Contacts of the helix formed by residues 151 - 163 (chain A) in PDB entry 3LX9
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 TYR 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ARG* 3.4 48.5 - - - +
104A GLY* 3.3 33.2 - - - -
147A GLY 4.6 2.0 - - - -
148A SER 2.8 7.5 + - - +
149A PHE 3.3 17.5 - - - -
150A GLY* 1.3 85.5 - - - +
152A TYR* 1.3 58.7 + - - +
153A ASP 3.4 2.2 - - - -
154A ILE* 3.2 23.4 + - + -
155A ASP* 2.8 32.7 + - - +
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Residues in contact with TYR 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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137A VAL* 2.6 38.9 + - + +
148A SER 3.3 19.4 + - - -
149A PHE* 3.5 21.7 - + - -
150A GLY* 3.8 10.0 - - - -
151A TYR* 1.3 76.5 - - - +
153A ASP* 1.3 59.5 + - - +
156A ALA* 2.9 31.7 + - - +
169A PHE* 3.8 15.3 - + - -
179A ASN 4.7 2.3 + - - -
183A GLY* 3.5 24.3 - - - -
186A HIS* 3.5 41.5 - + + +
187A MET* 3.5 31.0 - - + +
190A ALA* 4.2 2.0 - - - -
639A NAG 5.0 0.3 - - - +
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Residues in contact with ASP 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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151A TYR 3.4 0.4 - - - -
152A TYR* 1.3 75.4 - - - +
154A ILE* 1.3 59.8 + - + +
156A ALA* 3.7 1.0 - - - +
157A GLN* 2.8 47.9 + - - +
186A HIS* 3.3 20.5 + - - -
190A ALA* 3.6 10.4 - - - +
193A ARG* 2.9 30.3 + - - -
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Residues in contact with ILE 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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103A GLU 4.5 11.0 - - - +
104A GLY* 3.6 25.1 - - - +
105A ARG* 4.3 8.1 - - + -
150A GLY 5.3 1.3 - - - +
151A TYR* 3.2 33.0 + - + +
153A ASP* 1.3 77.7 - - + +
155A ASP* 1.3 59.6 + - - +
157A GLN* 3.4 13.7 + - - +
158A THR* 2.6 43.7 + - - +
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Residues in contact with ASP 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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100A ARG* 2.9 39.8 + - - -
106A LEU* 3.6 16.6 + - - +
148A SER* 2.7 30.6 + - - +
151A TYR* 2.8 20.7 + - - +
152A TYR 4.0 1.8 - - - +
154A ILE* 1.3 75.0 - - - +
156A ALA* 1.3 59.0 + - - +
158A THR* 3.5 5.9 + - - -
159A PHE* 2.9 53.5 + - + -
187A MET* 4.2 5.2 - - + -
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Residues in contact with ALA 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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152A TYR 2.9 18.7 + - - +
153A ASP* 3.7 2.7 - - - +
155A ASP* 1.3 76.1 - - - +
157A GLN* 1.3 61.9 + - - +
159A PHE* 3.3 3.7 + - - +
160A ALA* 3.0 24.3 + - - +
187A MET* 3.9 9.5 - - - -
190A ALA* 3.6 37.7 - - + +
191A LEU* 3.8 18.3 - - + +
194A THR* 3.6 4.9 - - + +
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Residues in contact with GLN 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 ASP* 2.8 33.3 + - - +
154A ILE* 3.6 15.4 - - - +
156A ALA* 1.3 73.2 - - + +
158A THR* 1.3 57.6 + - - +
160A ALA* 3.5 2.0 + - - +
161A ASP* 3.0 30.9 + - - +
190A ALA 6.0 0.2 - - - +
194A THR* 4.2 13.0 - - + -
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Residues in contact with THR 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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105A ARG* 4.1 25.0 - - + +
106A LEU* 4.6 7.9 - - + +
154A ILE* 2.6 35.2 + - - +
155A ASP* 3.2 9.9 + - - -
157A GLN* 1.3 76.4 - - - +
159A PHE* 1.3 59.7 + - + +
161A ASP* 3.3 7.5 + - - +
162A TRP* 3.0 68.1 + - + +
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Residues in contact with PHE 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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95A TRP* 4.0 13.9 - + - -
106A LEU* 3.9 23.6 - - + -
133A ILE* 3.9 18.8 - - + -
135A ALA* 4.0 15.3 - - + -
155A ASP* 2.9 34.5 + - + +
156A ALA* 3.8 6.5 - - - +
158A THR* 1.3 78.3 - - - +
160A ALA* 1.3 61.7 + - - +
162A TRP* 3.3 30.9 + + - -
163A GLY 3.1 4.7 + - - -
164A VAL* 2.9 45.7 + - + +
167A LEU* 3.7 36.8 - - + -
187A MET* 5.2 1.8 - - + -
191A LEU* 5.0 2.5 - - + -
198A ILE* 5.0 5.6 - - + -
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Residues in contact with ALA 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 ALA 3.0 13.4 + - - +
157A GLN* 3.7 4.3 - - - +
159A PHE* 1.3 74.9 - - - +
161A ASP* 1.3 64.0 + - - +
163A GLY* 3.1 11.3 + - - -
194A THR* 3.5 37.0 - - + +
196A ARG* 3.6 31.0 + - + +
198A ILE* 4.5 5.9 - - + +
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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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118A ARG* 2.8 49.1 + - - +
157A GLN 3.0 17.7 + - - +
158A THR* 3.6 6.7 - - - +
160A ALA* 1.3 77.8 - - - +
162A TRP* 1.3 65.6 + - - +
163A GLY* 3.3 1.4 + - - -
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Residues in contact with TRP 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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95A TRP* 3.6 36.8 - + - -
105A ARG* 6.2 0.4 - - - -
106A LEU* 3.8 17.9 - - + -
107A GLN* 5.1 0.7 - - - -
108A ALA* 4.8 5.2 - - + -
117A ILE* 3.4 43.4 - - + +
118A ARG* 3.8 48.7 - - + +
121A ALA* 3.3 19.6 - - - +
122A ASN* 4.8 3.1 + - - -
133A ILE* 4.1 2.5 - - + -
158A THR* 3.0 35.5 + - + +
159A PHE* 3.3 33.6 + + - +
161A ASP* 1.3 78.2 + - - +
163A GLY* 1.3 57.5 + - - +
164A VAL* 4.3 3.8 - - + -
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Residues in contact with GLY 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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121A ALA* 4.1 5.2 - - - +
122A ASN* 6.1 0.2 - - - -
125A HIS* 3.0 32.2 + - - -
131A LEU* 4.8 0.7 - - - +
160A ALA 3.1 8.7 + - - -
161A ASP 3.2 1.3 - - - -
162A TRP* 1.3 80.2 - - - +
164A VAL* 1.3 67.2 + - - +
165A ASP* 3.6 0.9 - - - +
196A ARG* 3.2 25.1 + - - -
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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