Contacts of the helix formed by residues 111 - 130 (chain B) in PDB entry 2BTO
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 GLY 111 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ALA 3.3 4.8 + - - -
107B VAL* 3.0 13.1 + - - -
109B TYR 3.9 0.2 - - - -
110B LEU* 1.3 78.9 - - - +
112B ALA* 1.3 65.3 + - - -
113B GLY 2.9 5.1 + - - -
114B ARG* 3.0 13.2 + - - +
115B GLU* 3.5 12.8 - - - +
406B GLU* 4.7 10.3 + - - -
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 4.2 18.2 - - + -
97B ARG* 6.1 2.2 - - + -
99B GLU* 6.1 5.4 - - + -
107B VAL* 3.1 22.1 + - + +
111B GLY* 1.3 70.3 - - - -
113B GLY* 1.3 60.4 + - - +
114B ARG 3.3 0.2 - - - -
115B GLU* 3.2 34.0 + - - +
116B VAL* 3.4 16.6 - - - +
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Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 4.6 5.3 - - - +
107B VAL 3.1 7.1 + - - -
108B GLY* 3.1 27.5 - - - -
111B GLY 2.9 2.2 + - - -
112B ALA* 1.3 77.8 - - - +
114B ARG* 1.3 61.2 + - - +
116B VAL* 3.2 19.4 + - - +
117B LEU 3.4 8.3 + - - -
151B PHE* 3.5 15.4 - - - -
154B LEU* 3.9 4.7 - - - +
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLY 4.3 0.4 + - - -
109B TYR* 2.6 45.4 + - - -
110B LEU* 3.5 33.8 - - - +
111B GLY 3.0 12.1 + - - +
113B GLY* 1.3 75.7 - - - +
115B GLU* 1.3 61.6 + - + +
117B LEU* 3.6 10.1 + - + +
118B PRO* 3.5 18.0 - - - +
154B LEU* 3.5 31.4 - - + +
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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
----------------------------------------------------------
97B ARG* 4.1 17.4 + - - +
111B GLY 3.5 10.6 - - - +
112B ALA* 3.2 32.6 + - - +
114B ARG* 1.3 79.1 - - + +
116B VAL* 1.3 64.4 + - + +
118B PRO* 3.5 10.4 - - - +
119B GLU* 5.1 0.9 + - - +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 4.1 9.4 - - + -
72B ASP 5.2 2.7 - - - +
73B LEU* 3.6 21.3 - - + -
95B ILE* 4.8 6.1 - - + -
96B SER 5.9 0.2 - - - -
97B ARG* 3.7 34.3 - - + +
112B ALA 3.4 15.0 - - - +
113B GLY* 3.2 6.9 + - - +
115B GLU* 1.3 78.1 - - - +
117B LEU* 1.3 63.9 + - - +
118B PRO* 3.5 0.4 - - - -
119B GLU* 3.2 8.3 + - - +
120B VAL* 3.1 28.4 + - + +
151B PHE* 3.3 35.9 - - + -
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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
----------------------------------------------------------
113B GLY 3.4 10.4 + - - +
114B ARG* 3.7 15.0 - - + +
116B VAL* 1.3 75.0 - - - +
118B PRO* 1.3 68.3 - - + +
120B VAL* 3.2 0.7 + - - +
121B MET* 2.8 52.8 + - + +
151B PHE* 3.7 26.7 - - + -
154B LEU* 4.3 20.6 - - + -
155B LEU* 4.1 11.4 - - + -
158B SER* 3.6 27.8 - - - +
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Residues in contact with PRO 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 ARG 3.5 14.6 - - - +
115B GLU 3.5 11.4 - - - +
116B VAL 3.6 0.4 - - - -
117B LEU* 1.3 91.4 - - + +
119B GLU* 1.3 56.1 + - - +
121B MET* 3.9 4.9 - - + +
122B SER* 2.9 30.3 + - - -
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ALA 4.5 5.9 - - - +
95B ILE* 3.6 29.7 - - + +
97B ARG* 3.4 30.8 + - - +
115B GLU 5.1 0.4 + - - +
116B VAL 3.2 9.5 + - - +
118B PRO* 1.3 75.1 - - - +
120B VAL* 1.3 66.6 + - - +
122B SER* 3.2 7.3 + - - -
123B ARG* 3.0 31.6 + - + +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 5.2 0.9 - - + -
69B ILE* 4.6 7.7 - - + +
71B VAL* 3.6 41.7 - - + -
95B ILE* 3.9 19.1 - - + -
116B VAL* 3.1 17.6 + - + +
117B LEU 3.8 2.9 - - - +
119B GLU* 1.3 76.6 - - - +
121B MET* 1.3 61.3 + - - +
123B ARG* 3.1 5.9 + - - +
124B LEU* 3.0 25.0 + - + +
151B PHE* 3.7 17.5 - - + -
155B LEU* 3.8 27.4 - - + -
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Residues in contact with MET 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 LEU* 2.8 42.4 + - + +
118B PRO* 4.0 5.2 - - + +
120B VAL* 1.3 74.9 - - - +
122B SER* 1.3 56.9 + - - +
124B LEU* 3.2 26.4 + - - +
125B ASP* 3.0 35.2 + - - +
155B LEU* 3.9 11.4 - - - -
