Contacts of the helix formed by residues 164 - 175 (chain A) in PDB entry 1LA5
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 GLY 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A TYR 3.4 12.1 - - - -
151A ARG 3.5 7.6 - - - -
152A ALA 3.9 1.3 - - - -
153A GLY* 3.6 7.0 - - - -
162A TRP* 3.1 14.7 - - - +
163A LEU* 1.3 79.4 - - - +
165A ASN* 1.3 61.5 + - - -
166A GLU 3.3 2.7 - - - -
167A ASN* 3.2 7.1 + - - +
168A LEU* 2.8 28.4 + - - +
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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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147A TRP* 4.9 0.6 - - - +
150A TYR* 2.9 26.3 + - - +
151A ARG* 3.1 1.0 + - - +
162A TRP* 3.1 28.1 + - - -
164A GLY* 1.3 69.4 - - - -
166A GLU* 1.3 58.9 + - - +
168A LEU* 3.2 5.6 + - - +
169A HIS* 2.8 30.1 + - - +
200A LEU* 4.1 6.1 - - + +
207A TYR* 2.9 53.4 - - + +
231A PHE* 3.5 35.9 - - - -
254A TRP* 4.8 0.3 - - - -
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Residues in contact with GLU 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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104A SER* 5.3 7.4 + - - +
151A ARG* 2.9 48.9 + - + +
152A ALA* 5.5 2.4 - - - -
164A GLY 3.3 0.6 - - - -
165A ASN* 1.3 77.7 - - - +
167A ASN* 1.3 62.7 + - - +
169A HIS* 3.4 5.9 + - - +
170A GLN* 2.8 37.8 + - + +
203A GLU* 3.3 12.2 - - + +
207A TYR* 3.5 10.5 - - + +
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Residues in contact with ASN 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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104A SER* 2.7 28.9 + - - -
106A TRP* 3.4 3.4 - - - -
117A LEU* 2.9 40.2 - - + +
151A ARG 5.7 0.2 - - - +
152A ALA 4.4 7.4 - - - +
163A LEU* 3.8 32.4 - - + +
164A GLY* 3.2 9.5 + - - +
165A ASN 3.2 0.2 - - - -
166A GLU* 1.3 79.0 - - - +
168A LEU* 1.3 62.4 + - - +
170A GLN* 3.0 3.9 + - - +
171A LEU* 2.7 31.8 + - - +
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Residues in contact with LEU 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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131A LEU* 5.9 2.7 - - + -
133A PHE* 4.0 38.1 - - + -
162A TRP* 5.3 7.4 - - + -
163A LEU* 4.4 7.8 - - + +
164A GLY 2.8 16.7 + - - +
165A ASN* 3.2 8.0 + - - +
167A ASN* 1.3 75.5 - - - +
169A HIS* 1.3 63.3 + - - +
171A LEU* 3.3 4.4 + - + +
172A THR* 2.9 44.4 + - + +
198A PHE* 3.8 18.6 - - + -
200A LEU* 3.0 36.3 - - + -
254A TRP* 6.3 0.2 - - + -
298A LEU* 5.5 4.3 - - + -
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Residues in contact with HIS 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 2.8 15.4 + - - +
166A GLU* 3.5 7.4 - - - +
168A LEU* 1.3 76.8 - - - +
170A GLN* 1.3 86.8 + - - +
172A THR* 3.2 1.8 + - - -
173A LEU* 3.1 50.8 + - + +
200A LEU* 3.0 29.7 + - + +
201A LEU* 3.2 20.8 - - + +
202A GLY* 3.1 37.3 + - - -
207A TYR* 5.0 1.3 - - + -
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Residues in contact with GLN 170 (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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98A SER* 3.9 8.7 + - - +
99A GLN* 4.7 3.0 - - - +
100A GLY* 4.3 16.2 - - - -
103A LEU* 5.1 9.8 - - - +
104A SER* 3.9 12.1 - - - -
106A TRP* 3.0 39.5 - - + -
166A GLU* 2.8 25.3 + - + +
167A ASN 3.0 3.5 + - - +
169A HIS* 1.3 102.1 - - - +
171A LEU* 1.3 64.1 + - - +
173A LEU* 4.0 7.5 - - - +
174A GLN* 3.5 13.7 + - - +
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Residues in contact with LEU 171 (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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78A GLY 4.5 3.1 - - - +
79A ASP* 4.7 3.4 - - + -
96A LEU* 4.2 13.5 - - + -
98A SER* 4.3 5.2 - - - +
106A TRP* 3.6 10.1 - - + -
117A LEU* 3.6 27.4 - - + -
131A LEU* 2.9 46.7 - - + -
163A LEU* 4.7 4.0 - - + -
167A ASN* 2.7 34.5 + - + +
168A LEU* 4.2 4.5 - - + +
170A GLN* 1.3 75.6 - - - +
172A THR* 1.3 65.7 + - + +
174A GLN* 3.0 40.0 + - - +
177A TRP* 3.0 9.3 - - - -
298A LEU* 4.8 6.7 - - + -
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Residues in contact with THR 172 (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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168A LEU* 2.9 46.6 + - + +
169A HIS* 3.2 7.3 + - - -
171A LEU* 1.3 75.3 - - - +
173A LEU* 1.3 56.4 + - - +
175A GLY 2.6 24.3 - - - +
176A ASN* 4.9 0.2 - - - -
177A TRP* 4.0 7.0 - - - -
198A PHE* 3.8 23.0 - - + +
199A ARG* 3.2 36.9 - - - +
200A LEU 3.6 5.4 + - - -
298A LEU* 4.1 10.1 - - + -
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Residues in contact with LEU 173 (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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169A HIS* 3.1 41.6 + - + +
170A GLN* 4.0 7.9 - - - +
172A THR* 1.3 77.4 + - - +
174A GLN* 1.3 65.0 + - - +
175A GLY* 3.2 5.4 + - - +
199A ARG* 3.9 32.3 - - - +
201A LEU* 6.1 2.5 - - + -
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Residues in contact with GLN 174 (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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78A GLY* 3.9 23.0 + - - -
79A ASP* 4.5 5.4 - - - +
98A SER* 3.4 21.6 + - - -
99A GLN* 3.2 43.7 - - + +
170A GLN 3.5 7.3 + - - +
171A LEU* 3.0 29.6 + - - +
173A LEU* 1.3 79.4 - - - +
175A GLY* 1.3 55.5 + - - +
177A TRP* 2.9 34.7 - - + -
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Residues in contact with GLY 175 (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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172A THR 2.6 23.0 - - - +
173A LEU 3.2 2.8 - - - -
174A GLN* 1.3 76.6 - - - +
176A ASN* 1.4 57.2 + - - -
177A TRP* 2.8 27.1 - - - -
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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