Contacts of the helix formed by residues 120 - 135 (chain F) in PDB entry 4P9U
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 120 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116F ALA 3.2 9.2 + - - +
119F LEU* 1.3 89.7 - - - +
121F LYS* 1.3 53.7 + - - +
122F GLU* 2.8 24.6 - - - +
123F SER* 4.0 11.9 - - - +
124F ALA* 2.9 29.5 + - - +
195F HIS* 3.5 41.7 + - + +
197F GLY* 5.3 3.4 - - - +
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Residues in contact with LYS 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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116F ALA 3.6 3.2 + - - -
117F PHE 3.5 20.6 + - - +
118F LYS 4.8 4.0 - - - +
119F LEU 3.6 5.1 + - - -
120F ASN* 1.3 74.6 - - - +
122F GLU* 1.3 58.3 + - - +
124F ALA 3.4 0.2 + - - -
125F GLU* 2.7 67.0 + - - +
240F CYS* 3.4 38.6 - - - +
241F GLN* 4.0 13.8 - - - +
243F GLY* 5.6 4.3 - - - +
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Residues in contact with GLU 122 (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 LEU 5.0 1.1 - - - +
120F ASN* 2.8 30.2 - - - +
121F LYS* 1.3 75.6 + - - +
123F SER* 1.3 79.7 + - - -
125F GLU* 3.2 16.5 - - - +
126F ARG* 2.9 65.6 + - - +
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Residues in contact with SER 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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120F ASN* 4.0 4.7 - - - +
122F GLU* 1.3 105.9 + - - -
124F ALA* 1.3 59.8 + - - +
126F ARG* 3.3 21.0 + - - +
127F ILE* 2.9 35.5 + - - +
195F HIS* 3.3 32.5 - - - -
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Residues in contact with ALA 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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116F ALA* 3.9 13.9 - - + +
117F PHE* 4.0 15.7 - - + -
120F ASN* 2.9 19.5 + - + +
121F LYS 3.5 4.7 - - - +
122F GLU 3.2 0.2 - - - -
123F SER* 1.3 76.8 - - - +
125F GLU* 1.3 63.8 + - - +
127F ILE* 3.1 6.5 - - - +
128F MET* 2.9 30.0 + - - +
192F LEU* 3.7 25.1 - - + -
195F HIS* 4.8 3.1 - - + -
240F CYS* 4.0 0.9 - - - -
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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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121F LYS* 2.7 53.6 + - - +
122F GLU* 3.2 17.0 - - - +
124F ALA* 1.3 77.1 - - - +
126F ARG* 1.3 57.8 + - + +
128F MET* 3.7 2.8 - - - +
129F ILE* 2.8 39.9 + - + +
237F LEU* 3.6 22.0 - - + -
240F CYS* 4.0 7.5 - - - -
241F GLN* 3.2 27.7 + - - +
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Residues in contact with ARG 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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122F GLU* 2.9 63.5 + - - +
123F SER* 3.2 30.8 + - - +
124F ALA 3.2 0.2 - - - -
125F GLU* 1.3 78.4 - - + +
127F ILE* 1.3 61.6 + - + +
129F ILE* 3.4 9.4 + - - +
130F ASN* 2.9 29.0 + - - +
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Residues in contact with ILE 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 SER* 2.9 21.0 + - - +
124F ALA* 3.1 16.2 - - - +
126F ARG* 1.3 79.4 - - + +
128F MET* 1.3 57.4 + - + +
130F ASN* 3.4 8.3 - - - +
131F VAL* 2.9 33.8 + - + +
187F MET* 5.6 1.4 - - + +
188F LEU* 5.0 2.2 - - - +
191F ARG* 3.6 59.9 - - + +
192F LEU* 3.8 19.1 - - + +
195F HIS* 4.2 18.6 - - + +
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Residues in contact with MET 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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117F PHE* 4.0 28.7 - - - -
