Contacts of the helix formed by residues 116 - 129 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99C GLY 3.8 19.3 - - - -
100C LYS* 3.5 39.7 - - + +
101C PRO* 3.6 22.2 - - + -
109C ILE* 4.0 10.3 - - + -
110C ASP* 3.9 5.3 + - - -
115C SER* 1.3 73.9 - - - +
117C ASP* 1.3 62.5 + - - +
119C PHE* 3.4 16.7 + + + -
120C LYS* 2.9 65.3 + - + +
192C TRP* 4.6 3.6 - + - -
197C TRP* 3.6 29.8 - + - -
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Residues in contact with ASP 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C SER* 3.2 9.3 + - - +
116C PHE* 1.3 81.2 - - - +
118C ARG* 1.3 65.2 + - - +
120C LYS* 3.4 20.2 + - - +
121C GLN* 3.1 37.3 + - - +
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Residues in contact with ARG 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C TYR* 3.3 24.2 - - + +
115C SER* 3.2 12.1 + - - +
117C ASP* 1.3 76.0 - - - +
119C PHE* 1.3 67.8 + - - +
121C GLN* 2.9 38.3 + - - +
122C VAL* 2.8 46.1 + - - +
125C GLU* 4.9 8.9 + - - -
4E ILE* 6.1 1.8 - - + -
55E LEU* 3.0 21.6 + - - +
56E ILE* 2.9 36.5 + - - +
57E LYS 5.0 0.2 - - - -
58E GLY* 4.7 4.2 - - - +
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Residues in contact with PHE 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ILE* 3.7 23.8 - - + -
113C TYR* 3.6 42.8 - + + +
115C SER 3.1 11.7 + - - +
116C PHE* 3.5 23.8 - + - +
118C ARG* 1.3 79.9 - - - +
120C LYS* 1.3 58.9 + - - +
122C VAL* 3.7 0.7 - - - +
123C PHE* 2.8 53.6 + + + +
138C LEU* 3.8 41.3 - - + -
149C ILE* 4.6 2.5 - - + -
167C LEU* 4.0 11.0 - - + -
192C TRP* 4.1 21.1 - + - -
197C TRP* 4.4 7.6 - + - -
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Residues in contact with LYS 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C PHE* 2.9 52.5 + - + +
117C ASP* 3.6 18.8 + - - +
119C PHE* 1.3 76.8 - - - +
121C GLN* 1.3 59.5 + - + +
124C SER* 3.0 35.6 + - - +
192C TRP* 3.4 56.6 - - + +
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Residues in contact with GLN 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C ASP* 3.1 28.1 + - - +
118C ARG* 2.9 42.2 + - - +
120C LYS* 1.3 77.9 - - + +
122C VAL* 1.3 56.8 + - - +
124C SER* 3.5 4.7 + - - -
125C GLU* 3.0 29.7 + - - +
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Residues in contact with VAL 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C TYR* 4.5 11.0 - - + -
118C ARG* 2.8 56.0 + - - +
119C PHE 3.9 3.4 - - - +
121C GLN* 1.3 69.9 - - - +
123C PHE* 1.3 64.9 + - - +
125C GLU* 3.4 8.4 + - - +
126C SER* 2.9 33.2 + - - +
149C ILE* 3.9 19.1 - - + -
52E LEU* 5.2 7.0 - - + -
55E LEU* 4.5 13.7 - - + -
56E ILE* 4.4 20.2 - - + -
67E LEU* 5.0 3.1 - - + +
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Residues in contact with PHE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C PHE* 2.8 39.0 + + + +
120C LYS 4.0 2.7 - - - +
122C VAL* 1.3 73.5 - - - +
124C SER* 1.3 59.5 + - - +
126C SER* 3.4 4.1 + - - -
127C ALA* 2.9 28.0 + - + +
136C THR* 3.6 30.5 - - + +
137C VAL* 4.3 7.0 - - - -
138C LEU* 4.2 16.4 - - + -
149C ILE* 4.2 21.9 - - + +
167C LEU* 4.1 20.0 - - + -
169C VAL* 3.4 31.9 - - + -
188C LEU* 6.3 0.2 - - + -
191C TRP* 3.8 9.6 - + - -
192C TRP* 3.7 25.8 - + + -
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Residues in contact with SER 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LYS* 3.0 23.4 + - - +
121C GLN* 3.8 5.4 - - - -
123C PHE* 1.3 76.5 - - - +
125C GLU* 1.3 59.6 - - - +
127C ALA* 3.3 7.3 + - - +
128C ASN* 2.9 43.1 + - - +
188C LEU* 5.5 5.9 - - - +
189C ASN* 4.9 7.1 + - - -
192C TRP* 3.2 24.4 + - - -
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Residues in contact with GLU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ARG* 4.9 8.7 + - - -
121C GLN 3.0 17.9 + - - +
122C VAL* 3.7 9.3 - - - +
124C SER* 1.3 77.2 - - - +
126C SER* 1.3 61.3 + - - +
128C ASN* 3.5 7.0 + - - +
129C SER* 3.2 21.8 + - - -
55E LEU* 4.7 9.3 - - - +
62E GLN* 3.6 20.1 + - - +
65E TYR* 2.5 39.3 + - - -
67E LEU* 3.9 14.4 - - + +
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Residues in contact with SER 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C VAL* 2.9 23.1 + - - +
123C PHE 3.6 4.5 - - - -
124C SER 3.2 0.2 - - - -
125C GLU* 1.3 75.2 - - - +
127C ALA* 1.3 62.4 + - - +
129C SER* 2.8 21.2 + - - -
130C LEU 3.5 0.2 + - - -
136C THR* 4.7 0.9 - - - -
149C ILE* 3.8 27.9 - - - +
151C THR* 3.2 16.2 - - - +
67E LEU* 3.6 21.1 - - - +
71E LEU* 4.0 14.9 - - - +
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Residues in contact with ALA 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C PHE* 2.9 23.3 + - + +
124C SER* 3.6 7.6 - - - +
126C SER* 1.3 77.0 - - - +
128C ASN* 1.3 60.5 + - - +
129C SER 3.4 0.7 + - - -
130C LEU* 3.4 9.2 + - - +
136C THR* 3.1 26.6 + - + +
169C VAL* 5.5 0.2 - - + -
171C GLU* 2.6 30.3 - - - +
184C ARG* 3.7 0.7 + - - -
188C LEU* 3.9 22.4 - - + -
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Residues in contact with ASN 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C SER* 2.9 32.8 + - - +
125C GLU* 3.9 6.4 - - - +
127C ALA* 1.3 76.5 - - - +
129C SER* 1.3 60.9 + - - +
130C LEU 3.3 1.3 + - - +
184C ARG* 3.6 17.6 + - - +
185C GLY* 3.7 19.4 + - - -
188C LEU* 3.5 23.0 - - - +
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Residues in contact with SER 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C GLU 3.2 12.0 + - - -
126C SER* 2.8 22.7 + - - -
128C ASN* 1.3 77.3 - - - +
130C LEU* 1.3 64.3 + - - +
131C PRO* 3.2 10.4 - - - +
151C THR* 4.2 0.7 - - - +
67E LEU* 4.3 13.8 - - - +
68E GLN* 3.0 33.0 + - - +
71E LEU* 4.3 3.6 - - - +
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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