Contacts of the helix formed by residues 109 - 130 (chain A) in PDB entry 2B2T
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 SER 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASN 4.8 0.7 - - - -
108A ALA* 1.3 75.6 - - - +
110A PRO* 1.3 68.3 - - - +
111A GLU* 2.9 20.8 - - - +
112A ASP* 2.8 35.0 + - - +
113A VAL* 3.0 12.4 + - - +
185B ARG* 4.5 19.4 + - - +
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Residues in contact with PRO 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA 4.6 0.9 - - - +
109A SER* 1.3 87.1 - - - +
111A GLU* 1.3 53.5 + - + +
113A VAL* 3.4 9.5 + - + +
114A GLU* 2.8 33.0 + - - +
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A SER* 2.9 14.8 - - - -
110A PRO* 1.3 81.3 - - + +
112A ASP* 1.3 62.1 + - - +
114A GLU* 3.5 8.7 - - - +
115A TYR* 2.9 28.1 + - - +
135B ARG* 3.8 19.1 + - - +
185B ARG* 5.5 6.6 - - - +
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA* 3.6 19.5 - - + +
109A SER* 2.8 35.8 + - - +
111A GLU* 1.3 79.0 - - - +
113A VAL* 1.3 58.5 + - - +
115A TYR* 3.5 3.5 + - - +
116A TYR* 3.0 27.4 + - - +
135B ARG* 2.7 40.6 + - - +
137B ILE* 6.5 1.1 - - + -
160B TYR* 5.0 1.2 + - - -
185B ARG* 5.0 11.5 - - - +
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 5.5 11.2 - - + -
107A ASN 4.4 13.2 - - - +
108A ALA* 4.7 5.6 - - + -
109A SER 3.0 14.1 + - - +
110A PRO* 3.8 11.0 - - + +
112A ASP* 1.3 74.7 - - - +
114A GLU* 1.3 65.2 + - - +
116A TYR* 3.8 7.0 - - + +
117A ASN* 3.0 43.0 + - - +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO 2.8 18.4 + - - +
111A GLU* 3.5 11.4 - - - +
112A ASP 3.2 0.2 - - - -
113A VAL* 1.3 79.0 - - - +
115A TYR* 1.3 62.6 + - - +
117A ASN* 4.1 4.6 - - - +
118A CYS* 3.1 55.9 + - - -
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Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLU 2.9 17.9 + - - +
112A ASP 3.7 4.7 - - - +
114A GLU* 1.3 75.8 - - - +
116A TYR* 1.3 59.3 + - - +
118A CYS* 3.2 5.6 + - + +
119A GLN* 2.9 69.0 + - + +
134B GLY* 3.2 25.0 + - - -
135B ARG* 3.4 45.8 - - + +
154B LYS* 4.9 7.7 + - + +
156B GLN* 5.5 1.4 + - - -
160B TYR* 3.2 27.4 - + - -
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Residues in contact with TYR 116 (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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101A THR* 4.4 11.3 - - + +
102A LYS* 4.1 17.3 + - - -
112A ASP 3.0 18.5 + - - +
113A VAL* 3.8 7.4 - - + +
114A GLU 3.4 0.4 - - - -
115A TYR* 1.3 77.3 - - - +
117A ASN* 1.3 82.2 + - - +
119A GLN* 3.9 1.0 - - - +
120A GLN* 3.0 53.1 + - + +
160B TYR* 3.5 58.7 - + + +
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Residues in contact with ASN 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 VAL* 3.0 43.2 + - - +
114A GLU* 4.2 5.5 - - - +
116A TYR* 1.3 93.6 - - - +
118A CYS* 1.3 63.2 + - - +
120A GLN* 3.6 4.3 + - - +
121A GLU* 3.4 22.3 + - - +
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Residues in contact with CYS 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 GLU* 3.1 47.6 + - - +
115A TYR* 3.7 5.8 - - + +
116A TYR 3.2 0.6 - - - -
117A ASN* 1.3 72.6 - - - +
119A GLN* 1.3 62.5 + - - +
120A GLN 2.9 3.6 - - - -
121A GLU* 2.8 32.7 + - - +
122A LEU* 3.2 16.3 + - + +
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Residues in contact with GLN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TYR* 2.9 66.7 + - + +
116A TYR 4.2 2.2 - - - +
118A CYS* 1.3 76.6 - - - +
120A GLN* 1.3 61.6 + - - +
121A GLU 3.4 0.4 - - - -
122A LEU* 3.7 30.9 + - - +
123A THR* 3.6 24.9 + - - +
154B LYS* 3.8 23.2 + - - +
156B GLN* 6.0 0.3 - - - -
157B GLY 5.4 3.8 + - - -
160B TYR* 4.2 8.7 - - + -
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Residues in contact with GLN 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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116A TYR* 3.0 43.5 + - + +
117A ASN* 3.9 6.5 - - - +
118A CYS 2.9 1.2 - - - -
119A GLN* 1.3 81.8 - - - +
121A GLU* 1.3 60.4 + - - +
122A LEU 3.4 0.4 - - - -
123A THR* 3.5 9.3 + - - +
124A ASP* 3.2 29.9 + - - +
