Contacts of the helix formed by residues 148 - 164 (chain A) in PDB entry 2LBP
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 GLN 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ASP* 2.9 41.2 + - - +
147A LYS* 1.3 91.0 + - - +
149A GLN* 1.3 69.0 + - - +
150A TYR* 4.1 8.7 - - + +
151A GLY 4.5 2.9 - - - +
152A GLU* 2.8 36.7 + - - +
177A ALA* 3.7 11.1 - - - +
202A TYR* 5.5 7.6 - - + -
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Residues in contact with GLN 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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147A LYS 4.1 4.0 + - - +
148A GLN* 1.3 81.2 - - - +
150A TYR* 1.3 66.5 + - - +
152A GLU* 5.0 0.9 - - - -
153A GLY* 2.9 21.5 + - - +
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Residues in contact with TYR 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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121A ASP* 4.0 30.1 - - + -
124A GLN* 4.0 2.5 + - - -
148A GLN* 3.4 3.9 - - + +
149A GLN* 1.3 81.1 - - - +
151A GLY* 1.3 75.0 + - - +
153A GLY* 3.6 0.3 - - - -
154A LEU* 3.0 47.0 + - + +
201A GLY* 3.9 20.2 - - - -
202A TYR* 3.5 45.8 - + + +
225A PRO* 3.7 5.8 - - + +
226A GLU* 3.6 18.2 + - + +
227A GLY* 2.9 24.8 + - - -
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Residues in contact with GLY 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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145A HIS* 3.3 14.7 - - - +
146A ASP* 3.9 9.5 + - - -
148A GLN* 3.8 3.0 + - - +
150A TYR* 1.3 81.4 - - - +
152A GLU* 1.3 56.4 + - - +
154A LEU* 4.8 1.1 - - - -
155A ALA* 3.1 23.4 + - - +
200A GLY* 3.2 33.7 - - - -
201A GLY* 3.6 2.9 - - - -
202A TYR* 5.6 0.2 - - - -
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Residues in contact with GLU 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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145A HIS* 3.4 40.3 + - + +
147A LYS* 3.9 21.0 - - - +
148A GLN 2.8 28.4 + - - +
149A GLN* 4.4 1.1 - - - +
151A GLY* 1.3 71.0 - - - +
153A GLY* 1.3 58.3 + - - +
155A ALA* 3.9 0.9 - - - +
156A ARG* 3.0 54.1 + - - +
172A PHE* 4.8 7.5 - - + -
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Residues in contact with GLY 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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149A GLN 2.9 18.6 + - - -
150A TYR 3.6 0.2 - - - -
152A GLU* 1.3 78.1 - - - +
154A LEU* 1.3 60.5 + - - +
156A ARG* 4.1 18.5 + - - +
157A SER* 3.3 20.8 + - - -
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Residues in contact with LEU 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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121A ASP* 3.1 30.7 - - + +
122A SER* 4.1 6.5 - - - -
124A GLN* 4.0 8.3 - - + +
125A GLY* 3.7 22.9 - - - +
150A TYR* 3.0 56.6 + - + +
151A GLY* 4.4 3.1 - - - +
153A GLY* 1.3 75.1 - - - +
155A ALA* 1.3 59.9 + - - +
157A SER* 3.4 16.6 - - - -
158A VAL* 3.5 15.9 - - - +
198A TYR* 3.8 12.9 - - + +
200A GLY* 5.3 0.9 - - - -
225A PRO* 3.7 17.7 - - + -
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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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143A ILE* 3.7 23.3 - - + +
144A ILE 4.2 5.2 - - - +
145A HIS* 4.0 15.3 - - + -
151A GLY 3.1 19.0 + - - +
152A GLU 3.4 2.9 + - - +
154A LEU* 1.3 73.9 - - - +
156A ARG* 1.3 63.6 + - - +
157A SER 3.1 0.2 - - - -
158A VAL* 3.3 3.6 + - - +
159A GLN* 2.8 29.6 + - - +
172A PHE* 3.9 11.4 - - + -
198A TYR* 4.0 12.5 - - + -
200A GLY 4.9 0.2 - - - +
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Residues in contact with ARG 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 GLU* 3.0 52.5 + - - +
