Contacts of the helix formed by residues 151 - 163 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B ARG* 3.3 48.2 - - - +
104B GLY* 3.5 32.0 - - - -
147B GLY 4.6 1.3 - - - -
148B SER 2.8 7.0 + - - +
149B PHE 3.2 22.4 - - - -
150B GLY* 1.3 87.0 - - - +
152B TYR* 1.3 58.5 + - - +
153B ASP 3.4 2.0 - - - -
154B ILE* 3.4 21.6 + - + -
155B ASP* 2.8 30.8 + - - +
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Residues in contact with TYR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B VAL* 2.6 39.0 + - + +
148B SER* 3.4 19.5 - - - -
149B PHE* 3.6 29.4 - + - -
150B GLY* 3.9 5.1 - - - -
151B TYR* 1.3 77.1 - - - +
153B ASP* 1.3 59.5 + - - +
155B ASP* 3.9 2.6 - - - -
156B ALA* 2.9 31.9 + - - +
169B PHE* 3.8 27.4 - + - -
179B ASN 4.8 1.7 + - - -
183B GLY* 3.6 20.9 - - - -
186B HIS* 3.6 42.8 - + + +
187B MET* 3.7 17.0 - - + +
190B ALA* 4.3 1.8 - - - -
1E NAG 5.1 0.3 - - - +
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Residues in contact with ASP 153 (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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151B TYR 3.4 0.2 - - - -
152B TYR* 1.3 72.1 - - - +
154B ILE* 1.3 62.9 + - + +
156B ALA* 3.5 1.4 + - - +
157B GLN* 2.9 36.5 + - + +
186B HIS* 3.2 19.7 + - - -
190B ALA* 3.6 8.1 - - - +
193B ARG* 2.6 32.6 + - - -
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Residues in contact with ILE 154 (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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103B GLU 4.7 10.1 - - - +
104B GLY* 3.7 23.6 - - - +
105B ARG* 4.4 8.5 - - + -
150B GLY 5.4 1.6 - - - +
151B TYR* 3.4 33.0 + - + +
153B ASP* 1.3 79.4 - - + +
155B ASP* 1.3 57.3 + - - +
157B GLN* 3.3 4.9 + - - +
158B THR* 2.6 44.4 + - - +
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Residues in contact with ASP 155 (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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100B ARG* 2.9 40.1 + - - -
106B LEU* 3.5 19.2 + - + +
148B SER* 2.7 31.5 + - - +
151B TYR* 2.8 20.5 + - - +
152B TYR 4.0 2.0 - - - +
154B ILE* 1.3 73.3 - - - +
156B ALA* 1.3 61.4 + - - +
158B THR* 3.2 6.9 + - - -
159B PHE* 2.9 49.3 + - + -
187B MET* 4.4 4.3 - - + -
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Residues in contact with ALA 156 (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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152B TYR 2.9 19.9 + - - +
153B ASP 3.7 2.9 - - - +
155B ASP* 1.3 76.9 - - - +
157B GLN* 1.3 57.4 + - + +
159B PHE* 3.3 5.4 + - - +
160B ALA* 3.0 28.6 + - - +
187B MET* 4.0 9.1 - - - +
190B ALA* 3.7 36.3 - - + +
191B LEU* 3.9 17.8 - - + +
194B THR* 3.7 4.4 - - + +
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Residues in contact with GLN 157 (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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153B ASP* 2.9 20.9 + - + +
154B ILE* 3.8 4.9 - - - +
156B ALA* 1.3 73.4 - - + +
158B THR* 1.3 59.8 + - - +
160B ALA* 4.6 1.4 - - - +
161B ASP* 2.8 64.5 + - - +
193B ARG* 4.6 3.8 - - - +
194B THR* 3.9 32.4 + - + +
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Residues in contact with THR 158 (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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105B ARG* 4.5 21.1 - - + +
106B LEU* 4.6 8.7 - - + +
154B ILE* 2.6 38.3 + - - +
155B ASP* 3.2 10.7 + - - -
157B GLN* 1.3 73.0 - - - +
159B PHE* 1.3 59.5 + - + +
161B ASP* 3.7 6.0 - - - +
162B TRP* 2.8 75.1 + - + +
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Residues in contact with PHE 159 (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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95B TRP* 4.1 12.3 - + - -
106B LEU* 3.8 25.8 - - + -
133B ILE* 3.9 21.1 - - + -
135B ALA* 4.0 12.8 - - + -
155B ASP* 2.9 27.4 + - + +
156B ALA* 3.7 8.3 - - - +
158B THR* 1.3 78.2 - - + +
160B ALA* 1.3 61.6 + - - +
162B TRP* 3.2 30.1 + + - -
163B GLY 3.0 5.0 + - - -
164B VAL* 2.9 45.1 + - + +
167B LEU* 3.8 27.4 - - + -
187B MET* 3.9 17.9 - - + -
191B LEU* 4.9 1.8 - - + -
198B ILE* 4.9 6.5 - - + -
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Residues in contact with ALA 160 (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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156B ALA 3.0 12.1 + - - +
157B GLN* 3.9 6.5 - - - +
159B PHE* 1.3 75.9 - - - +
161B ASP* 1.3 64.2 + - - +
163B GLY* 3.1 11.4 + - - -
194B THR* 3.5 36.3 - - + +
196B ARG* 3.6 33.0 + - + +
198B ILE* 4.3 6.0 - - + +
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Residues in contact with ASP 161 (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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118B ARG* 3.1 26.3 + - - +
157B GLN* 2.8 48.2 + - - +
158B THR* 3.7 6.2 + - - +
160B ALA* 1.3 76.7 - - - +
162B TRP* 1.3 62.6 + - + +
163B GLY* 3.4 0.9 + - - -
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Residues in contact with TRP 162 (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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95B TRP* 3.7 35.2 - + - -
105B ARG* 6.1 1.3 - - + -
106B LEU* 3.6 21.3 - - + -
107B GLN* 5.2 0.7 - - - -
108B ALA* 4.8 5.2 - - + -
117B ILE* 3.7 34.1 - - + +
118B ARG* 3.8 51.3 - - + +
121B ALA* 3.4 18.9 - - - +
122B ASN* 4.8 2.9 - - - +
133B ILE* 4.1 2.0 - - + -
158B THR* 2.8 38.9 + - + +
159B PHE* 3.5 31.0 - + - +
161B ASP* 1.3 77.9 - - + +
163B GLY* 1.3 56.6 + - - +
164B VAL* 4.4 5.8 - - + -
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Residues in contact with GLY 163 (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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121B ALA* 4.3 4.5 - - - +
125B HIS* 3.1 33.1 + - - -
131B LEU* 4.9 0.5 - - - +
159B PHE 3.0 2.6 + - - -
160B ALA 3.1 13.5 + - - -
161B ASP 3.2 0.8 - - - -
162B TRP* 1.3 78.8 - - - +
164B VAL* 1.3 66.5 + - - +
165B ASP* 3.5 0.9 - - - +
196B ARG* 3.3 18.5 + - - -
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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