Contacts of the helix formed by residues 133 - 148 (chain F) in PDB entry 1U1C
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 ASP 133 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131F VAL 4.0 0.8 + - - -
132F ALA* 1.3 71.4 - - - +
134F PHE* 1.3 60.1 + - - +
135F GLU* 3.0 32.4 + - - +
136F CYS* 3.0 15.9 + - - +
137F THR* 2.8 31.1 + - - -
211F LEU 5.2 0.9 - - - +
212F ARG* 3.5 29.0 - - - +
213F ALA* 2.8 32.5 + - - +
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Residues in contact with PHE 134 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B THR* 4.2 19.3 - - + +
134B PHE* 4.2 12.3 - + - -
137B THR* 3.8 29.2 - - + -
138B THR* 3.8 34.8 - - + -
141B VAL* 4.1 29.6 - - + -
153B VAL* 4.3 13.7 - - + -
132F ALA 3.6 4.1 + - - -
133F ASP* 1.3 75.2 + - - +
135F GLU* 1.3 67.6 + - + +
137F THR* 3.7 4.5 - - - -
138F THR* 2.8 55.3 + - + -
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Residues in contact with GLU 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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133F ASP* 3.0 10.3 + - - +
134F PHE* 1.3 82.6 - - + +
136F CYS* 1.3 60.2 + - - +
138F THR* 3.5 5.9 + - - -
139F ALA* 3.0 29.8 + - - +
212F ARG* 3.0 37.3 + - - +
252F LEU* 3.6 8.6 - - + +
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Residues in contact with CYS 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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88F THR* 3.7 29.2 - - - -
90F LEU* 4.0 7.9 - - + -
133F ASP* 3.0 18.8 + - - +
135F GLU* 1.3 76.9 - - - +
137F THR* 1.3 57.6 + - - +
139F ALA* 3.5 2.6 + - - +
140F LEU* 3.0 35.7 + - - +
212F ARG* 3.8 11.9 - - - -
213F ALA 3.6 29.2 - - - +
214F GLY* 3.7 10.5 - - - -
252F LEU* 3.9 15.6 - - - +
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Residues in contact with THR 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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134B PHE* 3.9 24.9 - - + -
109F VAL* 3.8 19.7 - - + -
110F THR 4.1 7.7 + - - +
111F THR* 4.5 12.0 - - + -
132F ALA* 3.3 22.5 + - - +
133F ASP 2.8 19.1 + - - -
134F PHE* 3.7 6.3 - - - -
136F CYS* 1.3 74.1 - - - +
138F THR* 1.3 59.3 + - - +
140F LEU* 3.3 9.3 + - - +
141F VAL* 2.9 35.5 + - + +
153F VAL* 4.9 0.2 - - + -
214F GLY* 5.2 0.9 - - - -
215F MET 5.6 0.2 + - - -
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Residues in contact with THR 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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134B PHE* 3.7 20.3 - - + -
138B THR* 5.0 2.4 + - + -
134F PHE* 2.8 52.4 + - + -
135F GLU* 3.7 6.7 - - - -
137F THR* 1.3 72.4 - - - +
139F ALA* 1.3 57.2 + - - +
141F VAL* 3.4 1.7 + - - +
142F GLU* 2.9 52.1 + - + +
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Residues in contact with ALA 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 GLU 3.0 19.0 + - - +
136F CYS 3.6 4.5 - - - +
138F THR* 1.3 75.6 - - - +
140F LEU* 1.3 57.2 + - - +
142F GLU* 3.8 5.4 - - - +
143F ALA* 2.8 32.9 + - - +
248F ALA* 3.7 25.7 - - + +
251F ARG* 4.1 15.8 - - + +
252F LEU* 3.8 15.0 - - + -
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Residues in contact with LEU 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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90F LEU* 4.3 6.5 - - + -
91F ARG 5.6 0.2 - - - +
109F VAL* 4.2 15.8 - - + +
136F CYS 3.0 21.1 + - - +
137F THR* 3.3 7.6 + - - +
139F ALA* 1.3 77.2 - - - +
141F VAL* 1.3 57.4 + - - +
144F ALA* 3.0 30.1 + - - +
214F GLY* 3.9 9.2 - - - -
215F MET 3.5 40.2 - - - +
216F VAL* 3.8 27.4 - - + -
