Contacts of the helix formed by residues 144 - 164 (chain A) in PDB entry 1L4E
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 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A MET* 1.3 82.6 - - - +
145A ARG* 1.3 65.3 + - - +
146A LEU* 3.4 17.4 + - - +
147A GLN* 3.0 43.0 + - - +
148A ALA 3.1 9.4 + - - -
236A SER* 3.9 1.6 - - - -
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Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A MET 4.1 0.6 + - - -
144A SER* 1.3 72.2 - - - +
146A LEU* 1.3 74.2 + - + +
148A ALA* 3.1 2.6 + - - +
149A GLU* 2.9 46.3 + - - +
230A ASP* 2.9 39.7 + - - -
232A ILE* 3.8 28.7 - - + +
233A ASP* 3.8 18.5 + - - +
236A SER* 4.1 15.5 + - - +
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A SER* 3.7 17.3 - - - +
145A ARG* 1.3 88.0 - - + +
147A GLN* 1.3 58.4 + - + +
149A GLU* 3.5 13.2 + - - +
150A ALA* 3.0 29.7 + - - +
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Residues in contact with GLN 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A VAL* 3.6 39.8 + - + +
131A ALA* 5.2 5.1 - - - +
143A MET* 3.4 17.5 - - + +
144A SER* 3.0 42.0 + - - +
146A LEU* 1.3 74.1 - - + +
148A ALA* 1.3 65.7 + - - +
150A ALA* 3.5 5.8 + - - +
151A LEU* 3.2 23.2 + - - +
241A PHE* 5.0 2.1 - - - -
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A MET* 3.8 22.4 - - - -
144A SER 3.1 4.0 + - - -
145A ARG 3.1 8.4 + - - +
147A GLN* 1.3 78.9 - - - +
149A GLU* 1.3 63.7 + - - +
151A LEU 3.3 1.6 + - - -
152A LEU* 3.0 30.4 + - + +
232A ILE* 4.3 12.1 - - + +
235A LEU* 5.3 2.0 - - + -
236A SER* 3.9 20.2 - - - +
244A VAL* 3.7 16.4 - - + +
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Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.9 31.5 - - + +
145A ARG* 2.9 51.8 + - - +
146A LEU* 4.0 12.6 - - - +
148A ALA* 1.3 75.5 - - - +
150A ALA* 1.3 63.5 + - - +
152A LEU* 3.4 5.5 + - - +
153A LEU* 3.1 23.6 + - - +
232A ILE* 4.0 18.3 - - + +
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU 3.0 18.7 + - - +
147A GLN* 3.9 7.0 - - - +
149A GLU* 1.3 78.3 - - - +
151A LEU* 1.3 61.6 + - - +
153A LEU* 3.4 6.8 + - - +
154A GLU* 3.0 23.8 + - - +
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A VAL* 3.9 18.2 - - + -
128A MET* 3.6 40.2 - - + +
130A VAL* 4.1 22.0 - - + -
143A MET* 6.0 0.9 - - - -
147A GLN 3.2 17.6 + - - +
148A ALA* 4.8 0.2 - - - -
150A ALA* 1.3 73.4 - - - +
152A LEU* 1.3 66.9 + - - +
154A GLU* 3.3 4.7 + - - +
155A VAL* 2.9 38.9 + - + +
241A PHE* 3.5 32.5 - - + +
244A VAL* 3.6 20.4 - - + -
245A GLY 4.1 1.8 - - - +
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.2 14.4 - - + -
7A LEU* 5.5 0.7 - - - -
148A ALA* 3.0 20.3 + - + +
149A GLU* 3.6 8.7 - - - +
151A LEU* 1.3 75.5 - - - +
153A LEU* 1.3 57.0 + - - +
155A VAL* 4.0 0.9 - - - +
156A SER* 2.9 36.3 + - - -
232A ILE* 4.2 32.1 - - + -
235A LEU* 4.9 5.6 - - + -
244A VAL* 3.5 30.5 - - + +
247A THR* 3.9 15.3 - - + -
248A GLY* 3.6 20.2 - - - +
251A LEU* 4.2 15.9 - - + -
277A ILE* 4.5 5.6 - - + -
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR 3.9 13.5 - - - +
4A LEU* 3.4 48.9 - - + +
7A LEU* 4.2 11.7 - - + -
149A GLU 3.1 7.9 + - - +
150A ALA* 3.5 11.4 - - - +
151A LEU 3.2 0.2 - - - -
152A LEU* 1.3 77.2 - - - +
154A GLU* 1.3 67.1 + - - +
156A SER* 3.3 4.7 + - - -
157A ARG* 3.0 26.3 + - + +
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Residues in contact with GLU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ASN 5.5 0.3 - - - +
128A MET* 3.2 45.2 - - + +
150A ALA 3.0 13.7 + - - +
151A LEU* 3.9 5.3 - - - +
153A LEU* 1.3 78.9 - - - +
155A VAL* 1.3 62.7 + - - +
157A ARG* 3.3 6.5 + - - +
158A TYR* 3.0 22.6 + - + +
