYS* 3.4 10.0 + - + +
128B GLY* 3.0 22.3 + - - -
153B ALA* 3.4 26.8 - - - +
154B TYR 4.3 0.2 + - - -
156B GLU* 3.8 28.5 - - - +
157B ALA* 3.7 25.4 - - + +
160B ILE* 3.9 27.8 - - + -
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Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 2.9 19.4 + - + +
122B PHE* 3.4 12.4 + - + +
124B LEU* 1.3 75.1 - - - +
126B MET* 1.3 63.9 - - - +
128B GLY* 3.1 2.3 + - - +
129B ASP* 2.8 60.4 + - - +
154B TYR* 3.8 11.2 - - + -
157B ALA* 4.2 0.8 - - - +
171B ILE* 4.8 9.4 - - + +
174B GLY 3.8 13.2 - - - -
175B LEU* 3.8 39.5 - - + +
178B ASN* 3.6 19.3 - - + +
506H LEU* 4.0 24.2 - - - +
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Residues in contact with MET 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 4.8 18.6 - - + +
46B SER* 4.2 26.2 - - - +
49B TYR* 5.2 2.0 - - + -
100B VAL* 3.6 29.8 - - + -
104B LEU* 3.9 21.1 - - + -
122B PHE* 3.0 38.4 + - + +
123B TYR* 3.2 13.2 + - - +
125B LYS* 1.3 77.4 - - - +
127B LYS* 1.3 59.2 + - - +
129B ASP* 3.0 11.9 + - - +
130B TYR* 2.8 53.2 + - + +
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.9 8.0 - - + +
104B LEU* 4.0 15.2 - - + +
105B ASP* 2.7 37.8 + - - +
109B ILE* 4.0 14.6 - - + +
123B TYR 2.9 13.7 + - - +
124B LEU* 3.6 14.2 - - + +
125B LYS 3.2 0.2 - - - -
126B MET* 1.3 75.9 - - - +
128B GLY* 1.3 62.4 + - - +
130B TYR 3.4 0.2 + - - -
131B TYR* 3.1 53.6 + - + -
149B SER* 5.4 2.2 - - - -
153B ALA* 3.7 17.0 - - + -
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU 3.0 12.0 + - - -
125B LYS 3.5 2.9 - - - -
127B LYS* 1.3 79.0 - - - +
129B ASP* 1.3 62.3 + - - +
131B TYR 3.5 0.2 + - - -
132B ARG* 3.0 18.4 + - - +
150B SER* 3.0 16.9 + - - -
153B ALA* 3.6 14.5 - - - +
154B TYR* 3.3 24.6 + - - -
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Residues in contact with ASP 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LYS* 6.0 1.0 - - - +
125B LYS* 2.8 49.2 + - - +
126B MET* 3.0 11.3 + - - +
128B GLY* 1.3 72.9 - - - +
130B TYR* 1.3 62.7 + - + +
132B ARG* 3.0 8.2 + - - +
133B TYR* 2.9 53.4 + - + +
154B TYR* 2.7 26.8 + - - -
178B ASN* 2.9 25.6 + - - +
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER 4.5 1.7 + - - -
49B TYR* 3.2 31.5 + - + +
50B LYS* 3.3 12.2 + - + +
53B VAL* 3.8 23.6 - - + -
96B VAL* 5.1 0.2 - - + -
97B CYS* 3.8 26.1 - - + -
100B VAL* 3.9 28.0 - - + -
101B LEU* 3.8 24.9 - - + -
126B MET* 2.8 55.8 + - + +
129B ASP* 1.3 75.0 - - + +
131B TYR* 1.3 60.4 + - - +
133B TYR* 3.3 22.0 + + - +
134B LEU* 3.1 30.5 + - - +
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Residues in contact with TYR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLN* 5.5 2.3 + - - -
101B LEU* 3.8 27.9 - - + +
105B ASP* 4.8 6.6 + - - -
127B LYS* 3.1 53.7 + - + +
130B TYR* 1.3 74.0 - - - +
132B ARG* 1.3 54.3 + - - +
134B LEU* 3.3 21.8 + - + +
