Contacts of the helix formed by residues 133 - 148 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131E VAL 4.0 0.8 + - - -
132E ALA* 1.3 71.2 - - - +
134E PHE* 1.3 60.0 + - - +
135E GLU* 3.0 32.4 + - - +
136E CYS* 3.1 12.1 + - + +
137E THR* 2.9 30.8 + - - -
211E LEU 5.2 0.7 - - - +
212E ARG* 3.6 31.4 - - + +
213E ALA 2.9 31.7 + - - +
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Residues in contact with PHE 134 (chain E).
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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111D THR* 4.1 20.7 - - + +
134D PHE* 4.0 14.4 - + - -
137D THR* 3.8 27.6 - - + -
138D THR* 3.8 37.9 - - + -
141D VAL* 3.9 32.1 - - + -
153D VAL* 4.2 15.5 - - + -
132E ALA 3.6 3.3 + - - -
133E ASP* 1.3 76.3 + - - +
135E GLU* 1.3 62.6 + - + +
137E THR* 3.5 3.7 + - - -
138E THR* 2.7 56.5 + - + -
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Residues in contact with GLU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E ASP* 3.0 11.1 + - - +
134E PHE* 1.3 83.4 - - + +
136E CYS* 1.3 58.5 + - - +
138E THR* 3.5 6.9 + - - -
139E ALA* 3.0 28.9 + - - +
212E ARG* 3.2 38.0 + - - +
252E LEU* 3.6 6.9 - - + +
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Residues in contact with CYS 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E THR* 3.8 29.4 - - - -
90E LEU* 4.0 8.3 - - + -
133E ASP* 3.1 10.5 + - - +
134E PHE 3.3 0.2 - - - -
135E GLU* 1.3 74.7 - - - +
137E THR* 1.3 63.6 + - - +
139E ALA* 3.3 3.1 + - - +
140E LEU* 3.0 30.2 + - - +
212E ARG* 3.8 19.3 - - - -
213E ALA 3.7 28.3 - - - +
214E GLY* 3.7 11.0 - - - -
252E LEU* 4.0 15.1 - - - +
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Residues in contact with THR 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D PHE* 3.7 25.8 - - + -
109E VAL* 3.9 18.8 - - + -
110E THR 4.0 7.9 + - - +
111E THR* 4.4 13.2 - - + -
132E ALA* 3.4 22.2 + - - +
133E ASP 2.9 18.7 + - - -
134E PHE* 3.9 5.2 - - - -
136E CYS* 1.3 72.2 - - - +
138E THR* 1.3 65.6 + - - +
140E LEU* 3.3 10.2 + - - +
141E VAL* 3.0 31.3 + - + +
153E VAL* 4.7 0.7 - - + -
214E GLY* 5.1 0.5 - - - -
215E MET 5.8 0.2 + - - -
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Residues in contact with THR 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D PHE* 3.7 19.0 - - + -
138D THR* 5.0 4.4 + - + +
134E PHE* 2.7 46.2 + - + -
135E GLU* 3.6 7.4 - - - -
137E THR* 1.3 76.7 - - - +
139E ALA* 1.3 55.9 + - - +
141E VAL* 3.3 3.5 + - - +
142E GLU* 2.8 55.4 + - - +
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Residues in contact with ALA 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E GLU 3.0 18.8 + - - +
136E CYS 3.7 4.5 - - - +
138E THR* 1.3 76.9 - - - +
140E LEU* 1.3 57.7 + - - +
142E GLU* 4.0 6.4 - - - +
143E ALA* 3.0 29.5 + - - +
248E ALA* 3.6 26.1 - - + +
251E ARG* 4.1 16.4 - - + +
252E LEU* 3.8 15.3 - - + -
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Residues in contact with LEU 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E LEU* 4.3 7.4 - - + -
91E ARG 5.6 0.4 - - - +
109E VAL* 4.0 18.7 - - + +
136E CYS 3.0 21.6 + - - +
137E THR* 3.7 4.9 - - - +
138E THR 3.3 0.2 - - - -
139E ALA* 1.3 75.0 - - - +
141E VAL* 1.3 59.4 + - - +
143E ALA* 3.5 0.4 + - - -
144E ALA* 3.0 28.6 + - - +
214E GLY* 3.9 10.8 - - - -
215E MET 3.6 35.7 - - - +
216E VAL* 3.7 30.3 - - + -
244E ILE* 3.8 9.2 - - + +
245E VAL* 4.2 14.6 - - + -
248E ALA* 3.6 22.0 - - + -
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Residues in contact with VAL 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D PHE* 4.0 27.6 - - + -
109E VAL* 3.9 20.9 - - + -
137E THR* 3.0 21.7 + - + +
138E THR 3.8 3.1 - - - +
140E LEU* 1.3 76.0 - - - +
142E GLU* 1.3 65.2 + - - +
144E ALA* 3.4 7.3 + - - +
145E LYS* 3.3 23.2 + - + +
151E THR* 5.4 3.4 - - + -
153E VAL* 4.0 25.8 - - + -
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Residues in contact with GLU 142 (chain E).
