Contacts of the helix formed by residues 153 - 169 (chain A) in PDB entry 1LUA
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 LYS 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A GLY* 4.3 3.3 - - - -
152A ARG* 1.3 85.2 - - + +
154A LEU* 1.3 65.2 + - - +
155A ASP* 3.2 24.0 + - - +
156A LYS* 3.3 11.0 + - + +
157A ALA* 3.1 19.6 + - - +
176A GLU* 3.8 5.6 - - - +
456A NAP 4.9 2.6 + - - -
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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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153A LYS* 1.3 71.2 - - - +
155A ASP* 1.3 57.7 + - - +
157A ALA* 4.2 2.9 - - - -
158A GLN* 2.8 38.4 + - + +
174A ALA* 4.5 10.5 - - + +
175A ALA* 4.2 14.4 - - - +
176A GLU* 2.8 47.5 + - + +
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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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153A LYS* 3.4 29.2 + - - +
154A LEU* 1.3 75.6 - - - +
156A LYS* 1.3 75.2 + - - +
158A GLN* 3.3 5.0 + - - +
159A ALA* 2.9 29.2 + - - +
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Residues in contact with LYS 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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129A THR* 3.8 21.7 - - + +
152A ARG* 4.8 2.0 - - - +
153A LYS* 3.3 11.8 + - + +
155A ASP* 1.3 86.5 + - - +
157A ALA* 1.3 62.7 + - - +
159A ALA* 3.3 7.8 + - + +
160A ALA* 3.0 22.9 + - - +
456A NAP 2.9 46.2 + - - +
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Residues in contact with ALA 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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129A THR* 3.8 13.7 - - + +
149A LEU* 4.0 10.2 - - - +
151A GLY* 4.1 11.0 - - - +
153A LYS 3.1 16.4 + - - +
154A LEU* 3.6 6.1 - - - +
156A LYS* 1.3 78.6 - - - +
158A GLN* 1.3 60.0 + - - +
160A ALA* 3.4 4.0 + - - +
161A ALA* 3.2 17.2 + - - +
174A ALA* 3.5 18.2 - - + +
175A ALA 3.8 22.2 - - - +
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Residues in contact with GLN 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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154A LEU* 2.8 30.1 + - + +
155A ASP* 3.8 5.4 - - - +
157A ALA* 1.3 70.8 - - - +
159A ALA* 1.3 66.4 + - - +
161A ALA* 3.3 9.9 + - - +
162A ASP* 2.9 58.2 + - - +
165A ASN* 5.6 1.0 - - - +
172A VAL 5.3 3.2 + - - -
173A THR* 5.7 1.2 - - - +
174A ALA* 3.7 22.3 + - + +
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Residues in contact with ALA 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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155A ASP 2.9 17.9 + - - +
156A LYS* 3.6 8.3 - - + +
158A GLN* 1.3 76.6 - - - +
160A ALA* 1.3 58.4 + - - +
162A ASP* 3.3 10.1 + - - +
163A SER* 2.9 30.2 + - - -
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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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129A THR* 4.2 9.2 - - + +
134A MET* 3.8 27.7 - - + +
149A LEU* 4.0 22.2 - - + -
156A LYS 3.0 12.8 + - - +
157A ALA 3.6 9.4 - - - +
158A GLN 3.2 0.2 - - - -
159A ALA* 1.3 78.6 - - - +
161A ALA* 1.3 56.6 + - - +
163A SER* 3.3 2.9 + - - -
164A VAL* 3.0 32.6 + - - +
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Residues in contact with ALA 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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149A LEU* 4.3 4.6 - - + +
157A ALA 3.2 11.4 + - - +
158A GLN* 3.3 11.6 + - - +
160A ALA* 1.3 80.0 - - - +
162A ASP* 1.3 54.1 + - - +
164A VAL* 3.7 3.2 - - - +
165A ASN* 2.7 42.1 + - - +
172A VAL* 3.8 39.7 - - + +
173A THR 4.4 0.7 - - - -
174A ALA* 4.3 12.8 - - + -
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Residues in contact with ASP 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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158A GLN* 2.9 50.1 + - - +
159A ALA* 3.5 8.5 - - - +
161A ALA* 1.3 77.1 - - - +
163A SER* 1.3 63.2 + - - +
165A ASN* 3.3 9.6 + - - +
166A LYS* 3.0 25.8 + - - +
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Residues in contact with SER 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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134A MET* 3.7 18.5 - - - +
159A ALA 2.9 18.3 + - - -
160A ALA* 3.5 5.2 - - - -
161A ALA 3.2 0.2 - - - -
162A ASP* 1.3 77.9 - - - +
164A VAL* 1.3 63.3 + - - +
166A LYS* 3.4 4.3 + - - +
167A ARG* 3.1 25.1 + - - +
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Residues in contact with VAL 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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134A MET* 3.6 43.3 - - + +
137A ALA* 4.7 0.4 - - + -
138A ALA* 3.8 33.7 - - + +
149A LEU* 4.7 5.6 - - + -
160A ALA 3.0 21.1 + - - +
161A ALA* 3.7 6.1 - - - +
163A SER* 1.3 75.6 - - - +
165A ASN* 1.3 64.1 + - - +
167A ARG* 4.9 0.9 - - - -
168A PHE* 3.0 32.6 + - + +
170A VAL* 4.0 12.3 - - + +
172A VAL* 4.2 11.0 - - + -
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Residues in contact with ASN 165 (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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158A GLN* 5.6 1.0 - - - +
161A ALA* 2.7 31.5 + - - +
162A ASP* 3.7 11.8 + - - +
163A SER 3.3 0.2 - - - -
164A VAL* 1.3 74.2 - - - +
166A LYS* 1.3 54.9 + - - +
169A LYS* 2.7 34.1 + - - -
170A VAL* 2.8 32.0 + - - +
171A ASN* 4.1 7.9 + - - -
172A VAL* 2.7 46.3 + - - +
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Residues in contact with LYS 166 (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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162A ASP 3.0 17.6 + - - +
163A SER* 3.9 4.5 - - - +
165A ASN* 1.3 77.3 - - - +
167A ARG* 1.3 64.2 + - - +
169A LYS* 3.7 14.3 + - - +
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Residues in contact with ARG 167 (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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74A GLU* 4.8 13.7 + - - +
78A GLU* 5.8 1.4 + - - -
81A LYS* 6.1 0.8 - - - +
135A ARG* 5.1 1.1 - - - +
163A SER* 3.1 16.2 + - - +
164A VAL* 4.9 0.2 - - - -
166A LYS* 1.3 81.4 - - - +
168A PHE* 1.3 92.5 + - + +
169A LYS* 4.7 4.3 - - - +
276A ASP* 3.0 31.5 + - - +
278A GLU* 2.8 40.4 + - - -
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Residues in contact with PHE 168 (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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134A MET 5.4 0.7 - - - -
135A ARG* 3.9 38.6 - - - -
138A ALA* 3.4 33.9 - - + +
139A LEU* 5.7 3.4 - - + -
164A VAL* 3.0 25.9 + - + +
167A ARG* 1.3 118.4 - - + +
169A LYS* 1.3 76.6 + - - +
170A VAL* 3.5 18.2 + - + +
277A ALA* 4.0 11.2 - - + -
278A GLU* 3.6 22.4 - - + -
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Residues in contact with LYS 169 (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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165A ASN 2.7 20.2 + - - -
166A LYS 4.0 12.6 - - - +
167A ARG 4.7 3.1 - - - +
168A PHE* 1.3 78.8 - - - +
170A VAL* 1.3 59.8 + - - +
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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