153A GLY* 4.1 15.1 + - - +
155A ALA* 1.3 77.8 - - - +
157A SER* 1.3 53.6 + - - +
159A GLN* 3.2 12.6 + - - +
160A ASP* 2.8 56.5 + - - +
172A PHE* 4.0 15.9 - - + -
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Residues in contact with SER 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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122A SER* 4.5 5.9 + - - -
125A GLY* 4.0 19.2 - - - -
126A PRO* 4.2 11.3 - - - +
129A ALA* 5.3 0.7 - - - +
153A GLY 3.3 12.6 + - - -
154A LEU* 3.4 14.1 - - - -
156A ARG* 1.3 79.3 - - - +
158A VAL* 1.3 56.2 + - - +
160A ASP* 3.2 11.4 - - - +
161A GLY* 3.1 22.9 + - - -
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Residues in contact with VAL 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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125A GLY* 3.2 31.4 - - - +
128A ALA* 4.0 3.6 - - + -
129A ALA* 4.3 6.2 - - - +
132A ILE* 4.2 10.5 - - + -
143A ILE* 3.9 16.4 - - + -
154A LEU 3.5 13.2 - - - +
155A ALA 3.6 7.2 - - - +
157A SER* 1.3 75.0 - - - +
159A GLN* 1.3 58.2 + - - +
160A ASP 3.1 1.3 - - - -
161A GLY 3.7 0.2 - - - -
162A LEU* 2.7 53.3 + - + +
198A TYR* 3.9 36.3 - - + -
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Residues in contact with GLN 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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143A ILE* 3.5 19.5 - - + -
155A ALA 2.8 17.7 + - - +
156A ARG* 3.2 16.8 + - - +
158A VAL* 1.3 76.9 - - - +
160A ASP* 1.3 61.9 + - - +
162A LEU* 3.7 2.4 - - - +
163A LYS* 3.1 29.4 + - + +
169A VAL* 4.9 12.5 - - + +
172A PHE* 2.9 49.1 - - + +
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Residues in contact with ASP 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 ARG* 2.8 37.5 + - - +
157A SER* 3.2 13.3 - - - +
159A GLN* 1.3 80.4 + - - +
161A GLY* 1.3 60.0 + - - +
163A LYS* 4.3 1.4 - - - +
164A ALA* 3.1 31.9 + - - +
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Residues in contact with GLY 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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129A ALA* 4.2 16.6 - - - -
133A LEU* 4.1 3.2 - - - +
157A SER 3.1 11.0 + - - -
158A VAL 3.7 2.2 - - - -
159A GLN 3.4 0.2 - - - -
160A ASP* 1.3 77.0 - - - +
162A LEU* 1.3 57.3 + - - +
164A ALA* 2.4 28.3 - - - +
165A ALA* 3.6 5.4 - - - +
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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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129A ALA* 3.8 28.0 - - - +
132A ILE* 4.1 18.2 - - + -
133A LEU* 3.9 16.8 - - + -
141A ILE* 3.6 39.7 - - + -
143A ILE* 3.7 15.0 - - + -
158A VAL* 2.7 32.1 + - + +
159A GLN* 3.7 6.1 - - - +
161A GLY* 1.3 75.3 - - - +
163A LYS* 1.3 57.3 + - - +
165A ALA* 3.9 5.5 - - - +
167A ALA* 3.0 32.8 + - + +
169A VAL* 4.2 9.6 - - + -
198A TYR* 6.0 0.2 - - + -
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Residues in contact with LYS 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 GLN* 3.1 18.0 + - + +
160A ASP* 4.6 1.3 - - - +
162A LEU* 1.3 71.7 - - - +
164A ALA* 1.3 59.2 + - - +
165A ALA 2.5 3.2 + - - -
166A ASN* 2.4 49.0 + - + +
167A ALA 2.8 27.6 + - - -
168A ASN* 4.7 4.0 - - - +
169A VAL* 5.0 10.8 - - + +
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Residues in contact with ALA 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 ASP 3.1 18.0 + - - +
161A GLY* 2.4 25.8 - - - +
163A LYS* 1.3 76.4 - - - +
165A ALA* 1.3 58.5 + - - +
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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