Contacts of the helix formed by residues 156 - 169 (chain A) in PDB entry 2LNT
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 ASP 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A LEU* 6.3 0.2 - - + -
127A ARG* 4.2 3.8 - - - +
147A ASN* 4.1 3.8 + - - -
148A ARG 4.2 1.2 - - - +
149A LEU 3.7 8.0 - - - +
150A TYR* 3.7 10.5 + - - -
151A ALA* 3.0 48.4 + - + +
152A TYR* 5.1 0.4 - - - -
153A GLU 2.8 10.6 + - - +
155A ALA* 1.3 76.4 - - - +
157A THR* 1.3 54.1 + - - +
158A ALA 3.3 1.1 - - - -
159A LEU* 3.9 16.3 - - - +
160A LEU* 2.7 64.9 + - + +
163A ASN* 4.1 4.5 + - - -
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Residues in contact with THR 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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87A LEU* 4.0 10.3 - - + -
90A VAL* 3.5 39.5 - - + +
91A PHE* 5.4 1.1 - - - +
94A ASN* 3.8 26.0 + - - +
97A ILE* 4.4 4.7 - - + +
154A PRO* 2.6 29.7 + - + +
155A ALA 3.0 1.7 + - - -
156A ASP* 1.3 78.5 - - - +
158A ALA* 1.3 62.7 + - - +
160A LEU* 3.7 13.4 - - + +
161A LEU* 3.6 14.4 + - - +
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Residues in contact with ALA 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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147A ASN* 5.6 4.9 - - - +
155A ALA 3.9 6.1 + - - +
156A ASP 3.3 0.4 - - - -
157A THR* 1.3 77.9 + - - +
159A LEU* 1.3 66.8 + - + +
161A LEU* 3.1 23.5 - - - +
162A ASP* 3.5 5.0 + - - +
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Residues in contact with LEU 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 GLY* 6.3 0.7 - - - -
146A SER* 4.2 21.5 - - - +
147A ASN* 4.7 9.9 - - - +
148A ARG 3.0 28.7 - - - +
149A LEU* 3.7 31.9 - - + +
155A ALA 4.9 0.4 + - - +
156A ASP* 3.7 18.8 - - - +
158A ALA* 1.3 75.2 - - + +
160A LEU* 1.3 57.1 + - - +
161A LEU 2.8 3.1 + - - -
162A ASP* 2.8 11.8 + - + +
163A ASN* 2.6 55.2 + - - +
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Residues in contact with LEU 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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87A LEU* 4.9 12.6 - - + -
91A PHE* 5.2 11.4 - - + -
97A ILE* 4.5 16.4 - - + -
127A ARG* 3.6 28.0 - - + +
128A ILE* 3.7 28.9 - - + -
156A ASP* 2.7 46.6 + - + +
157A THR* 3.7 22.9 - - + +
159A LEU* 1.3 71.4 - - - +
161A LEU* 1.3 56.3 - - - +
163A ASN* 4.0 5.6 - - - +
164A MET* 2.8 32.1 + - - +
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Residues in contact with LEU 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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94A ASN* 5.8 1.1 - - - +
96A GLU* 3.4 52.7 - - + +
97A ILE* 4.9 9.2 - - + +
157A THR 3.6 7.6 + - - +
158A ALA* 3.1 17.3 + - - +
159A LEU 2.8 1.0 + - - -
160A LEU* 1.3 82.7 - - - +
162A ASP* 1.3 63.3 + - + +
164A MET* 3.2 16.7 + - + +
165A LYS* 3.3 32.6 - - + +
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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 ALA 3.5 4.9 + - - +
159A LEU* 2.8 15.9 + - + +
161A LEU* 1.3 79.9 - - + +
163A ASN* 1.3 69.2 + - - +
165A LYS* 3.2 13.8 + - - +
166A LYS* 3.1 22.2 + - - +
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Residues in contact with ASN 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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128A ILE* 5.4 8.2 - - + +
