Contacts of the helix formed by residues 127 - 143 (chain C) in PDB entry 1U5T
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 SER 127 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C LEU* 4.6 10.1 - - - +
126C LYS* 1.3 79.6 - - - +
128C LEU* 1.3 71.8 + - - +
129C ASP* 4.0 11.3 + - - +
130C SER* 3.6 20.0 + - - -
131C TRP* 2.8 26.6 + - - +
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Residues in contact with LEU 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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104C LEU* 5.3 17.3 - - + -
122C PHE* 5.2 9.4 - - + -
124C LEU* 4.5 27.4 - - + -
127C SER* 1.3 80.5 + - - +
129C ASP* 1.3 63.4 + - - +
130C SER 2.3 17.9 + - - -
131C TRP* 2.5 17.6 + - + +
132C ALA* 3.2 10.9 + - - +
175C TYR* 4.2 28.7 - - + +
176C CYS* 4.8 7.4 - - + +
179C PRO* 4.7 13.9 - - + -
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Residues in contact with ASP 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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127C SER* 4.0 8.0 + - - +
128C LEU* 1.3 78.6 - - - +
130C SER* 1.3 56.6 + - - +
132C ALA* 4.7 3.3 - - - +
133C SER* 4.6 8.3 + - - -
179C PRO* 4.2 21.5 - - + +
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Residues in contact with SER 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C LYS* 4.5 12.2 - - - +
127C SER* 3.6 28.1 + - - -
128C LEU 2.3 16.2 + - - +
129C ASP* 1.3 70.4 - - - +
131C TRP* 1.3 54.3 + - - -
132C ALA 2.6 17.3 + - - -
133C SER* 2.6 26.8 + - - -
134C LEU* 3.6 2.9 + - - +
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Residues in contact with TRP 131 (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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44C TRP* 3.1 32.1 - + - -
122C PHE* 4.8 8.5 - + - -
123C ILE 4.0 17.0 - - - -
124C LEU* 4.5 3.8 - - + -
125C TRP* 4.1 30.3 - + - -
126C LYS* 3.9 37.6 - - + +
127C SER 2.8 17.5 + - - +
128C LEU* 2.5 15.4 + - + +
130C SER* 1.3 74.1 - - - +
132C ALA* 1.3 58.9 + - - +
134C LEU* 3.8 15.8 + - + +
135C ILE* 3.5 16.9 + - + +
164C GLU* 3.7 24.7 - - + +
165C PHE* 3.9 24.3 - + + +
168C MET* 4.5 15.0 - - + -
176C CYS* 4.8 11.7 - - + +
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Residues in contact with ALA 132 (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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128C LEU 3.2 7.2 + - - +
129C ASP 5.2 2.7 - - - -
130C SER 2.6 6.4 + - - -
131C TRP* 1.3 72.4 - - - +
133C SER* 1.3 50.3 + - - +
134C LEU 2.3 19.5 + - - -
135C ILE* 2.4 23.7 + - - -
136C LEU* 2.7 15.5 + - - -
176C CYS 3.1 26.6 + - - +
179C PRO* 4.7 4.7 - - + -
180C LEU* 3.5 28.7 - - + +
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Residues in contact with SER 133 (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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129C ASP 4.6 4.9 + - - -
130C SER* 2.6 25.0 + - - +
132C ALA* 1.3 72.8 - - - +
134C LEU* 1.3 54.5 + - - -
136C LEU* 4.2 19.1 - - - +
137C GLN* 3.0 32.5 + - - +
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Residues in contact with LEU 134 (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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126C LYS* 4.6 23.6 - - + +
130C SER 3.6 2.5 + - - +
131C TRP* 4.0 17.3 - - + +
132C ALA 2.3 16.4 + - - -
133C SER* 1.3 69.8 - - - +
135C ILE* 1.3 68.6 + - - +
137C GLN* 3.7 27.6 - - - +
138C TRP 3.0 2.4 + - - -
162C ASN 5.1 2.0 - - - +
163C TRP* 2.8 66.1 - - + -
164C GLU 4.8 3.1 - - - +
165C PHE* 3.2 18.6 - - + -
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Residues in contact with ILE 135 (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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131C TRP* 3.5 17.0 - - + +
132C ALA* 2.4 23.4 + - - +
134C LEU* 1.3 67.1 - - - +
