Contacts of the helix formed by residues 136 - 150 (chain B) in PDB entry 1L3C
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A LEU* 4.8 1.8 - - + -
169A ARG* 3.6 50.9 - - + +
170A GLY* 4.1 4.0 - - - +
171A THR 3.4 14.6 - - - +
172A MSE 3.8 24.7 - - + +
109B SER* 5.6 3.4 - - - +
135B ILE* 1.3 86.9 + - + +
137B LEU* 1.3 65.0 + - - +
138B GLU* 3.2 13.5 - - + +
139B THR* 3.3 28.3 + - - +
140B LYS* 3.4 18.7 + - - +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A THR* 3.2 18.1 + - + +
173A MSE 5.2 10.0 - - + +
135B ILE 4.0 1.0 + - - -
136B LEU* 1.3 72.9 - - - +
138B GLU* 1.3 67.8 + - - +
140B LYS* 3.4 28.7 + - + +
141B PHE* 3.4 12.4 + - + +
137D LEU* 5.0 10.0 - - + +
140D LYS* 4.2 25.1 - - + +
141D PHE* 4.6 12.3 - - + +
144D MSE 3.7 42.8 - - + -
156D ILE* 4.0 22.0 - - + -
158D GLU* 5.8 1.6 - - - +
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ARG 5.4 1.1 - - - +
170A GLY* 3.7 8.8 - - - -
171A THR* 3.3 38.0 + - - -
136B LEU* 3.7 8.2 - - + +
137B LEU* 1.3 85.4 + - + +
139B THR* 1.3 59.1 + - - +
141B PHE* 3.3 1.9 + - - +
142B GLU* 2.8 34.1 + - + +
141D PHE* 3.9 29.9 - - + -
144D MSE 3.8 13.9 - - - +
148D ARG* 4.6 6.4 + - - -
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B SER* 4.0 19.5 + - - +
113B LEU* 3.8 20.2 - - + -
132B VAL* 4.4 11.2 - - + -
133B THR 4.4 3.1 - - - +
134B ALA* 3.8 22.4 - - + -
136B LEU* 3.3 30.9 + - - +
138B GLU* 1.3 74.6 - - - +
140B LYS* 1.3 67.3 + - - +
142B GLU* 4.4 5.8 - - - -
143B ALA* 2.8 24.8 + - - +
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A MSE 4.2 22.2 - - - +
134B ALA* 3.6 21.8 - - + -
135B ILE 4.5 3.4 + - - -
136B LEU 3.4 20.2 + - - +
137B LEU* 3.6 19.8 - - + +
138B GLU 3.3 0.6 - - - -
139B THR* 1.3 77.8 - - - +
141B PHE* 1.3 61.3 + - - +
143B ALA* 4.1 1.0 - - - +
144B MSE 2.9 31.0 + - - +
156B ILE* 4.5 5.6 - - + -
158B GLU* 3.1 34.4 + - - +
178B PRO* 4.9 8.8 + - - +
180B ALA* 3.8 19.7 - - + +
182B ILE* 4.0 13.5 - - + +
137D LEU* 4.5 16.4 - - + -
158D GLU* 5.7 1.2 + - - -
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Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU* 3.4 5.4 + - + +
138B GLU 3.3 5.7 + - - +
139B THR 3.2 0.2 - - - -
140B LYS* 1.3 78.8 - - - +
142B GLU* 1.3 71.2 + - + +
144B MSE 3.3 8.1 + - + +
145B GLU* 3.0 54.2 + - + +
137D LEU* 4.7 11.2 - - + +
138D GLU* 4.0 34.5 - - + -
141D PHE* 3.5 65.5 - + + -
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 3.8 22.0 - - + +
114B GLN* 3.6 25.9 + - - +
138B GLU* 2.8 24.3 + - + +
139B THR* 4.0 2.5 - - - +
141B PHE* 1.3 81.1 - - + +
143B ALA* 1.3 55.9 + - - +
145B GLU* 3.3 18.8 + - - +
146B CYS* 2.9 42.1 + - - +
141D PHE* 6.4 0.2 - - + -
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 3.9 10.9 - - + +
117B LEU* 4.5 6.1 - - - -
132B VAL* 4.0 30.7 - - + -
