Contacts of the helix formed by residues 146 - 159 (chain A) in PDB entry 3L6D
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 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ASN* 4.4 8.3 - - - +
121A HIS* 3.1 29.1 + - - +
122A TYR 2.9 25.6 + - - +
123A VAL* 3.8 2.6 - - - +
144A THR 3.8 1.8 + - - -
145A GLY* 1.3 68.9 - - - +
147A ARG* 1.3 57.5 + - - +
148A GLU* 3.4 12.3 + - - +
149A ALA* 2.9 38.6 + - + +
150A PHE* 2.9 28.2 + - - +
166A PHE* 3.8 1.8 - - - -
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Residues in contact with ARG 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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145A GLY 3.4 5.6 + - - +
146A ASP* 1.3 73.7 + - - +
148A GLU* 1.3 58.0 + - - +
150A PHE* 3.3 3.1 + - - +
151A GLU* 2.9 42.7 + - + +
166A PHE* 3.5 56.6 + - + +
168A PRO* 4.3 19.0 - - - +
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Residues in contact with GLU 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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121A HIS* 5.9 3.6 - - - +
146A ASP* 3.4 8.5 - - - +
147A ARG* 1.3 78.3 - - - +
149A ALA* 1.3 58.4 + - - +
151A GLU* 3.3 6.4 + - - +
152A GLN* 3.0 32.8 + - - +
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Residues in contact with ALA 149 (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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96A THR* 3.5 28.3 - - + +
121A HIS* 3.6 22.0 - - + +
123A VAL* 4.1 2.9 - - + -
146A ASP* 2.9 23.5 + - + +
148A GLU* 1.3 73.1 - - - +
150A PHE* 1.3 67.3 + - - +
152A GLN* 3.3 10.1 + - - +
153A HIS* 3.0 31.1 + - - +
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Residues in contact with PHE 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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123A VAL* 3.8 13.5 - - + +
143A HIS* 3.6 39.9 - + + -
146A ASP 2.9 14.8 + - - +
147A ARG* 3.5 7.6 - - + +
149A ALA* 1.3 75.9 - - - +
151A GLU* 1.3 82.9 + - - +
153A HIS* 3.0 5.0 + - - -
154A ARG* 2.8 53.8 + - + -
157A LEU* 4.3 14.1 - - + -
164A THR* 3.6 28.0 - - + -
166A PHE* 3.6 42.6 - + + -
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Residues in contact with GLU 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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147A ARG* 2.9 33.7 + - + +
148A GLU* 3.3 6.9 + - - +
149A ALA 3.2 0.2 - - - -
150A PHE* 1.3 85.9 - - - +
152A GLN* 1.3 63.6 + - - +
153A HIS 3.4 0.3 + - - -
154A ARG* 3.1 55.9 + - - +
166A PHE* 5.0 2.3 - - - +
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Residues in contact with GLN 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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67A PRO* 5.6 1.2 - - - +
96A THR* 5.2 1.5 + - - -
121A HIS* 6.4 0.4 - - - -
148A GLU* 3.0 16.9 + - - +
149A ALA* 3.3 15.3 - - - +
151A GLU* 1.3 80.0 - - - +
153A HIS* 1.3 85.6 + - + +
154A ARG 3.7 0.2 + - - -
155A ALA* 5.0 1.7 + - - +
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Residues in contact with HIS 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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11A ASP 5.8 0.2 + - - -
67A PRO* 3.9 33.6 + - + +
68A ALA* 4.0 14.8 - - + +
96A THR* 3.4 37.5 + - + -
98A VAL* 5.5 1.6 - - + -
149A ALA 3.0 21.2 + - - +
150A PHE 3.0 5.8 + - - +
152A GLN* 1.3 102.6 + - + +
154A ARG* 1.3 65.3 + - - +
155A ALA 3.2 2.7 - - - -
156A LEU* 3.1 24.4 + - + +
157A LEU* 3.0 31.4 + - + +
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Residues in contact with ARG 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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150A PHE* 2.8 40.0 + - + +
151A GLU* 3.1 49.9 + - - +
152A GLN 3.4 0.4 - - - -
153A HIS* 1.3 76.5 - - - +
155A ALA* 1.3 57.8 + - - +
157A LEU* 3.2 6.4 + - - +
158A GLU* 2.9 51.5 + - - +
164A THR* 3.6 30.2 + - + +
165A VAL* 5.4 0.2 - - - +
166A PHE* 5.1 4.9 - - - +
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Residues in contact with ALA 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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33A LYS* 5.1 3.5 + - - -
151A GLU 5.2 0.2 + - - -
152A GLN 5.0 1.7 + - - +
153A HIS 3.2 0.8 - - - -
154A ARG* 1.3 78.6 - - - +
156A LEU* 1.3 64.8 + - - +
158A GLU* 3.4 22.2 + - - +
159A GLY* 3.4 8.0 + - - -
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Residues in contact with LEU 156 (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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11A ASP* 4.0 15.0 - - + +
12A VAL* 4.0 41.1 - - + -
28A LEU* 4.1 16.5 - - + +
33A LYS* 3.9 27.7 - - + +
68A ALA* 4.3 17.0 - - + -
70A ILE* 5.7 1.1 - - + -
153A HIS* 3.1 23.3 + - + +
155A ALA* 1.3 79.9 - - - +
157A LEU* 1.3 68.4 + - + +
159A GLY* 3.0 21.1 + - - -
160A LEU* 4.1 1.6 + - - +
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Residues in contact with LEU 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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70A ILE* 4.6 7.9 - - + -
98A VAL* 3.7 33.9 - - + -
100A TYR* 3.7 14.3 + - - +
123A VAL* 4.7 2.7 - - + -
141A SER* 5.0 4.0 + - - -
143A HIS* 3.6 36.7 - - + +
150A PHE* 4.3 16.4 - - + +
153A HIS* 3.0 24.8 + - + +
154A ARG* 3.2 5.6 + - - +
156A LEU* 1.3 88.7 - - + +
158A GLU* 1.3 56.6 + - - +
160A LEU* 3.0 36.5 + - + +
161A ALA 3.5 4.3 + - - +
164A THR* 5.7 2.9 - - + +
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Residues in contact with GLU 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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137A ARG* 2.9 33.5 + - - +
154A ARG* 2.9 53.2 + - - +
155A ALA* 3.6 15.8 - - - +
156A LEU 3.3 0.2 - - - -
157A LEU* 1.3 70.5 - - - +
159A GLY* 1.3 60.8 + - - +
160A LEU 3.1 1.8 - - - -
161A ALA 3.3 19.9 - - - +
162A GLY 4.2 14.4 - - - +
164A THR* 4.1 15.4 + - + +
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Residues in contact with GLY 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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27A VAL* 3.6 2.3 - - - +
28A LEU* 4.5 1.3 - - - -
31A GLN* 2.8 42.6 + - - -
33A LYS* 4.5 4.9 - - - -
135A GLY* 3.3 13.0 - - - -
137A ARG* 3.4 3.7 + - - -
155A ALA 3.4 6.6 + - - -
156A LEU 3.0 13.9 + - - -
158A GLU* 1.3 76.2 - - - +
160A LEU* 1.3 61.2 + - - +
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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