141A ILE* 3.8 27.6 - - + +
142A THR 5.3 1.4 - - - +
149A LEU* 4.3 12.4 + - - +
150A TYR* 5.7 4.3 - - - -
156A ASP* 4.1 7.5 + - - -
159A LEU* 2.6 52.8 + - - +
160A LEU* 3.8 9.8 - - + +
162A ASP* 1.3 77.8 - - - +
164A MET* 1.3 56.0 + - - +
166A LYS* 3.2 5.6 + - - +
167A ALA* 2.7 38.8 + - - +
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Residues in contact with MET 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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73A MET* 3.5 29.9 - - + +
75A ILE* 5.7 1.6 - - + -
91A PHE* 5.6 1.1 - - + -
96A GLU 4.6 0.9 - - - +
97A ILE* 3.2 55.9 - - + +
100A LEU* 3.5 31.5 - - + +
101A ALA* 3.8 13.9 - - + -
128A ILE* 5.3 9.4 - - + +
160A LEU 2.8 21.0 + - - +
161A LEU* 3.2 10.1 + - + +
163A ASN* 1.3 76.0 - - - +
165A LYS* 1.3 60.6 + - + +
167A ALA* 4.4 4.5 - - - -
168A LEU* 3.0 30.5 + - - +
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Residues in contact with LYS 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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96A GLU* 5.0 5.7 + - - +
100A LEU* 3.8 29.9 - - + +
161A LEU* 3.3 33.9 - - + +
162A ASP* 3.3 13.9 - - - +
163A ASN 3.1 0.4 - - - -
164A MET* 1.3 77.8 - - + +
166A LYS* 1.3 60.4 + - - +
168A LEU* 3.2 5.2 + - - +
169A LYS* 2.9 28.1 + - - +
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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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138A ARG* 5.5 1.0 - - - -
140A ASP* 2.7 36.5 + - - +
141A ILE* 3.8 31.2 - - + -
142A THR 5.6 1.8 - - - +
162A ASP* 3.1 12.7 + - - +
163A ASN* 3.8 8.5 - - - +
165A LYS* 1.3 79.4 - - - +
167A ALA* 1.3 62.5 + - - +
169A LYS* 3.4 30.0 + - - +
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Residues in contact with ALA 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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73A MET* 4.7 5.2 - - + -
128A ILE* 5.7 7.9 - - + -
130A PHE* 2.9 47.8 - - + -
138A ARG* 5.1 6.5 - - - +
140A ASP* 5.9 0.4 - - - -
141A ILE* 3.9 19.5 - - + +
163A ASN 2.7 23.3 + - - +
164A MET* 4.1 6.1 - - - +
166A LYS* 1.3 74.5 - - - +
168A LEU* 1.3 58.7 + - - +
169A LYS* 3.6 2.1 + - - +
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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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71A PRO* 4.7 0.7 - - + -
73A MET* 4.0 8.0 - - + +
100A LEU* 4.0 17.9 - - + -
104A PHE* 3.5 42.2 - - + -
130A PHE* 3.5 27.7 - - + -
164A MET 3.0 20.7 + - - +
165A LYS* 3.2 4.9 + - - +
167A ALA* 1.3 75.3 - - - +
169A LYS* 1.3 60.3 + - - +
170A LEU* 2.6 61.9 + - - +
171A LEU* 3.6 15.7 - - + +
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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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130A PHE* 5.7 0.9 - - + -
138A ARG* 4.0 41.1 - - - +
140A ASP* 5.8 0.9 - - - +
165A LYS 2.9 16.4 + - - +
166A LYS* 3.4 27.8 + - - +
167A ALA 3.3 3.1 - - - +
168A LEU* 1.3 76.9 - - - +
170A LEU* 1.3 76.4 + - + +
171A LEU 4.3 0.5 + - - -
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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