136C LEU* 1.3 54.5 + - - +
138C TRP* 2.2 40.5 + - - +
139C PHE* 3.5 14.9 + - + -
154C LEU* 3.9 22.4 - - + -
165C PHE* 3.2 48.2 - - + -
168C MET* 5.7 1.1 - - + -
173C LEU* 4.2 12.1 - - + -
176C CYS* 5.2 4.7 - - + -
177C LEU* 3.6 28.9 - - + -
180C LEU* 4.1 2.0 - - + -
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Residues in contact with LEU 136 (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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132C ALA 2.7 12.6 + - - +
133C SER* 4.2 18.4 - - - +
135C ILE* 1.3 75.2 - - - +
137C GLN* 1.3 53.0 + - + +
138C TRP 2.8 2.1 + - - -
139C PHE* 2.9 15.0 + - + +
140C GLU* 2.7 55.2 + - + +
145C LEU* 6.5 0.7 - - + -
180C LEU* 3.3 34.3 - - + +
199C ILE* 4.9 12.6 - - + -
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Residues in contact with GLN 137 (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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133C SER* 3.0 23.8 + - - +
134C LEU* 3.4 26.5 + - - +
135C ILE 3.1 1.0 - - - -
136C LEU* 1.3 76.9 - - + +
138C TRP* 1.3 54.2 + - - +
140C GLU* 3.5 17.7 - - + -
141C ASP* 3.1 34.0 - - + +
163C TRP* 2.8 26.7 - - + -
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Residues in contact with TRP 138 (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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134C LEU 3.0 3.1 + - - +
135C ILE 2.2 40.4 + - - +
137C GLN* 1.3 70.6 - - - +
139C PHE* 1.3 90.6 + + + +
141C ASP* 3.7 2.8 - - - +
142C SER* 2.6 46.2 + - - -
144C LYS* 4.4 24.5 - - + -
154C LEU* 5.3 4.2 - - + +
159C GLU* 3.3 56.1 + - + +
161C VAL* 5.5 0.9 - - + -
163C TRP* 3.2 33.6 - + - -
165C PHE* 3.4 28.0 - + + -
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Residues in contact with PHE 139 (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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135C ILE* 4.2 22.2 - - + -
136C LEU* 3.3 13.0 - - + +
138C TRP* 1.3 108.8 - + + +
140C GLU* 1.3 62.4 + - - +
142C SER* 2.8 1.3 + - - -
143C GLY* 2.4 39.3 + - - +
144C LYS* 4.7 11.0 - - + +
145C LEU* 4.4 21.3 - - + +
149C ILE* 4.7 14.8 - - + -
154C LEU* 4.6 19.7 - - + -
177C LEU* 5.7 2.5 - - + -
180C LEU* 5.8 1.1 - - + -
199C ILE* 3.3 48.0 - - + -
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Residues in contact with GLU 140 (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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136C LEU* 2.7 31.7 + - + +
137C GLN* 3.5 23.6 - - + -
139C PHE* 1.3 76.1 - - - +
141C ASP* 1.3 54.8 + - - +
142C SER 2.7 14.7 + - - +
143C GLY* 3.5 3.5 + - - -
145C LEU* 5.0 16.6 - - - +
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Residues in contact with ASP 141 (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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137C GLN* 3.1 41.3 + - - +
138C TRP 3.7 3.8 - - - +
139C PHE 3.3 0.4 - - - -
140C GLU* 1.3 77.2 - - - +
142C SER* 1.3 59.7 + - - +
163C TRP* 4.0 14.7 - - + -
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Residues in contact with SER 142 (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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138C TRP* 2.6 44.1 + - - -
139C PHE 2.8 5.0 + - - -
140C GLU 2.7 6.9 + - - +
141C ASP* 1.3 75.9 + - - +
143C GLY* 1.3 58.1 + - - -
144C LYS* 3.8 15.8 - - - -
163C TRP* 5.9 0.7 - - - -
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Residues in contact with GLY 143 (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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139C PHE 2.4 22.7 + - - -
140C GLU 4.1 3.1 - - - -
142C SER* 1.3 70.8 - - - +
144C LYS* 1.3 50.8 + - - +
145C LEU* 2.3 43.1 + - - +
146C ASN* 4.2 4.5 + - - -
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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