Contacts of the helix formed by residues 106 - 125 (chain A) in PDB entry 4BT9
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 ASN 106 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PHE 4.1 0.4 + - - +
105A PRO* 1.3 74.5 - - - +
107A ASP* 1.3 65.2 + - - +
108A GLU* 3.0 23.3 + - - +
109A ASP* 3.0 23.7 + - - +
110A GLN* 3.1 18.2 + - - +
75B ASN* 3.4 17.6 - - - +
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Residues in contact with ASP 107 (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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106A ASN* 1.3 76.8 - - - +
108A GLU* 1.3 58.3 + - - +
110A GLN* 3.2 3.6 + - - +
111A VAL* 3.0 36.8 + - + +
75B ASN* 2.7 33.1 + - - +
76B THR* 5.1 0.7 + - - -
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Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASN* 3.0 12.9 + - - +
107A ASP* 1.3 78.6 - - - +
109A ASP* 1.3 61.4 + - - +
111A VAL* 3.5 6.2 + - - +
112A GLY* 2.9 25.3 + - - -
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Residues in contact with ASP 109 (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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3A GLY 5.1 1.0 - - - -
4A PHE* 3.4 43.7 + - + +
105A PRO* 3.5 14.5 - - + +
106A ASN* 3.0 37.9 + - - +
108A GLU* 1.3 79.1 - - - +
110A GLN* 1.3 61.8 + - - +
112A GLY* 3.7 2.0 - - - +
113A ALA* 3.0 28.6 + - - +
71B MET* 4.2 5.7 - - - +
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Residues in contact with GLN 110 (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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106A ASN 3.1 12.7 + - - +
107A ASP 3.6 7.9 - - - +
109A ASP* 1.3 75.3 - - - +
111A VAL* 1.3 61.6 + - + +
113A ALA* 3.4 2.9 + - - +
114A ALA* 3.0 26.3 + - - +
152A GLU* 2.7 37.5 + - - +
68B PHE* 4.2 4.0 - - + -
71B MET* 4.2 12.5 - - + +
72B LYS* 3.5 30.5 - - + +
75B ASN* 2.9 23.6 + - + +
76B THR* 2.9 28.0 + - - +
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Residues in contact with VAL 111 (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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107A ASP* 3.0 24.1 + - + +
108A GLU* 3.9 6.1 - - - +
110A GLN* 1.3 74.4 - - + +
112A GLY* 1.3 66.9 + - - +
114A ALA* 3.2 7.4 + - - +
115A LYS* 2.9 51.6 + - + +
152A GLU* 5.9 1.1 - - - +
156A VAL* 4.7 16.2 - - + -
159A THR* 6.1 0.4 - - - +
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Residues in contact with GLY 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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108A GLU 2.9 16.8 + - - -
109A ASP* 3.7 3.1 - - - -
111A VAL* 1.3 79.7 - - - +
113A ALA* 1.3 55.2 + - - +
115A LYS* 3.3 9.5 + - - +
116A ALA* 3.1 27.0 + - - +
119A ARG* 4.5 2.8 + - - -
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Residues in contact with ALA 113 (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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109A ASP 3.0 16.8 + - - +
110A GLN 3.7 4.5 - - - +
111A VAL 3.2 0.2 - - - -
112A GLY* 1.3 73.6 - - - +
114A ALA* 1.3 65.6 + - - +
116A ALA* 3.4 7.4 + - - +
117A LEU* 3.1 22.3 + - - +
64B PRO 4.5 2.4 - - - +
67B ALA* 4.3 5.2 - - + +
68B PHE* 3.8 24.6 - - - +
71B MET* 3.8 23.6 - - + -
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Residues in contact with ALA 114 (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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110A GLN 3.0 13.8 + - - +
111A VAL* 3.5 8.7 - - - +
113A ALA* 1.3 77.6 - - - +
115A LYS* 1.3 61.2 + - - +
117A LEU* 3.2 5.1 + - - +
118A LEU* 3.0 28.2 + - - +
152A GLU* 5.0 1.6 - - - +
153A LEU* 3.8 21.1 - - + +
156A VAL* 3.9 24.7 - - + -
68B PHE* 3.7 17.2 - - + -
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Residues in contact with LYS 115 (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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111A VAL* 2.9 39.3 + - + +
112A GLY* 3.7 7.4 - - - +
113A ALA 3.3 0.2 - - - -
114A ALA* 1.3 75.9 - - - +
116A ALA* 1.3 56.8 + - - +
