Contacts of the helix formed by residues 111 - 131 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ALA 3.2 3.0 + - - -
107A VAL 3.2 9.1 + - - -
110A LEU* 1.3 77.6 - - - +
112A ALA* 1.3 60.6 + - - -
113A GLY 3.2 0.2 - - - -
114A ARG* 2.9 26.9 + - - +
115A GLU* 3.6 9.4 + - - +
406A GLU* 4.2 17.2 + - - -
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 4.0 19.5 - - + +
97A ARG* 5.6 1.9 - - + +
100A GLY 5.3 3.8 - - - +
107A VAL* 3.0 23.7 + - + +
111A GLY* 1.3 71.1 - - - -
113A GLY* 1.3 61.7 + - - +
115A GLU* 3.1 28.8 + - - +
116A VAL* 3.4 10.6 + - - +
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 4.1 9.3 - - - +
107A VAL 3.1 9.3 + - - -
108A GLY* 3.2 24.5 - - - -
112A ALA* 1.3 73.9 - - - +
114A ARG* 1.3 64.3 + - - +
116A VAL* 3.4 6.6 - - - +
117A LEU* 3.2 18.2 + - - +
151A PHE* 3.3 22.2 - - - -
154A LEU* 4.0 1.1 - - - -
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLY 4.0 1.6 + - - -
109A TYR* 2.8 54.1 + - - -
110A LEU* 3.7 23.4 - - - +
111A GLY 2.9 16.1 + - - +
113A GLY* 1.3 77.2 - - - +
115A GLU* 1.3 60.4 + - + +
117A LEU* 3.5 9.9 + - + +
118A PRO* 3.5 17.0 - - - +
154A LEU* 3.4 34.6 - - - +
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG* 5.2 4.7 + - - +
111A GLY 4.0 9.9 - - - +
112A ALA* 3.1 24.0 + - - +
114A ARG* 1.3 80.5 - - + +
116A VAL* 1.3 59.8 + - + +
118A PRO* 3.4 12.6 - - - +
119A GLU* 5.1 0.5 + - - +
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 4.5 7.4 - - + -
72A ASP 5.5 1.3 - - - +
73A LEU* 4.0 21.8 - - + -
95A ILE* 4.9 6.3 - - + -
97A ARG* 3.2 57.4 - - + +
112A ALA 3.4 2.6 + - - +
113A GLY 3.4 13.2 - - - +
115A GLU* 1.3 75.7 - - + +
117A LEU* 1.3 66.4 + - - +
118A PRO 3.3 1.8 - - - -
119A GLU* 3.1 6.7 + - - +
120A VAL* 3.0 27.3 + - + +
151A PHE* 3.7 20.6 - - + -
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLY 3.2 12.3 + - - +
114A ARG* 3.5 15.7 - - + +
115A GLU 3.4 0.2 - - - -
116A VAL* 1.3 75.2 - - - +
118A PRO* 1.4 66.5 - - + +
120A VAL* 3.1 2.9 + - - +
121A MET* 2.8 45.2 + - + +
151A PHE* 3.7 19.7 - - + -
154A LEU* 3.9 27.1 - - + -
155A LEU* 4.1 12.3 - - + -
158A SER* 3.4 30.7 - - - +
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Residues in contact with PRO 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ARG 3.5 7.6 - - - +
115A GLU 3.4 17.3 - - - +
116A VAL 3.5 0.4 - - - -
117A LEU* 1.4 93.8 - - + +
119A GLU* 1.3 62.0 + - - +
121A MET* 3.2 6.6 + - + +
122A SER* 2.9 24.9 + - - -
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ALA 4.7 4.7 - - - +
94A LEU 5.5 0.2 - - - +
95A ILE* 3.6 35.8 - - + +
97A ARG* 2.7 35.4 + - - +
115A GLU 5.1 0.6 + - - +
116A VAL* 3.1 10.0 + - - +
118A PRO* 1.3 78.8 - - - +
120A VAL* 1.3 63.9 + - - +
122A SER* 3.2 9.9 + - - -
123A ARG* 3.1 27.0 + - + +
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Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 5.0 0.2 - - + -
69A ILE* 4.6 7.8 - - + +
71A VAL* 3.8 36.3 - - + -
95A ILE* 3.9 16.2 - - + -
116A VAL* 3.0 18.7 + - + +
117A LEU 3.6 5.2 - - - +
119A GLU* 1.3 76.1 - - - +
121A MET* 1.3 58.5 + - - +
123A ARG* 3.1 6.1 + - - +
124A LEU* 2.9 31.6 + - + +
151A PHE* 3.6 22.9 - - + -
155A LEU* 3.7 27.1 - - + -
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Residues in contact with MET 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 2.8 39.4 + - + +
118A PRO* 3.8 5.8 - - + +
120A VAL* 1.3 72.6 - - - +
122A SER* 1.3 53.1 + - - +
124A LEU* 3.4 6.1 + - + +
125A ASP* 2.8 43.3 + - - +
155A LEU* 3.7 22.0 - - + -
158A SER* 4.0 26.9 - - - +
159A LEU* 3.8 27.8 - - + -
162A LYS* 4.3 23.6 - - + +
163A TYR* 4.3 7.0 - - + -
