Contacts of the helix formed by residues 116 - 129 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99F GLY 3.9 18.4 - - - -
100F LYS* 3.6 34.9 - - + +
101F PRO* 3.5 19.7 - - + -
109F ILE* 4.0 12.1 - - + +
110F ASP* 3.9 4.8 + - - -
115F SER* 1.3 75.8 - - - +
117F ASP* 1.3 63.2 + - - +
119F PHE* 3.6 16.1 - + - +
120F LYS* 2.9 62.5 + - + +
192F TRP* 4.5 4.5 - + - -
197F TRP* 3.5 36.8 - + - -
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Residues in contact with ASP 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F SER* 3.2 11.3 + - - +
116F PHE* 1.3 80.9 - - - +
118F ARG* 1.3 64.5 + - - +
120F LYS* 3.5 19.8 + - - +
121F GLN* 3.1 34.7 + - - +
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Residues in contact with ARG 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 6.0 1.6 - - + -
55D LEU* 3.0 22.0 + - - +
56D ILE* 3.0 37.6 + - - +
58D GLY* 4.7 4.2 - - - +
113F TYR 3.2 22.4 - - - +
114F GLY* 5.4 0.2 - - - -
115F SER* 3.4 11.9 + - - +
116F PHE 3.3 0.2 - - - -
117F ASP* 1.3 75.5 - - - +
119F PHE* 1.3 62.0 + - - +
121F GLN* 2.9 37.2 + - - +
122F VAL* 2.8 50.1 + - - +
125F GLU* 5.0 7.9 + - - -
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Residues in contact with PHE 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F ILE* 3.7 23.6 - - + -
113F TYR* 3.9 41.1 - + + +
115F SER 3.2 11.9 + - - +
116F PHE* 3.6 21.3 - + - +
117F ASP 3.4 0.2 - - - -
118F ARG* 1.3 78.9 - - - +
120F LYS* 1.3 56.2 + - - +
122F VAL* 3.3 0.9 + - - +
123F PHE* 2.8 58.0 + + + +
138F LEU* 3.9 39.5 - - + -
147F LEU* 5.8 0.2 - - + -
149F ILE* 4.4 4.9 - - + -
167F LEU* 4.0 10.8 - - + -
192F TRP* 4.0 19.7 - + - -
197F TRP* 4.4 9.9 - + - -
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Residues in contact with LYS 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F PHE* 2.9 50.4 + - + +
117F ASP* 3.6 19.1 + - - +
118F ARG 3.2 0.2 - - - -
119F PHE* 1.3 79.9 - - - +
121F GLN* 1.3 58.7 + - + +
124F SER* 3.0 36.0 + - - +
192F TRP* 3.5 52.5 - - + +
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Residues in contact with GLN 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F ASP* 3.1 27.7 + - - +
118F ARG* 2.9 38.7 + - - +
120F LYS* 1.3 79.5 - - + +
122F VAL* 1.3 58.0 + - - +
124F SER* 3.8 4.1 - - - -
125F GLU* 3.0 30.3 + - - +
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Residues in contact with VAL 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 5.2 6.7 - - + -
55D LEU* 4.5 14.4 - - + -
56D ILE* 4.4 20.4 - - + -
67D LEU* 5.0 2.6 - - + +
113F TYR* 4.4 12.3 - - + -
118F ARG* 2.8 55.0 + - - +
119F PHE 3.9 3.6 - - - +
121F GLN* 1.3 69.4 - - - +
123F PHE* 1.3 65.5 + - - +
125F GLU* 3.4 10.1 + - + +
126F SER* 2.9 33.0 + - - +
149F ILE* 3.9 17.9 - - + -
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Residues in contact with PHE 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F PHE* 2.8 39.8 + + + +
120F LYS 4.0 3.1 - - - +
122F VAL* 1.3 73.1 - - - +
124F SER* 1.3 58.6 + - - +
126F SER* 3.3 3.8 + - - -
127F ALA* 2.9 31.1 + - + +
136F THR* 3.6 32.4 - - + +
137F VAL 4.2 17.9 - - - -
138F LEU* 4.3 4.7 - - + -
149F ILE* 4.1 20.6 - - + +
167F LEU* 4.2 19.7 - - + -
169F VAL* 3.4 31.2 - - + -
188F LEU* 6.1 0.2 - - + -
191F TRP* 3.8 11.0 - + - -
192F TRP* 3.6 26.7 - + + -
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Residues in contact with SER 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F LYS* 3.0 22.1 + - - +
121F GLN* 3.8 4.9 - - - -
123F PHE* 1.3 75.3 - - - +
125F GLU* 1.3 61.2 + - - +
127F ALA* 3.3 6.4 + - - +
128F ASN* 2.9 44.0 + - - +
188F LEU* 5.4 6.4 - - - +
189F ASN* 5.1 4.6 + - - -
192F TRP* 3.1 25.1 + - - -
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Residues in contact with GLU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 4.9 8.6 - - - +
62D GLN* 4.0 20.1 + - - +
65D TYR* 2.6 38.9 + - - -
67D LEU* 3.8 15.0 - - + +
118F ARG* 5.0 8.3 + - - -
121F GLN 3.0 18.4 + - - +
122F VAL* 3.7 11.1 - - - +
124F SER* 1.3 76.7 - - - +
126F SER* 1.3 62.0 + - - +
128F ASN* 3.4 6.8 + - - +
129F SER* 3.2 21.7 + - - -
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Residues in contact with SER 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D LEU* 3.8 19.3 - - - +
71D LEU* 4.0 14.8 - - - +
122F VAL* 2.9 24.5 + - - +
123F PHE 3.5 4.7 - - - -
125F GLU* 1.3 73.2 - - - +
127F ALA* 1.3 65.0 + - - +
129F SER* 2.8 22.0 + - - -
130F LEU 3.5 0.5 + - - -
136F THR* 4.6 1.1 - - - -
149F ILE* 3.8 27.7 - - - +
151F THR* 3.3 15.6 - - - +
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Residues in contact with ALA 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F PHE* 2.9 23.0 + - + +
124F SER* 3.7 7.0 - - - +
126F SER* 1.3 76.0 - - - +
128F ASN* 1.3 61.3 + - - +
129F SER 3.4 0.5 + - - -
130F LEU* 3.5 8.8 + - - +
136F THR* 3.1 27.1 + - + +
171F GLU* 2.5 30.2 - - - +
184F ARG* 3.6 0.9 + - - -
188F LEU* 3.8 22.9 - - + -
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Residues in contact with ASN 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F SER* 2.9 31.3 + - - +
125F GLU* 3.8 7.1 - - - +
126F SER 3.2 0.2 - - - -
127F ALA* 1.3 77.3 - - - +
129F SER* 1.3 60.3 + - - +
130F LEU 3.3 0.4 - - - +
184F ARG* 3.5 17.8 + - - +
185F GLY* 3.8 20.5 + - - -
188F LEU* 3.7 20.8 - - - +
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Residues in contact with SER 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU* 4.5 13.5 - - - +
68D GLN* 2.9 34.1 + - - +
71D LEU* 4.4 3.5 - - - +
125F GLU 3.2 11.8 + - - -
126F SER* 2.8 21.1 + - - -
128F ASN* 1.3 75.8 - - - +
130F LEU* 1.3 64.2 + - - +
131F PRO* 3.1 10.2 - - - +
151F THR* 4.3 0.3 - - - +
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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