118A LEU* 3.2 11.0 + - + +
119A ARG* 2.8 55.8 + - - +
156A VAL* 3.8 16.6 - - + -
159A THR* 5.0 2.0 - - - -
160A GLU* 3.3 41.4 + - + -
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Residues in contact with ALA 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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112A GLY 3.1 16.1 + - - +
113A ALA* 3.7 9.2 - - - +
114A ALA 3.3 0.2 - - - -
115A LYS* 1.3 74.4 - - - +
117A LEU* 1.3 60.6 + - - +
119A ARG* 3.5 19.3 + - - +
120A LEU* 3.1 26.5 + - - +
64B PRO* 4.0 15.3 - - + +
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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 ALA 3.1 12.9 + - - +
114A ALA 3.2 8.5 + - - +
116A ALA* 1.3 73.4 - - - +
118A LEU* 1.3 65.7 + - + +
120A LEU* 3.3 5.7 + - + +
121A GLN* 3.0 23.7 + - - +
131A ILE* 4.2 16.8 - - + -
145A LEU* 4.9 2.9 - - + -
153A LEU* 3.9 28.5 - - + -
169A TRP* 4.1 15.9 - - + -
64B PRO* 4.1 15.4 - - - +
65B VAL* 4.2 29.2 - - + +
68B PHE* 3.8 33.2 - - + -
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA 3.0 18.8 + - - +
115A LYS* 3.5 10.3 - - + +
117A LEU* 1.3 76.0 - - + +
119A ARG* 1.3 59.4 + - - +
121A GLN* 3.2 11.3 + - - +
122A ASP* 2.9 29.6 + - - +
153A LEU* 4.0 22.4 - - + +
156A VAL* 3.9 25.8 - - + -
157A ALA* 4.0 14.6 - - + +
160A GLU* 6.3 0.9 - - + -
162A ASP* 6.1 1.1 - - - +
165A HIS* 4.8 13.1 - - + +
169A TRP* 3.5 36.3 - - + +
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Residues in contact with ARG 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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112A GLY* 4.5 2.8 + - - -
115A LYS* 2.8 42.5 + - + +
116A ALA* 3.5 36.7 - - - +
118A LEU* 1.3 72.9 - - - +
120A LEU* 1.3 56.7 + - - +
122A ASP* 3.3 7.5 + - - +
123A THR* 2.7 40.8 + - - +
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Residues in contact with LEU 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 ALA 3.1 15.1 + - - +
117A LEU* 3.5 9.6 - - + +
119A ARG* 1.3 76.5 - - - +
121A GLN* 1.3 62.2 + - - +
123A THR* 3.3 3.5 + - - -
124A TYR* 3.1 53.6 + - + +
126A LEU* 3.9 20.4 - - + +
131A ILE* 5.8 2.2 - - + -
136A LEU* 5.1 0.2 - - + -
63B HIS* 3.8 30.7 - - + +
64B PRO* 4.3 24.5 - - + -
65B VAL* 4.7 8.1 - - + -
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Residues in contact with GLN 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* 3.0 14.0 + - + +
118A LEU* 3.5 16.8 - - - +
120A LEU* 1.3 76.0 - - - +
122A ASP* 1.3 57.4 + - - +
125A ASN* 2.9 25.6 + - - -
126A LEU* 3.0 43.2 + - - +
128A THR* 3.6 28.3 - - - +
131A ILE* 3.7 15.5 - - + +
165A HIS* 3.7 24.7 - - - +
168A LEU* 4.5 5.7 - - - +
169A TRP* 2.7 27.7 + - - +
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Residues in contact with ASP 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 LEU 2.9 17.3 + - - +
119A ARG* 3.6 7.6 - - - +
121A GLN* 1.3 76.9 - - - +
123A THR* 1.3 67.2 + - - +
125A ASN* 3.3 22.4 + - - +
162A ASP* 5.5 0.7 - - - +
164A TYR* 6.0 0.2 - - - -
165A HIS* 3.9 26.7 + - + -
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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
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119A ARG* 2.7 26.6 + - - +
120A LEU* 3.3 4.2 + - - -
122A ASP* 1.3 79.0 - - - +
124A TYR* 1.3 85.2 + - + +
125A ASN* 3.8 4.3 + - - -
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Residues in contact with TYR 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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120A LEU* 3.1 45.8 + - + +
123A THR* 1.3 94.6 - - + +
125A ASN* 1.3 73.0 + - - +
126A LEU* 3.3 24.1 + - + +
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Residues in contact with ASN 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 GLN 2.9 10.9 + - - -
122A ASP* 3.3 16.7 + - - +
123A THR 4.9 3.6 + - - -
124A TYR* 1.3 80.3 - - - +
126A LEU* 1.3 61.5 + - - +
127A ASP* 3.8 5.2 + - - +
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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