139B THR 2.8 23.2 + - - +
140B LYS 4.1 2.2 - - - +
142B GLU* 1.3 69.4 - - - +
144B MSE 1.3 67.3 + - - +
146B CYS* 3.9 0.2 - - - +
147B LEU* 3.1 31.0 + - - +
182B ILE* 4.1 18.6 - - + -
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Residues in contact with MSE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LYS 2.9 20.6 + - - +
141B PHE* 3.5 9.2 - - + +
143B ALA* 1.3 78.4 - - - +
145B GLU* 1.3 62.9 + - - +
148B ARG* 3.2 47.6 + - - +
154B VAL* 4.1 28.2 - - - +
155B ASN 4.9 1.1 - - - -
156B ILE* 4.0 28.3 - - + -
182B ILE* 4.2 9.0 - - + -
171C THR* 2.9 37.7 - - + +
137D LEU* 3.7 16.4 - - + -
138D GLU* 4.2 5.2 - - - +
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B PHE* 3.0 43.6 + - + +
142B GLU* 3.6 19.8 - - - +
144B MSE 1.3 78.9 - - - +
146B CYS* 1.3 65.7 + - - +
148B ARG* 3.3 6.8 + - - +
149B ASP* 2.9 45.8 + - - +
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Residues in contact with CYS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLN* 3.7 45.1 - - - -
117B LEU* 3.7 23.1 - - + -
142B GLU* 2.9 36.2 + - - +
143B ALA 3.9 0.2 - - - +
145B GLU* 1.3 72.6 - - - +
147B LEU* 1.3 59.4 + - - +
149B ASP* 2.9 9.6 + - - +
150B LEU* 2.8 36.9 + - + +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 3.7 30.1 - - + -
130B ILE* 4.2 13.2 - - + -
132B VAL* 4.4 15.7 - - + -
143B ALA 3.1 17.8 + - - +
146B CYS* 1.3 78.7 - - - +
148B ARG* 1.3 59.6 + - - +
150B LEU* 3.3 8.5 + - + -
151B GLY 3.4 0.3 + - - -
152B PHE* 3.0 47.9 + - + -
154B VAL* 3.5 18.4 - - + -
182B ILE* 3.8 27.1 - - + +
183B TYR 5.1 0.2 - - - -
184B THR* 4.0 19.3 - - + -
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Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B MSE 3.2 52.1 + - - +
145B GLU* 3.6 6.0 - - - +
146B CYS 3.1 0.4 - - - -
147B LEU* 1.3 77.1 - - - +
149B ASP* 1.3 66.1 + - - +
150B LEU 3.1 0.2 - - - -
151B GLY* 3.0 18.0 + - - -
152B PHE 3.9 12.9 + - - +
154B VAL* 3.7 16.3 + - + +
166C ALA* 5.4 12.9 - - - +
167C LEU 5.8 2.2 + - - -
170C GLY* 6.2 2.2 - - - -
171C THR* 3.8 7.3 + - - -
138D GLU* 5.6 2.4 + - - -
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Residues in contact with ASP 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLU* 2.9 42.5 + - - +
146B CYS* 2.9 8.6 + - - +
148B ARG* 1.3 82.2 - - - +
150B LEU* 1.3 63.0 + - + +
151B GLY 3.2 3.7 + - - -
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLN 5.6 0.2 - - - +
117B LEU* 3.8 39.9 - - + +
118B ARG* 4.0 26.2 - - + +
121B LYS* 2.9 47.5 + - + +
146B CYS* 2.8 22.9 + - + +
147B LEU* 3.8 8.7 - - + +
148B ARG 3.1 0.8 - - - -
149B ASP* 1.3 80.9 - - + +
151B GLY* 1.3 59.5 + - - +
152B PHE* 3.5 17.9 + - + -
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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