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Residues in contact with SER 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PRO 2.9 13.7 + - - -
119A GLU* 3.3 13.7 - - - -
121A MET* 1.3 77.4 - - - +
123A ARG* 1.3 64.2 + - - +
125A ASP* 3.3 14.0 + - - +
126A TYR* 3.1 26.2 + - - +
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Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ILE* 3.6 16.2 - - + -
90A ASN* 3.7 6.5 - - - +
92A ALA* 3.3 41.5 + - - +
93A ASN* 2.8 27.7 + - - +
95A ILE* 3.8 17.3 - - + -
119A GLU* 3.1 16.4 + - + +
120A VAL 3.1 7.0 + - - +
122A SER* 1.3 81.7 + - - +
124A LEU* 1.3 62.3 + - - +
126A TYR* 3.2 50.3 + - - +
127A GLU* 2.9 31.7 + - - +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.6 7.4 - - + -
9A VAL* 3.9 21.3 - - + -
69A ILE* 3.6 15.0 - - + +
120A VAL* 2.9 18.4 + - + +
121A MET* 3.5 13.2 - - + +
123A ARG* 1.3 74.1 - - - +
125A ASP* 1.3 65.9 + - - +
127A GLU* 3.2 1.6 + - - +
128A ILE* 2.8 42.8 + - + +
137A ILE* 3.9 26.7 - - + -
155A LEU* 3.7 40.4 - - + -
159A LEU* 3.9 18.6 - - + -
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Residues in contact with ASP 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A MET* 2.8 30.0 + - - +
122A SER* 3.3 15.6 - - - +
124A LEU* 1.3 71.1 - - - +
126A TYR* 1.3 58.3 + - - +
128A ILE* 3.5 2.1 + - - +
129A ASP* 3.0 30.1 + - - +
162A LYS* 2.8 28.0 + - - +
163A TYR* 2.7 35.4 + - - +
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Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ASN* 4.1 8.9 + - - -
122A SER 3.1 13.6 + - - +
123A ARG* 3.4 42.8 - - - +
124A LEU 3.1 0.4 - - - -
125A ASP* 1.3 78.3 - - - +
127A GLU* 1.3 87.9 + - + +
129A ASP* 3.4 9.8 + - - +
130A LYS* 3.1 59.2 + - + +
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Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.5 24.1 - - + +
54A SER* 5.1 1.4 + - - -
66A PRO 5.0 2.2 - - - +
67A ARG* 4.1 24.6 + - - +
68A ALA 5.1 0.7 - - - +
69A ILE* 4.1 11.0 - - + -
90A ASN* 4.2 3.6 + - - +
93A ASN* 3.0 31.3 + - - +
123A ARG 2.9 18.5 + - - +
124A LEU* 4.0 2.5 - - - +
126A TYR* 1.3 99.7 - - + +
128A ILE* 1.3 59.0 + - - +
130A LYS* 3.7 21.9 + - - +
131A CYS* 3.1 28.6 + - - -
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Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.6 6.3 - - + -
124A LEU* 2.8 32.0 + - + +
125A ASP 4.0 3.6 - - - +
127A GLU* 1.3 75.1 - - - +
129A ASP* 1.3 64.9 + - - +
131A CYS* 3.3 24.5 + - - +
134A VAL* 4.7 12.3 - - + +
137A ILE* 3.9 29.8 - - + -
159A LEU* 4.5 2.0 - - + -
163A TYR* 3.8 51.6 - - + +
166A ILE* 4.2 16.2 - - + -
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Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASP 3.0 18.8 + - - +
126A TYR* 3.8 9.7 - - - +
127A GLU 3.4 0.2 - - - -
128A ILE* 1.3 80.1 - - - +
130A LYS* 1.3 65.3 + - - +
131A CYS 3.1 9.6 + - - +
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Residues in contact with LYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A SER* 3.4 28.7 + - - +
55A LYS 5.9 0.6 + - - -
65A VAL* 5.9 3.4 - - - +
67A ARG* 4.3 9.8 + - - +
90A ASN* 5.3 3.0 - - - +
126A TYR* 3.1 57.8 + - + +
127A GLU* 3.7 27.7 + - - +
129A ASP* 1.3 80.0 - - - +
131A CYS* 1.3 59.7 + - - +
132A ASP* 3.6 9.2 + - - +
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Residues in contact with CYS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ASN* 3.4 32.8 - - + +
7A ILE* 3.9 16.4 - - - -
67A ARG* 3.8 13.0 - - - +
127A GLU 3.1 23.3 - - - -
128A ILE* 3.4 12.7 - - - +
129A ASP 3.1 10.7 - - - +
130A LYS* 1.3 75.8 - - - +
132A ASP* 1.3 65.2 + - - +
133A ASN* 4.6 0.2 - - - -
134A VAL* 4.0 20.9 + - + +
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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