Contacts of the helix formed by residues 131 - 145 (chain F) in PDB entry 5O6I
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 131 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19F ILE* 6.1 0.6 - - - +
129F ASN* 2.9 17.3 + - - +
130F LYS* 1.3 73.3 - - - +
132F LYS* 1.3 62.8 + - - +
133F ALA* 3.2 12.8 + - - +
134F LEU* 3.0 37.9 + - + +
135F LEU* 3.2 24.9 + - - +
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Residues in contact with LYS 132 (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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130F LYS 3.1 7.7 + - - +
131F ASN* 1.3 73.2 + - - +
133F ALA* 1.3 58.8 + - - +
135F LEU* 3.2 6.4 + - - +
136F GLU* 2.8 56.1 + - + +
151F ILE* 4.6 13.9 - - + -
161F TYR* 3.6 55.6 + - + +
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Residues in contact with ALA 133 (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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131F ASN* 3.2 9.1 + - - +
132F LYS* 1.3 78.1 - - - +
134F LEU* 1.3 61.1 + - - +
136F GLU* 3.4 14.6 + - - +
137F ILE* 3.1 31.9 + - + +
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Residues in contact with LEU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ILE* 3.6 30.5 - - + -
95F LEU* 5.3 6.5 - - + -
98F ILE* 4.5 10.1 - - + -
109F PHE* 3.8 32.8 - - + -
113F LEU* 4.5 14.1 - - + -
129F ASN* 4.6 15.3 - - + +
131F ASN* 3.0 31.3 + - - +
132F LYS 3.2 0.2 - - - -
133F ALA* 1.3 77.7 - - - +
135F LEU* 1.3 64.0 + - + +
137F ILE* 3.2 17.9 + - + +
138F VAL* 3.1 25.4 + - + +
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Residues in contact with LEU 135 (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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113F LEU* 4.8 10.8 - - + -
127F ILE* 4.1 27.1 - - + +
129F ASN* 3.8 25.4 - - + +
131F ASN 3.2 10.7 + - - +
132F LYS* 3.7 7.9 - - - +
134F LEU* 1.3 79.5 - - + +
136F GLU* 1.3 57.0 + - - +
138F VAL* 3.2 2.4 + - + -
139F SER* 2.8 26.5 + - - -
151F ILE* 3.6 14.8 - - + -
161F TYR* 3.7 39.3 - - + +
162F VAL 4.4 1.1 - - - -
163F LEU* 3.4 32.6 - - + +
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Residues in contact with GLU 136 (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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132F LYS* 2.8 52.0 + - + +
133F ALA* 3.6 15.2 - - - +
134F LEU 3.2 0.2 - - - -
135F LEU* 1.3 78.1 - - - +
137F ILE* 1.3 59.4 + - + +
139F SER* 3.4 3.6 + - - -
140F ARG* 3.2 33.0 + - + +
151F ILE* 3.8 17.9 - - + -
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Residues in contact with ILE 137 (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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98F ILE* 4.3 12.8 - - + -
99F ARG* 3.8 46.7 - - + +
133F ALA* 3.1 19.5 + - + +
134F LEU* 3.2 18.4 + - + +
136F GLU* 1.3 74.2 - - + +
138F VAL* 1.3 66.3 + - + +
140F ARG* 3.2 10.0 + - - +
141F TRP* 3.2 58.1 + - + +
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Residues in contact with VAL 138 (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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109F PHE* 4.1 19.7 - - + -
110F ILE* 4.0 28.3 - - + -
113F LEU* 3.9 24.7 - - + -
127F ILE* 4.7 7.9 - - + -
134F LEU* 3.1 15.4 + - + +
135F LEU* 3.6 7.6 - - - +
137F ILE* 1.3 76.6 - - + +
139F SER* 1.3 58.4 + - - +
141F TRP* 3.3 11.5 + - + +
142F LEU* 2.9 36.9 + - + +
163F LEU* 3.8 17.0 - - + -
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Residues in contact with SER 139 (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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135F LEU 2.8 20.1 + - - -
136F GLU* 3.5 7.2 - - - -
137F ILE 3.2 0.4 - - - -
138F VAL* 1.3 74.0 - - - +
140F ARG* 1.3 58.7 + - - +
142F LEU* 3.4 1.0 + - - -
143F ASN* 2.9 37.0 + - - -
149F ASN* 2.5 35.1 + - - +
151F ILE* 3.9 16.3 - - - +
163F LEU* 4.1 3.8 - - - -
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Residues in contact with ARG 140 (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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136F GLU* 3.2 19.8 + - - +
137F ILE* 3.2 8.5 + - - +
139F SER* 1.3 76.0 - - - +
141F TRP* 1.3 64.4 + - + +
143F ASN* 3.2 10.7 + - - +
144F ASN* 2.9 28.9 + - - +
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Residues in contact with TRP 141 (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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98F ILE* 3.1 45.8 - - + -
99F ARG* 4.2 11.4 + - - +
101F CYS* 4.1 7.2 - - + -
106F GLN* 3.4 61.9 - - + +
109F PHE* 3.9 24.9 - + + -
110F ILE* 4.2 19.7 - - + -
137F ILE* 3.2 34.7 + - + +
138F VAL* 3.7 10.3 - - + +
140F ARG* 1.3 80.3 - - + +
142F LEU* 1.3 61.6 + - - +
144F ASN* 3.2 8.7 + - + +
145F LEU* 3.0 29.6 + - + +
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Residues in contact with LEU 142 (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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110F ILE* 3.7 11.2 - - + -
127F ILE* 5.4 0.9 - - + -
138F VAL* 2.9 31.1 + - + +
139F SER 3.6 4.7 - - - +
141F TRP* 1.3 75.2 - - - +
143F ASN* 1.3 63.7 + - - +
145F LEU* 3.0 7.8 + - + -
147F VAL* 3.0 53.9 + - + +
149F ASN* 3.6 6.1 - - - +
163F LEU* 3.7 29.6 - - + -
165F ILE* 3.9 18.4 - - + -
173F PHE* 4.2 10.1 - - + -
177F ILE* 3.7 27.4 - - + -
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Residues in contact with ASN 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F SER* 2.9 33.9 + - - +
140F ARG* 3.2 12.0 + - - +
142F LEU* 1.3 74.6 - - - +
144F ASN* 1.3 62.4 + - - +
146F GLY* 3.1 13.0 + - - +
147F VAL 4.1 6.0 - - - +
148F ARG* 4.2 14.0 - - - +
149F ASN* 3.9 13.7 + - - +
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Residues in contact with ASN 144 (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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103F MET* 3.7 27.5 - - - +
106F GLN* 4.7 7.3 + - - +
140F ARG 2.9 12.7 + - - +
141F TRP* 3.2 12.8 + - + +
143F ASN* 1.3 76.3 - - - +
145F LEU* 1.3 59.7 + - - +
146F GLY 3.6 0.7 + - - -
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Residues in contact with LEU 145 (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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103F MET* 3.6 37.5 - - + -
106F GLN* 5.1 8.1 - - + +
107F ILE* 4.3 19.3 - - + -
110F ILE* 4.8 5.2 - - + -
141F TRP* 3.0 23.0 + - + +
142F LEU* 3.0 7.4 + - + +
144F ASN* 1.3 78.2 - - - +
146F GLY* 1.3 60.3 + - - +
147F VAL* 3.4 6.7 - - + -
172F LYS* 3.2 33.2 + - + +
176F THR* 5.0 9.4 - - + -
177F ILE* 3.9 28.0 - - + -
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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