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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138E THR* 2.8 39.8 + - - +
139E ALA* 4.0 5.9 - - - +
141E VAL* 1.3 78.8 - - + +
143E ALA* 1.3 57.2 + - - +
145E LYS* 3.7 4.9 + - - +
146E SER* 3.2 25.3 + - - -
251E ARG* 3.9 24.4 + - - +
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Residues in contact with ALA 143 (chain E).
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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139E ALA 3.0 20.8 + - - +
140E LEU 3.9 3.6 - - - +
141E VAL 3.3 0.2 - - - -
142E GLU* 1.3 74.5 - - - +
144E ALA* 1.3 66.4 + - - +
146E SER* 3.2 8.3 + - - -
147E ILE* 3.2 28.6 + - - +
244E ILE* 3.5 27.6 - - + +
247E GLU* 3.8 14.6 - - + +
248E ALA* 3.7 11.7 - - + +
251E ARG* 4.5 3.6 - - - +
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Residues in contact with ALA 144 (chain E).
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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107E VAL* 4.4 7.4 - - + -
109E VAL* 5.1 0.9 - - + -
140E LEU 3.0 18.6 + - - +
141E VAL 3.6 6.1 - - - +
143E ALA* 1.3 76.7 - - - +
145E LYS* 1.3 59.3 + - - +
147E ILE* 3.5 4.2 - - - +
148E GLY 3.2 16.1 + - - -
149E ALA* 3.3 12.9 + - - +
151E THR* 3.4 34.3 - - + +
244E ILE* 3.9 19.9 - - + +
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Residues in contact with LYS 145 (chain E).
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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141E VAL* 3.3 13.7 + - + +
142E GLU* 4.1 5.8 - - - +
144E ALA* 1.3 77.1 - - - +
146E SER* 1.3 64.5 + - - +
148E GLY* 3.4 13.1 + - - +
149E ALA 5.1 3.4 - - - +
151E THR* 4.9 0.6 + - - -
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Residues in contact with SER 146 (chain E).
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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142E GLU 3.2 19.1 + - - -
143E ALA* 3.2 10.9 + - - -
145E LYS* 1.3 79.1 - - - +
147E ILE* 1.3 63.4 + - - +
247E GLU* 4.9 4.7 - - - +
251E ARG* 3.8 18.6 + - - -
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Residues in contact with ILE 147 (chain E).
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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143E ALA 3.2 10.0 + - - +
144E ALA 3.5 10.3 - - - +
146E SER* 1.3 78.9 - - - +
148E GLY* 1.3 64.7 + - - +
149E ALA* 3.8 7.6 - - + -
240E HIS* 3.5 40.4 - - + +
243E LYS* 4.7 24.7 - - + +
244E ILE* 3.7 25.8 - - + -
247E GLU* 4.9 8.7 - - + -
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Residues in contact with GLY 148 (chain E).
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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144E ALA 3.2 6.5 + - - -
145E LYS* 3.4 9.5 + - - -
146E SER 3.4 3.6 - - - -
147E ILE* 1.3 81.4 - - - +
149E ALA* 1.3 60.0 + - - +
240E HIS* 4.2 9.4 - - - -
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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