Contacts of the helix formed by residues 106 - 120 (chain A) in PDB entry 3BIL
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 ASP 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A SER* 2.8 20.1 + - - +
104A ASN* 4.1 7.9 - - + +
105A GLU* 1.3 75.8 - - - +
107A ALA* 1.3 66.6 + - - +
108A THR* 3.4 14.8 + - - -
109A THR* 2.7 40.1 + - - +
110A MET* 3.2 13.4 + - - +
130A ASN* 4.0 3.3 - - - +
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Residues in contact with ALA 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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105A GLU 4.2 0.4 + - - -
106A ASP* 1.3 70.8 - - - +
108A THR* 1.3 58.0 + - - +
110A MET* 3.2 2.7 + - - -
111A SER* 2.8 30.7 + - - -
130A ASN* 3.8 14.7 - - - +
132A GLU* 3.7 37.5 - - + +
133A CYS* 3.6 19.5 - - - -
136A GLN* 5.7 0.2 - - - -
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Residues in contact with THR 108 (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 ASP* 3.4 12.4 + - - -
107A ALA* 1.3 77.0 - - - +
109A THR* 1.3 63.3 + - - +
111A SER* 3.2 9.8 - - - -
112A GLY* 2.9 19.4 + - - -
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Residues in contact with THR 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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102A ASN 4.1 9.0 - - - +
103A SER* 3.6 15.6 + - - +
104A ASN* 5.1 1.7 + - - +
106A ASP* 2.7 31.1 + - - +
108A THR* 1.3 75.6 - - - +
110A MET* 1.3 55.7 + - - +
112A GLY* 3.1 5.2 + - - -
113A SER* 3.0 29.0 + - - +
88B GLN* 4.1 23.6 - - - +
97B ALA* 6.6 0.2 - - + -
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Residues in contact with MET 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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71A ILE* 4.1 19.5 - - + -
73A PRO* 6.0 0.9 - - + -
103A SER* 3.8 27.2 - - - +
106A ASP 3.2 9.1 + - - +
107A ALA* 3.2 7.9 + - - +
109A THR* 1.3 71.2 - - - +
111A SER* 1.3 68.1 + - - +
113A SER* 3.1 7.5 + - - -
114A LEU* 3.0 41.2 + - + +
127A CYS* 4.5 8.1 - - - -
128A VAL 3.2 26.9 - - - +
129A PRO* 4.3 4.5 - - - -
130A ASN* 3.3 30.3 - - + +
133A CYS* 4.0 18.2 - - - -
137A LEU* 5.0 1.3 - - - -
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Residues in contact with SER 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 ALA 2.8 13.4 + - - -
108A THR* 3.2 16.6 - - - -
110A MET* 1.3 78.1 - - - +
112A GLY* 1.3 62.6 + - - -
114A LEU* 4.0 2.1 - - - +
115A GLU* 3.3 23.4 + - - +
133A CYS* 4.3 1.0 - - - -
136A GLN* 2.9 42.0 + - - +
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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 THR 2.9 14.6 + - - -
109A THR* 3.1 5.8 + - - -
111A SER* 1.3 76.7 - - - +
113A SER* 1.3 55.0 + - - +
115A GLU* 3.4 14.9 - - - +
116A PHE* 3.1 25.5 + - - +
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Residues in contact with SER 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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71A ILE* 4.2 9.9 - - - -
101A THR* 3.1 36.7 + - - +
102A ASN 5.3 1.6 + - - -
103A SER* 6.0 0.7 - - - -
109A THR* 3.0 16.4 + - - +
110A MET* 3.1 12.4 + - - -
112A GLY* 1.3 74.1 - - - +
114A LEU* 1.3 55.3 + - - +
116A PHE* 3.0 7.1 + - - +
117A LEU* 2.6 40.4 + - - +
98B THR 5.2 1.6 + - - -
99B ILE* 5.8 2.2 - - - +
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Residues in contact with LEU 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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71A ILE* 3.7 23.5 - - + +
110A MET* 3.0 40.1 + - + +
111A SER 4.0 1.8 - - - +
113A SER* 1.3 67.6 - - - +
115A GLU* 1.3 68.1 + - - +
117A LEU* 3.1 15.2 + - - +
118A THR* 3.1 21.2 + - - +
125A ILE* 4.3 12.8 - - + -
127A CYS* 5.0 1.6 - - - -
133A CYS* 4.9 2.9 - - - -
136A GLN* 4.2 23.8 - - + +
137A LEU* 3.9 32.1 - - + +
140A LEU* 3.9 26.7 - - + -
147A VAL* 5.6 0.2 - - + -
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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
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111A SER 3.3 16.1 + - - +
112A GLY* 3.4 16.4 - - - +
114A LEU* 1.3 80.1 - - - +
116A PHE* 1.3 70.4 + - - +
118A THR* 3.6 5.6 + - - -
119A SER* 3.2 27.1 + - - +
136A GLN* 5.6 0.9 + - - +
140A LEU* 5.9 1.8 - - - +
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Residues in contact with PHE 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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99A ILE* 6.0 0.4 - - + -
112A GLY 3.1 12.2 + - - +
113A SER* 3.0 10.6 + - - +
115A GLU* 1.3 86.5 + - - +
117A LEU* 1.3 76.2 + - + +
119A SER* 3.1 13.1 + - - -
120A HIS* 3.1 65.1 + + + -
67B THR* 3.9 34.1 - - + -
97B ALA* 6.4 0.4 - - + -
99B ILE* 3.5 35.4 - - + -
120B HIS* 5.1 2.0 - - + -
121B GLY 6.1 0.9 - - - -
122B VAL* 4.4 12.3 - - + -
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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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69A GLY* 3.8 28.5 - - - -
70A VAL 4.3 0.9 - - - +
71A ILE* 3.9 33.4 - - + -
99A ILE* 4.4 20.6 - - + -
101A THR* 4.5 13.5 - - + -
113A SER 2.6 21.1 + - - +
114A LEU 3.1 3.3 + - - +
116A PHE* 1.3 84.5 - - + +
118A THR* 1.3 62.2 + - - +
120A HIS* 3.4 9.3 + - - -
122A VAL* 3.3 45.3 + - + +
125A ILE* 4.0 18.2 - - + -
99B ILE* 5.3 0.2 - - + -
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Residues in contact with THR 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 LEU 3.1 16.1 + - - +
115A GLU* 3.6 5.2 + - - -
117A LEU* 1.3 72.1 - - - +
119A SER* 1.3 63.2 + - - +
120A HIS 3.1 6.5 + - - -
121A GLY* 3.5 9.2 + - - -
125A ILE* 3.7 10.5 - - + -
140A LEU* 3.7 30.4 - - + +
143A GLN* 5.2 5.3 + - - -
145A MET* 3.4 40.5 - - + +
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Residues in contact with SER 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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115A GLU* 3.2 20.3 + - - +
116A PHE* 3.1 10.9 + - - -
118A THR* 1.3 81.9 + - - +
120A HIS* 1.3 71.9 + - - +
121A GLY 3.6 0.4 - - - -
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Residues in contact with HIS 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 PHE* 3.1 62.5 + + + +
117A LEU* 3.4 4.6 + - - +
118A THR 3.1 1.2 - - - -
119A SER* 1.3 88.6 - - - +
121A GLY* 1.3 63.0 + - - +
122A VAL* 3.6 5.3 - - + +
116B PHE* 4.7 6.1 - - + -
120B HIS* 3.0 71.3 + + + -
121B GLY 5.5 1.0 + - - -
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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
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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