244F ILE* 3.6 8.9 - - + +
245F VAL* 4.2 15.3 - - + -
248F ALA* 3.6 22.0 - - + -
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Residues in contact with VAL 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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134B PHE* 4.0 29.2 - - + -
109F VAL* 3.9 16.8 - - + -
137F THR* 2.9 20.4 + - + +
138F THR 3.8 3.8 - - - +
140F LEU* 1.3 74.4 - - - +
142F GLU* 1.3 67.0 + - + +
144F ALA* 3.4 7.7 + - - +
145F LYS* 3.1 22.2 + - + +
151F THR* 5.4 3.0 - - + +
153F VAL* 3.8 31.2 - - + -
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Residues in contact with GLU 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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138F THR* 2.9 38.4 + - + +
139F ALA* 3.9 3.8 - - - +
141F VAL* 1.3 78.5 - - + +
143F ALA* 1.3 63.2 + - - +
145F LYS* 3.3 8.2 + - - +
146F SER* 3.1 25.3 + - - -
251F ARG* 3.0 27.3 + - - +
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Residues in contact with ALA 143 (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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139F ALA 2.8 20.1 + - - +
140F LEU 3.7 4.0 - - - +
142F GLU* 1.3 76.5 - - - +
144F ALA* 1.3 60.6 + - - +
146F SER* 3.5 11.5 + - - -
147F ILE* 3.6 19.4 + - - +
244F ILE* 3.4 29.3 - - + +
247F GLU* 3.8 17.0 - - + +
248F ALA* 3.6 13.7 - - + +
251F ARG* 4.4 4.9 - - - +
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Residues in contact with ALA 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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107F VAL* 4.4 0.9 - - + -
109F VAL* 5.2 1.1 - - + -
140F LEU 3.0 17.7 + - - +
141F VAL 3.7 5.2 - - - +
142F GLU 3.3 0.2 - - - -
143F ALA* 1.3 73.9 - - - +
145F LYS* 1.3 63.8 + - - +
147F ILE* 3.7 2.4 - - - +
148F GLY 3.3 3.3 + - - -
149F ALA* 3.2 26.3 + - - +
151F THR* 3.3 34.5 - - + +
244F ILE* 3.8 27.1 - - + +
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Residues in contact with LYS 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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141F VAL* 3.1 14.4 + - + +
142F GLU* 3.6 11.0 - - - +
143F ALA 3.3 0.4 - - - -
144F ALA* 1.3 74.7 - - - +
146F SER* 1.3 63.5 + - - +
148F GLY* 3.5 11.4 + - - +
149F ALA 5.3 2.0 - - - +
151F THR* 5.6 0.2 - - - -
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Residues in contact with SER 146 (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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142F GLU 3.1 13.9 + - - -
143F ALA* 3.7 11.2 - - - -
144F ALA 3.3 0.2 - - - -
145F LYS* 1.3 78.4 - - - +
147F ILE* 1.3 63.7 + - - +
148F GLY 3.6 0.5 + - - -
247F GLU* 5.1 5.6 - - - -
251F ARG* 3.1 22.5 + - - -
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Residues in contact with ILE 147 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143F ALA 3.6 11.1 + - - +
144F ALA 3.7 10.5 - - - +
146F SER* 1.3 79.1 - - - +
148F GLY* 1.3 61.3 + - - +
149F ALA* 3.8 20.4 - - + +
240F HIS* 3.8 49.5 + - + +
243F LYS* 4.4 26.0 - - + +
244F ILE* 3.8 12.6 - - + -
247F GLU* 5.4 6.3 - - + -
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Residues in contact with GLY 148 (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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144F ALA 3.3 4.2 + - - -
145F LYS* 3.5 10.5 + - - -
146F SER 3.3 4.2 - - - -
147F ILE* 1.3 80.6 - - - +
149F ALA* 1.3 63.0 + - - +
150F THR* 4.0 1.0 + - - -
240F HIS* 5.0 2.6 + - - -
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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