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 5.3 2.0 - - + -
66A MET* 4.2 18.4 - - + -
113A ILE* 5.6 2.7 - - + -
128A MET* 3.2 25.4 - - + -
151A LEU* 2.9 33.2 + - + +
152A LEU 4.1 1.3 - - - +
154A GLU* 1.3 75.5 - - - +
156A SER* 1.3 59.1 + - - +
158A TYR* 3.3 7.0 + - + +
159A THR* 2.9 35.1 + - - +
245A GLY* 3.4 26.9 - - - +
248A GLY* 4.3 3.4 - - - -
249A VAL* 3.6 24.0 - - + +
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.7 25.1 - - - +
152A LEU 2.9 22.8 + - - -
153A LEU* 3.6 5.4 - - - -
154A GLU 3.3 0.2 - - - -
155A VAL* 1.3 75.2 - - - +
157A ARG* 1.3 62.1 + - - +
159A THR 3.5 0.2 + - - -
160A CYS* 3.1 21.0 + - - +
248A GLY* 3.1 21.2 + - - -
251A LEU* 3.6 12.3 - - - +
252A GLY* 3.5 23.3 + - - -
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.0 23.7 + - + +
154A GLU* 3.6 6.1 - - - +
156A SER* 1.3 75.0 - - - +
158A TYR* 1.3 60.6 + - - +
160A CYS* 3.4 3.8 + - - +
161A ASP* 2.9 32.0 + - - +
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Residues in contact with TYR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 4.3 11.4 - - + -
111A HIS* 3.0 25.8 + - - +
113A ILE* 3.9 26.7 - - + -
126A VAL* 3.7 36.8 - - + +
128A MET* 4.9 8.3 - - - -
154A GLU* 3.0 14.1 + - + +
155A VAL* 3.6 11.4 - - + +
157A ARG* 1.3 75.9 - - - +
159A THR* 1.3 66.0 + - - +
161A ASP* 3.3 9.1 + - + +
162A LEU* 3.2 45.0 + - + +
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Residues in contact with THR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.6 19.2 - - + +
155A VAL* 2.9 21.4 + - - +
156A SER 3.7 5.6 - - - -
157A ARG 3.2 0.2 - - - -
158A TYR* 1.3 79.6 - - - +
160A CYS* 1.3 63.2 + - - +
162A LEU* 3.1 19.9 + - - +
163A ALA 3.5 0.2 + - - -
170A PHE* 3.4 35.8 - - + -
249A VAL* 3.7 34.2 - - + +
252A GLY* 4.1 4.3 - - - -
253A ALA* 3.8 11.9 - - - +
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Residues in contact with CYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A SER 3.1 14.3 + - - +
157A ARG* 4.2 3.4 - - - +
159A THR* 1.3 79.1 - - - +
161A ASP* 1.3 61.9 + - - +
163A ALA* 3.0 19.3 - - - +
164A GLN* 3.7 6.2 + - - +
252A GLY* 3.9 7.4 - - - +
255A ARG* 4.6 11.7 - - + -
256A CYS* 2.0 61.1 - - - -
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Residues in contact with ASP 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ARG 2.9 19.1 + - - +
158A TYR* 3.4 12.1 - - + +
159A THR 3.1 0.2 - - - -
160A CYS* 1.3 78.3 - - - +
162A LEU* 1.3 57.4 + - + +
164A GLN* 2.9 36.6 + - - +
165A ARG* 3.7 2.9 + - - +
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA* 4.6 4.3 - - + -
64A LEU* 4.2 15.0 - - + -
111A HIS* 3.6 33.0 - - + +
158A TYR* 3.2 39.9 + - + +
159A THR 3.1 8.1 + - - +
161A ASP* 1.3 72.2 - - - +
163A ALA* 1.3 58.0 + - - +
165A ARG* 2.6 38.5 + - + +
167A VAL* 3.4 23.6 + - + +
170A PHE* 4.0 20.0 - - + -
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A THR 3.5 3.3 + - - +
160A CYS* 3.0 16.5 + - - +
162A LEU* 1.3 79.0 - - - +
164A GLN* 1.3 59.8 + - + +
166A GLY* 3.2 13.7 + - - -
167A VAL* 3.5 14.2 + - - +
170A PHE* 4.4 1.7 - - + -
256A CYS* 3.3 23.6 - - - -
258A LEU* 3.6 18.8 - - + -
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Residues in contact with GLN 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A CYS 4.5 5.6 - - - +
161A ASP* 2.9 20.9 + - - +
163A ALA* 1.3 78.3 - - + +
165A ARG* 1.3 57.9 + - - +
166A GLY 3.2 1.9 + - - -
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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
------------------------------------------------------------
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