159B PRO* 4.0 9.5 - - - +
160B TYR* 3.4 46.5 + - - +
161B SER* 4.9 2.2 - - - +
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN 3.4 11.8 + - - +
118A CYS* 2.8 13.9 + - - +
120A GLN* 1.3 77.0 - - - +
122A LEU* 1.3 60.0 + - + +
124A ASP* 3.4 8.9 - - + +
125A ASP* 2.7 43.4 + - - +
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Residues in contact with LEU 122 (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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118A CYS* 3.2 12.0 + - + +
119A GLN* 3.7 40.8 - - - +
120A GLN 3.4 0.2 - - - -
121A GLU* 1.3 76.2 - - + +
123A THR* 1.3 61.2 + - + +
125A ASP* 3.5 6.4 + - - +
126A LEU* 3.0 35.4 + - + +
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Residues in contact with THR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN 3.6 16.5 + - - +
120A GLN* 3.5 17.0 + - - -
122A LEU* 1.3 75.1 - - + +
124A ASP* 1.3 67.1 + - - +
126A LEU* 3.3 10.3 - - + +
127A HIS* 3.0 38.3 + - - -
154B LYS* 5.2 0.9 - - - +
157B GLY* 4.2 12.8 - - - +
158B LEU 3.8 7.9 - - - +
159B PRO* 3.7 42.6 - - + +
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Residues in contact with ASP 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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21A ASP* 4.2 16.2 - - - +
120A GLN* 3.2 22.6 + - - +
121A GLU* 3.4 13.5 - - + +
122A LEU 3.2 0.2 - - - -
123A THR* 1.3 84.7 + - - +
125A ASP* 1.3 62.8 + - - +
127A HIS* 3.4 10.1 + - - +
128A LYS* 3.3 27.9 + - - +
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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 GLU* 2.7 28.1 + - - +
122A LEU* 3.8 6.9 - - - +
124A ASP* 1.3 77.2 - - - +
126A LEU* 1.3 71.9 + - + +
128A LYS* 2.9 32.4 + - - +
129A GLN* 3.2 16.3 + - + +
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Residues in contact with LEU 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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122A LEU* 3.0 24.4 + - + +
123A THR* 3.3 15.0 - - + +
125A ASP* 1.3 76.2 - - + +
127A HIS* 1.3 63.0 + - + +
129A GLN* 2.9 43.7 + - - +
130A TYR* 3.6 28.1 + - + +
157A GLY* 4.9 9.6 - - - +
126B LEU* 5.9 8.3 - - + -
157B GLY 5.9 3.4 - - - +
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Residues in contact with HIS 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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18A ARG* 4.2 8.7 + - - -
20A MSE 3.5 39.9 - - + +
69A HIS* 5.0 2.1 + - - +
123A THR* 3.0 23.0 + - - -
124A ASP* 3.6 9.9 - - - +
125A ASP 3.2 0.2 - - - -
126A LEU* 1.3 75.7 - - + +
128A LYS* 1.3 65.8 + - - +
130A TYR* 3.2 45.0 + + + +
131A GLN* 4.1 6.4 + - - +
159B PRO* 3.8 29.7 - - + +
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Residues in contact with LYS 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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124A ASP* 3.3 19.3 + - - +
125A ASP* 2.9 26.4 + - - +
127A HIS* 1.3 76.9 - - - +
129A GLN* 1.3 65.3 + - + +
131A GLN* 3.0 33.8 + - - +
132A ILE* 3.8 8.3 - - - +
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Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASP* 3.6 15.8 - - - +
126A LEU* 2.9 23.9 + - - +
128A LYS* 1.3 73.3 - - + +
130A TYR* 1.3 60.7 + - - +
131A GLN 2.9 7.4 + - - -
132A ILE* 3.0 28.7 + - + +
156A GLN* 3.3 40.3 + - + +
157A GLY* 4.5 9.8 + - - -
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Residues in contact with TYR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 4.7 10.2 + - - -
20A MSE 4.5 1.8 - - + -
69A HIS* 3.4 56.3 + + + +
70A ILE 4.9 0.2 + - - -
126A LEU* 3.7 23.7 - - + +
127A HIS* 3.2 44.2 + + - +
129A GLN* 1.3 74.6 - - - +
131A GLN* 1.3 57.8 + - - +
132A ILE 3.5 0.2 - - - -
155A TRP* 3.3 28.9 - - - +
156A GLN 3.5 16.2 - - - -
157A GLY* 3.7 13.9 + - - -
158A LEU* 3.4 31.6 - - + +
130B TYR* 5.3 4.5 + - - -
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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
------------------------------------------------------------
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