Contacts of the helix formed by residues 136 - 150 (chain C) in PDB entry 1L3B
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 LEU 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109C SER* 5.3 4.5 - - - +
134C ALA* 4.0 2.5 - - - +
135C ILE* 1.3 87.8 - - + +
137C LEU* 1.3 65.8 + - - +
138C GLU* 4.1 8.5 - - + +
139C THR* 3.5 29.5 + - - +
140C LYS* 3.6 16.5 + - - -
167F LEU* 3.6 29.8 - - + -
169F ARG* 4.0 43.1 - - + +
170F GLY* 4.3 1.8 - - - +
171F THR 3.2 17.5 - - - +
172F MSE 4.0 5.8 - - + -
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Residues in contact with LEU 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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135C ILE 4.0 0.4 + - - -
136C LEU* 1.3 72.6 - - - +
138C GLU* 1.3 67.8 + - - +
140C LYS* 3.0 46.4 + - + +
141C PHE* 3.7 5.9 + - - +
171F THR* 2.7 21.9 + - + +
173F MSE 3.8 30.1 - - + -
137G LEU* 6.4 1.1 - - + -
140G LYS* 5.1 17.5 - - + +
141G PHE* 4.6 7.9 - - + +
144G MSE 4.7 12.3 - - + -
156G ILE* 3.5 36.6 - - + -
158G GLU* 6.0 3.4 - - - +
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Residues in contact with GLU 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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136C LEU* 4.1 4.9 - - + +
137C LEU* 1.3 78.0 + - - +
139C THR* 1.3 64.1 + - - +
141C PHE* 3.3 6.6 + - - +
142C GLU* 3.2 20.8 + - - +
169F ARG 5.6 2.0 - - - +
170F GLY* 3.6 10.5 - - - -
171F THR* 2.7 53.2 + - - +
141G PHE* 3.7 29.8 - - + -
144G MSE 3.5 13.1 - - - +
148G ARG* 4.6 3.6 + - - -
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Residues in contact with THR 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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109C SER* 3.8 20.4 + - - +
113C LEU* 3.9 19.5 - - + +
132C VAL* 4.9 4.7 - - + -
133C THR 4.4 6.1 - - - +
134C ALA* 3.5 24.0 - - + -
135C ILE 5.0 0.4 - - - +
136C LEU* 3.5 30.6 + - - +
137C LEU 3.3 0.4 - - - -
138C GLU* 1.3 75.8 - - - +
140C LYS* 1.3 65.1 + - - +
142C GLU* 3.9 6.0 - - - +
143C ALA* 2.9 22.6 + - + +
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Residues in contact with LYS 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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134C ALA* 3.9 10.0 + - + -
135C ILE 5.4 2.3 + - - -
136C LEU 3.6 15.7 + - - -
137C LEU* 3.0 41.0 + - + +
138C GLU 3.2 0.4 - - - -
139C THR* 1.3 81.1 - - - +
141C PHE* 1.3 63.4 + - - +
143C ALA* 3.3 2.1 + - - +
144C MSE 3.1 28.7 + - - +
156C ILE* 4.1 14.1 - - + -
158C GLU* 2.9 25.5 + - - +
178C PRO* 5.5 1.8 + - - +
180C ALA* 3.5 20.4 - - + -
182C ILE* 3.8 24.6 - - + +
173F MSE 4.8 5.3 - - - +
137G LEU* 4.4 18.3 - - + +
158G GLU* 5.8 0.8 + - - -
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Residues in contact with PHE 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 LEU 3.7 2.5 + - - +
138C GLU 3.3 8.6 + - - +
140C LYS* 1.3 79.3 - - - +
142C GLU* 1.3 60.6 + - + +
144C MSE 3.1 11.0 + - + +
145C GLU* 3.0 52.3 + - + +
137G LEU* 5.1 6.7 - - + +
138G GLU* 3.8 40.4 - - + -
141G PHE* 3.3 60.8 - + + -
142G GLU* 5.2 2.7 - - + -
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Residues in contact with GLU 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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113C LEU* 4.3 19.3 - - + -
114C GLN* 4.4 15.3 + - - +
138C GLU 3.2 11.6 + - - +
139C THR* 4.0 5.4 - - - +
141C PHE* 1.3 80.5 - - + +
143C ALA* 1.3 65.8 + - - +
145C GLU* 3.1 16.7 + - - +
146C CYS* 3.0 56.0 + - - -
