Contacts of the helix formed by residues 116 - 129 (chain A) in PDB entry 1B06
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 PHE 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A GLY 3.8 19.3 - - - -
100A LYS* 3.5 38.8 - - + +
101A PRO* 3.4 28.0 - - + -
109A ILE* 4.0 10.3 - - + -
110A ASP* 3.7 5.5 + - - -
115A SER* 1.3 74.3 - - - +
117A ASP* 1.3 63.3 + - - +
119A PHE* 4.3 14.8 - + - -
120A LYS* 2.9 65.7 + - + +
192A TRP* 4.6 3.1 - + - -
197A TRP* 3.5 27.8 - + - -
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Residues in contact with ASP 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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115A SER* 3.2 9.2 + - - +
116A PHE* 1.3 81.2 - - - +
118A ARG* 1.3 64.2 + - - +
120A LYS* 3.4 18.6 + - - +
121A GLN* 3.1 35.3 + - - +
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Residues in contact with ARG 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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113A TYR* 3.3 25.4 - - + +
115A SER* 3.4 12.5 + - - +
116A PHE 3.4 0.2 - - - -
117A ASP* 1.3 74.5 - - - +
119A PHE* 1.3 68.4 + - - +
121A GLN* 2.9 39.8 + - - +
122A VAL* 2.8 48.8 + - - +
125A GLU* 4.7 10.3 + - - -
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Residues in contact with PHE 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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109A ILE* 3.7 29.2 - - + -
113A TYR* 3.9 43.8 - + + +
115A SER 3.1 11.9 + - - +
116A PHE* 3.6 21.1 - + - +
118A ARG* 1.3 80.2 - - - +
120A LYS* 1.3 58.5 + - - +
122A VAL* 3.2 0.7 + - - +
123A PHE* 2.7 57.5 + + - +
138A LEU* 3.9 37.2 - - + -
149A ILE* 4.5 2.7 - - + -
167A LEU* 4.1 10.5 - - + -
192A TRP* 4.1 19.7 - + - -
197A TRP* 4.4 6.1 - + - -
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Residues in contact with LYS 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* 2.9 51.7 + - + +
117A ASP* 3.5 19.3 + - - +
118A ARG 3.2 0.2 - - - -
119A PHE* 1.3 80.0 - - + +
121A GLN* 1.3 58.0 + - + +
124A SER* 2.9 36.4 + - - +
192A TRP* 3.5 53.4 - - + +
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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 ASP* 3.1 26.7 + - - +
118A ARG* 2.9 43.4 + - - +
120A LYS* 1.3 78.2 - - + +
122A VAL* 1.3 57.2 + - - +
124A SER* 3.8 4.2 - - - -
125A GLU* 2.9 30.5 + - - +
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Residues in contact with VAL 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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113A TYR* 4.5 19.3 - - + -
118A ARG* 2.8 55.8 + - - +
119A PHE 3.8 2.9 - - - +
121A GLN* 1.3 70.5 - - - +
123A PHE* 1.3 65.2 + - - +
125A GLU* 3.3 11.1 + - + +
126A SER* 2.9 34.0 + - - +
149A ILE* 4.0 16.2 - - + -
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Residues in contact with PHE 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 PHE* 2.7 40.6 + + + +
120A LYS 4.0 2.9 - - - +
122A VAL* 1.3 72.8 - - - +
124A SER* 1.3 58.9 + - - +
126A SER* 3.4 4.5 + - - -
127A ALA* 3.0 28.3 + - + +
136A THR* 3.5 32.9 - - + +
137A VAL* 4.3 6.7 - - - -
138A LEU* 4.2 15.3 - - + -
149A ILE* 4.0 21.2 - - + +
167A LEU* 4.1 19.7 - - + -
169A VAL* 3.4 31.4 - - + -
191A TRP* 3.8 9.0 - + - -
192A TRP* 3.8 25.1 - + + -
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Residues in contact with SER 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 LYS* 2.9 24.6 + - - +
121A GLN* 3.8 4.9 - - - -
123A PHE* 1.3 76.7 - - - +
125A GLU* 1.3 60.2 + - - +
127A ALA* 3.3 6.4 + - - +
128A ASN* 2.9 43.2 + - - +
188A LEU* 5.5 5.8 - - - +
189A ASN* 5.1 4.9 + - - -
192A TRP* 3.2 25.3 + - - -
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Residues in contact with GLU 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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118A ARG* 4.7 10.2 + - - -
121A GLN 2.9 19.3 + - - +
122A VAL* 3.3 12.6 + - + +
124A SER* 1.3 76.9 - - - +
126A SER* 1.3 63.3 + - - +
128A ASN* 3.5 6.6 + - - +
129A SER* 3.2 22.4 + - - -
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Residues in contact with SER 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 VAL* 2.9 23.9 + - - +
123A PHE 3.6 4.7 - - - -
125A GLU* 1.3 75.7 - - - +
127A ALA* 1.3 63.7 + - - +
129A SER* 2.7 24.9 + - - -
130A LEU 3.5 0.5 + - - -
136A THR* 4.7 1.1 - - - -
149A ILE* 3.8 28.0 - - - +
151A THR* 3.2 21.7 - - - +
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Residues in contact with ALA 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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123A PHE* 3.0 22.8 + - + +
124A SER* 3.3 8.0 + - - +
126A SER* 1.3 76.4 - - - +
128A ASN* 1.3 60.5 + - - +
129A SER 3.4 0.5 + - - -
130A LEU* 3.5 8.7 + - - +
136A THR* 3.2 27.1 + - + +
169A VAL* 5.5 0.2 - - + -
171A GLU* 2.6 31.5 - - - +
184A ARG* 3.7 0.7 + - - -
188A LEU* 3.9 23.6 - - + -
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Residues in contact with ASN 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 SER* 2.9 33.5 + - - +
125A GLU* 3.9 6.4 - - - +
126A SER 3.2 0.2 - - - -
127A ALA* 1.3 76.5 - - - +
129A SER* 1.3 59.5 + - - +
130A LEU 3.3 0.8 - - - +
184A ARG* 3.6 18.2 + - - +
185A GLY* 3.7 19.8 + - - -
188A LEU* 3.4 23.5 - - - +
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Residues in contact with SER 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 GLU* 3.2 12.4 + - - -
126A SER* 2.7 22.3 + - - -
128A ASN* 1.3 77.7 - - - +
130A LEU* 1.3 65.0 + - - +
131A PRO* 3.2 10.6 - - - +
151A THR* 4.3 5.5 + - - +
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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
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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