158B SER* 3.7 34.5 - - - +
159B LEU* 4.3 7.6 - - + +
162B LYS* 4.1 30.1 - - + +
163B TYR* 4.8 4.5 - - + -
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PRO 2.9 20.7 + - - -
119B GLU* 3.2 7.8 + - - -
121B MET* 1.3 78.7 - - - +
123B ARG* 1.3 66.8 + - - +
125B ASP* 3.3 15.5 - - - +
126B TYR* 3.2 21.1 + - - +
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 3.7 16.6 - - + -
90B ASN* 3.3 23.2 - - - +
92B ALA* 3.2 36.1 + - - +
93B ASN* 2.7 28.0 + - - +
95B ILE* 3.7 14.8 - - + -
119B GLU* 3.0 25.0 + - + +
120B VAL 3.1 7.2 + - - +
122B SER* 1.3 79.3 + - - +
124B LEU* 1.3 66.4 + - - +
126B TYR* 3.4 38.1 + - - +
127B GLU* 3.0 29.1 + - - +
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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
----------------------------------------------------------
7B ILE* 4.4 7.9 - - + -
9B VAL* 3.9 24.5 - - + -
69B ILE* 3.9 12.6 - - + -
120B VAL* 3.0 17.0 + - + +
121B MET* 3.2 18.4 + - - +
123B ARG* 1.3 73.8 - - - +
125B ASP* 1.3 67.1 + - - +
127B GLU* 3.4 1.7 + - - +
128B ILE* 2.8 37.1 + - + +
137B ILE* 4.3 21.3 - - + -
155B LEU* 3.7 34.1 - - + -
159B LEU* 3.7 20.9 - - + -
163B TYR* 4.6 3.6 - - + -
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Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B MET* 3.0 23.4 + - - +
122B SER* 3.3 17.6 - - - +
124B LEU* 1.3 75.6 - - - +
126B TYR* 1.3 62.5 + - - +
128B ILE* 3.5 2.3 - - - +
129B ASP* 3.0 26.8 + - - +
162B LYS* 3.5 25.4 + - - -
163B TYR* 2.4 35.9 + - - -
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Residues in contact with TYR 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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90B ASN* 4.4 8.0 + - - -
122B SER 3.2 10.1 + - - +
123B ARG* 3.6 42.4 - - - +
124B LEU 3.3 0.2 - - - -
125B ASP* 1.3 80.5 - - - +
127B GLU* 1.3 74.8 + - - +
129B ASP* 3.5 8.2 + - - +
130B LYS* 2.9 63.0 + - + +
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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
----------------------------------------------------------
7B ILE* 3.9 23.3 - - + +
54B SER* 4.9 2.4 + - - -
65B VAL* 6.1 1.0 - - - +
66B PRO 4.8 1.6 - - - +
67B ARG* 3.7 28.9 + - - +
68B ALA 5.1 0.4 - - - +
69B ILE* 4.0 16.8 - - + -
90B ASN* 4.5 2.4 + - - +
93B ASN* 2.9 27.6 + - - +
123B ARG 3.0 20.3 + - - +
124B LEU 3.8 3.6 - - - +
126B TYR* 1.3 93.5 - - + +
128B ILE* 1.3 63.4 + - - +
130B LYS* 3.1 31.2 - - - +
131B CYS* 3.3 12.6 - - - -
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Residues in contact with ILE 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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7B ILE* 3.9 15.5 - - + +
124B LEU* 2.8 36.2 + - + +
125B ASP* 3.5 6.1 - - - +
127B GLU* 1.3 72.4 - - - +
129B ASP* 1.3 63.7 + - + +
131B CYS* 3.1 25.4 + - - +
134B VAL* 4.4 17.3 - - + +
137B ILE* 4.0 21.3 - - + -
163B TYR* 4.2 31.2 - - + +
166B ILE* 3.6 27.1 - - + -
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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
----------------------------------------------------------
125B ASP 3.0 17.1 + - - +
126B TYR* 4.0 7.5 - - - +
128B ILE* 1.3 78.8 - - + +
130B LYS* 1.3 61.1 + - - +
131B CYS 3.1 11.2 + - - +
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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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54B SER* 3.7 29.6 + - - +
55B LYS 5.9 1.7 + - - -
56B LEU* 6.1 3.2 - - - +
67B ARG* 3.6 17.5 + - - +
90B ASN* 5.9 0.4 - - - +
126B TYR* 2.9 58.1 + - + +
127B GLU* 3.1 33.6 + - - +
129B ASP* 1.3 77.1 + - - +
131B CYS* 1.3 57.3 + - - +
132B ASP* 4.3 1.6 + - - +
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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) + - + + + + + -
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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