124F ALA 2.9 27.6 + - - +
125F GLU* 3.7 5.2 - - - +
127F ILE* 1.3 74.9 - - - +
129F ILE* 1.3 60.6 + - - +
131F VAL* 3.1 7.8 + - - +
132F ILE* 2.9 36.3 + - + +
188F LEU* 4.5 11.4 - - + -
192F LEU* 4.0 21.5 - - + -
233F TYR* 3.2 30.3 - - - +
236F LEU* 3.4 16.4 - - + -
237F LEU* 3.3 30.5 - - + +
240F CYS* 4.8 1.3 - - - -
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Residues in contact with ILE 129 (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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125F GLU* 2.8 31.5 + - + +
126F ARG* 3.7 8.3 - - - +
128F MET* 1.3 74.9 - - - +
130F ASN* 1.3 65.5 + - - +
132F ILE* 3.3 7.8 + - - -
133F GLU* 2.9 51.2 + - + +
237F LEU* 3.7 20.4 - - + -
241F GLN* 4.5 17.0 - - - +
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Residues in contact with ASN 130 (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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126F ARG 2.9 17.9 + - - +
127F ILE* 3.4 10.3 - - - +
129F ILE* 1.3 78.2 - - - +
131F VAL* 1.3 58.9 + - - +
133F GLU* 3.6 5.3 + - - +
134F SER* 2.9 44.9 + - - -
184F TYR* 4.6 3.5 - - - -
187F MET* 4.2 18.9 - - - +
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Residues in contact with VAL 131 (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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127F ILE* 2.9 20.4 + - + +
128F MET 3.1 6.9 + - - +
130F ASN* 1.3 76.8 - - - +
132F ILE* 1.3 58.0 + - - +
134F SER* 3.3 2.9 + - - -
135F CYS* 2.9 28.3 + - - +
184F TYR* 3.8 41.2 - - + +
187F MET* 4.4 18.2 - - + -
188F LEU* 3.8 37.7 - - + +
191F ARG* 6.0 0.4 - - - -
233F TYR* 4.2 17.5 - - + -
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Residues in contact with ILE 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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128F MET* 2.9 27.4 + - + +
129F ILE* 3.8 4.3 - - - +
131F VAL* 1.3 74.2 - - + +
133F GLU* 1.3 60.2 + - + +
135F CYS* 3.1 16.5 + - + +
136F GLU* 2.9 23.1 - - - +
230F MET* 5.0 5.8 - - + +
233F TYR* 3.7 48.0 - - + +
234F ARG* 4.0 42.0 - - + +
237F LEU* 3.9 26.5 - - + -
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Residues in contact with GLU 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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129F ILE* 2.9 40.3 + - + +
130F ASN* 4.2 4.3 - - - +
132F ILE* 1.3 74.2 - - + +
134F SER* 1.3 65.3 + - - +
135F CYS 3.1 1.6 - - - -
136F GLU* 3.3 25.6 + - + +
147F PHE* 4.4 13.3 - - + -
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Residues in contact with SER 134 (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 ASN* 2.9 30.7 + - - -
131F VAL 3.6 1.8 - - - -
133F GLU* 1.3 73.5 - - - +
135F CYS* 1.3 57.4 + - - +
136F GLU 3.0 9.6 + - - -
137F ALA* 4.0 1.9 + - - +
144F TRP* 3.3 30.7 - - - -
147F PHE* 5.0 4.9 - - - -
148F ILE* 5.3 7.6 - - - +
184F TYR* 3.3 41.1 + - - -
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Residues in contact with CYS 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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131F VAL* 2.9 20.4 + - - +
132F ILE* 3.4 9.9 - - - +
133F GLU 3.1 1.2 - - - -
134F SER* 1.3 75.9 - - - +
136F GLU* 1.3 64.5 + - - +
137F ALA* 3.1 10.3 + - - +
138F LEU* 3.4 11.4 - - - +
181F PHE* 3.7 31.2 - - + -
184F TYR* 3.8 26.7 - - - -
230F MET* 3.4 24.8 - - + +
233F TYR* 4.3 13.9 - - - -
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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