135B ALA* 2.8 32.7 + - - +
145B THR* 6.4 0.7 - - + -
146B VAL* 3.6 22.9 - - + +
149B SER* 3.7 36.7 + - - -
150B SER* 3.5 22.0 - - - -
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 4.1 3.0 - - - +
128B GLY 3.0 16.8 + - - +
129B ASP* 3.0 27.8 + - - +
131B TYR* 1.3 72.8 - - - +
133B TYR* 1.3 71.0 + - - +
135B ALA* 3.0 8.2 + - - +
136B GLU* 2.9 35.5 + - - +
150B SER* 3.8 10.9 + - - +
154B TYR* 2.9 16.1 + - - +
178B ASN* 3.3 20.0 + - - +
181B VAL* 4.0 15.8 - - - +
182B PHE* 3.9 31.2 - - + +
186B ILE* 3.8 19.1 - - + -
505H SEP 2.8 45.3 + - - -
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Residues in contact with TYR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LYS* 3.1 19.3 - - - +
53B VAL* 4.1 15.3 - - + -
57B ARG* 3.3 44.9 - - - -
93B LEU* 4.0 15.3 - - + +
97B CYS* 3.9 9.9 - - - -
129B ASP* 2.9 38.3 + - + +
130B TYR* 3.6 44.4 - + - +
131B TYR 3.3 0.2 - - - -
132B ARG* 1.3 84.6 - - - +
134B LEU* 1.3 65.5 + - - +
136B GLU* 3.3 23.1 + - - +
137B VAL* 3.8 5.0 + - - +
178B ASN* 4.9 0.2 + - - -
505H SEP 2.6 25.5 + - - -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 4.9 0.9 - - + -
94B GLU* 3.9 34.2 - - + +
97B CYS* 3.6 22.0 - - + -
98B GLN* 4.6 10.5 - - + +
101B LEU* 4.0 17.0 - - + -
130B TYR 3.1 14.7 + - - +
131B TYR* 3.4 34.1 - - + +
133B TYR* 1.3 75.2 - - - +
135B ALA* 1.3 63.0 + - - +
137B VAL* 3.2 9.0 + - - +
138B ALA* 3.1 23.4 + - + +
146B VAL* 3.9 20.4 - - + -
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B TYR 2.8 20.6 + - - +
132B ARG* 3.0 11.6 + - - +
134B LEU* 1.3 73.6 - - - +
136B GLU* 1.3 61.3 + - - +
137B VAL 3.1 0.9 + - - -
138B ALA* 3.4 15.5 + - - +
143B ARG* 4.0 13.7 + - - +
146B VAL* 3.7 17.9 - - + +
147B VAL* 4.0 24.2 - - + +
182B PHE* 5.7 0.2 - - + -
186B ILE* 4.1 15.7 - - + -
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 2.7 51.0 + - - +
60B TRP* 3.8 20.4 - - + -
61B ARG* 4.6 8.7 + - - -
132B ARG* 2.9 27.3 + - - +
133B TYR* 3.5 13.6 - - - +
134B LEU 3.3 0.2 - - - -
135B ALA* 1.3 77.1 - - - +
137B VAL* 1.3 63.2 + - + +
138B ALA 4.9 1.0 - - - +
185B GLU* 5.2 5.2 - - - +
186B ILE* 4.1 16.7 - - + +
505H SEP 4.4 0.2 + - - -
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TRP* 3.5 49.8 - - + +
90B GLU* 4.1 23.0 - - + +
93B LEU* 4.0 20.0 - - + -
94B GLU* 3.9 30.1 - - + +
133B TYR 3.8 8.9 + - - +
134B LEU* 3.6 10.1 - - - +
135B ALA 3.1 0.2 - - - -
136B GLU* 1.3 81.4 - - + +
138B ALA* 1.3 66.3 + - - +
139B THR* 4.0 9.6 - - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU* 5.4 4.9 - - - +
134B LEU* 3.1 16.4 + - + +
135B ALA 3.4 4.1 + - - +
136B GLU 4.9 1.0 - - - +
137B VAL* 1.3 82.2 - - + +
139B THR* 1.3 64.9 + - - +
142B LYS* 4.1 13.7 - - + +
143B ARG* 3.2 45.5 + - + +
146B VAL* 4.2 7.6 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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