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Residues in contact with ALA 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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113C LEU* 4.2 15.0 - - + +
117C LEU* 4.6 6.3 - - - -
132C VAL* 4.5 13.9 - - + -
139C THR 2.9 20.4 + - - +
140C LYS 3.6 4.5 - - - +
142C GLU* 1.3 77.0 - - - +
144C MSE 1.3 61.9 + - - +
147C LEU* 3.3 31.9 + - - +
182C ILE* 3.9 28.7 - - + -
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Residues in contact with MSE 144 (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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171B THR* 3.3 38.4 - - + +
140C LYS 3.1 16.6 - - - +
141C PHE* 3.1 7.7 + - + +
143C ALA* 1.3 76.2 - - - +
145C GLU* 1.3 63.3 + - - +
148C ARG* 3.0 55.1 + - - +
154C VAL* 4.1 21.5 - - + +
155C ASN 4.7 3.8 - - - +
156C ILE* 3.8 30.7 - - + -
182C ILE* 4.2 11.0 - - + -
137G LEU* 3.9 16.6 - - + -
138G GLU* 4.0 5.4 - - + +
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Residues in contact with GLU 145 (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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141C PHE* 3.0 41.8 + - + +
142C GLU* 3.1 20.9 + - - +
144C MSE 1.3 76.6 - - - +
146C CYS* 1.3 52.6 + - - +
148C ARG* 3.1 12.0 + - - +
149C ASP* 2.7 53.8 + - - +
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Residues in contact with CYS 146 (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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113C LEU* 5.6 0.2 - - - -
114C GLN* 3.7 37.0 - - + +
117C LEU* 4.1 19.5 - - + -
118C ARG* 6.2 0.9 - - + -
142C GLU* 3.0 46.5 + - - +
145C GLU* 1.3 73.4 - - - +
147C LEU* 1.3 68.9 + - - +
148C ARG 3.0 1.1 - - - -
149C ASP* 2.9 8.7 + - - -
150C LEU* 2.9 34.0 + - + +
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Residues in contact with LEU 147 (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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117C LEU* 3.7 38.1 - - + -
130C ILE* 4.2 11.9 - - + -
132C VAL* 4.4 10.5 - - + -
143C ALA 3.3 19.0 + - - +
146C CYS* 1.3 79.0 - - - +
148C ARG* 1.3 58.1 + - - +
150C LEU* 3.5 5.9 + - + -
152C PHE* 3.0 40.8 + - + +
154C VAL* 3.1 21.1 - - + -
182C ILE* 3.5 27.1 - - + +
184C THR* 3.8 26.0 - - + +
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Residues in contact with ARG 148 (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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171B THR* 4.7 2.6 + - - -
144C MSE 3.0 53.6 + - - +
145C GLU* 3.1 8.6 + - - +
146C CYS 3.0 0.6 - - - -
147C LEU* 1.3 78.9 - - - +
149C ASP* 1.3 58.8 + - - +
150C LEU 3.1 0.2 - - - -
151C GLY* 2.8 22.7 + - - -
152C PHE 3.9 10.5 + - - +
154C VAL* 3.1 27.4 - - + +
138G GLU* 4.0 12.7 + - - +
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Residues in contact with ASP 149 (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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145C GLU* 2.7 38.9 + - - +
146C CYS* 2.9 9.2 + - - +
148C ARG* 1.3 77.7 - - - +
150C LEU* 1.3 62.6 + - + +
151C GLY 3.1 3.8 + - - -
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Residues in contact with LEU 150 (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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117C LEU* 3.6 37.5 - - + +
118C ARG* 4.0 28.5 - - + +
121C LYS* 2.9 49.4 + - + +
146C CYS* 2.9 26.6 + - + +
147C LEU* 3.5 4.7 + - + -
148C ARG 3.1 0.8 - - - -
149C ASP* 1.3 83.4 - - + +
151C GLY* 1.3 62.1 + - - +
152C PHE* 3.4 18.6 + - + -
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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