Contacts of the strand formed by residues 150 - 160 (chain A) in PDB entry 3LON
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 ALA 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ILE* 3.9 31.2 - - + -
94A LEU* 4.0 18.6 - - + +
95A THR 2.9 16.6 + - - +
96A PRO* 3.5 5.7 - - + +
97A CYS* 2.8 24.5 + - - +
142A PRO* 5.4 0.9 - - + -
143A LEU 3.8 5.4 - - - +
144A LEU* 4.1 4.4 - - + +
148A GLY 4.1 0.6 + - - -
149A HIS* 1.3 70.0 - - - +
151A VAL* 1.3 60.6 + - - +
152A GLY 4.8 5.8 - - - +
172A VAL* 3.7 9.6 - - + +
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Residues in contact with VAL 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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97A CYS* 3.8 23.1 - - + -
101A SER 5.2 2.2 - - - +
104A LEU* 3.7 43.3 - - + -
118A ARG* 4.0 24.4 + - - +
143A LEU* 2.8 13.2 + - + +
145A CYS* 3.8 21.5 - - + +
150A ALA* 1.3 73.4 - - - +
152A GLY* 1.3 60.5 + - - +
169A PHE* 4.4 4.7 - - + -
171A PRO* 3.4 6.8 - - - +
172A VAL* 2.8 27.2 + - - +
173A GLU* 4.9 0.7 - - - +
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Residues in contact with GLY 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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142A PRO* 3.5 1.4 - - - +
143A LEU* 2.8 32.3 + - - +
150A ALA* 3.7 3.4 - - - +
151A VAL* 1.3 81.9 + - - +
153A LEU* 1.3 72.0 + - - +
169A PHE* 3.9 11.9 - - - -
170A ILE 3.1 13.2 - - - -
172A VAL* 4.0 4.5 - - - -
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A THR* 4.1 14.4 - - + +
48A ILE* 3.8 24.9 - - + -
53A TRP* 3.6 36.3 - - + -
54A THR* 4.5 4.7 - - - +
55A VAL* 6.4 0.2 - - + -
82A LEU* 4.0 19.7 - - + -
140A GLY* 3.6 18.8 - - - +
141A GLY 3.2 4.5 - - - +
142A PRO* 4.5 2.9 - - + -
150A ALA* 5.6 0.2 - - + -
152A GLY* 1.3 81.3 - - - +
154A PHE* 1.3 65.9 + - - +
155A ARG 3.2 0.7 + - - -
169A PHE* 3.3 3.6 - - - +
170A ILE* 3.0 43.3 + - + +
175A LEU* 4.5 9.2 - - + -
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Residues in contact with PHE 154 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A VAL* 4.4 2.6 - - - +
106A LEU* 3.5 27.6 - - + -
135A LEU* 3.8 32.5 - - + -
138A SER* 3.3 35.7 - - - +
139A SER* 3.4 7.9 - - - -
140A GLY* 2.8 28.2 + - - -
141A GLY 2.7 10.7 + - - +
143A LEU* 3.5 10.0 - - + +
153A LEU* 1.3 69.1 - - - +
155A ARG* 1.3 63.5 + - - +
156A ALA* 3.4 33.0 - - - -
157A ALA* 4.0 4.5 - - + -
167A VAL* 3.6 28.0 - - + -
168A ASP 4.0 5.8 - - - -
169A PHE* 4.3 0.2 - - - -
170A ILE* 5.7 0.2 - - - -
999A NNA 3.8 27.1 - - + -
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Residues in contact with ARG 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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55A VAL* 4.4 3.1 - - + -
57A HIS* 3.4 12.5 - - + -
79A ASP 5.9 0.6 + - - -
80A GLN 4.8 0.4 + - - -
81A ASP* 2.8 38.2 + - - +
139A SER* 3.5 4.4 + - - -
153A LEU 3.2 0.4 + - - -
154A PHE* 1.3 75.6 - - - +
156A ALA* 1.3 59.1 + - - +
168A ASP* 2.8 38.8 + - - +
169A PHE* 4.1 5.6 - - - -
170A ILE* 3.9 24.9 - - + -
999A NNA 3.0 73.3 + - - +
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A PHE* 3.4 11.3 - - - -
155A ARG* 1.3 81.0 - - - +
157A ALA* 1.3 59.7 + - - +
168A ASP* 2.7 38.8 + - + +
999A NNA 3.2 63.3 - - + +
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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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132A ILE* 4.4 3.6 - - + -
135A LEU* 4.5 3.8 - - + -
154A PHE* 4.0 9.0 - - + -
156A ALA* 1.3 73.7 - - - +
158A VAL* 1.3 56.6 + - - +
159A CYS 3.5 1.4 + - - -
164A ALA* 4.2 21.3 - - + -
166A ALA 3.9 4.9 - - - +
999A NNA 2.8 76.0 + - + +
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ARG* 3.5 36.3 - - - +
157A ALA* 1.3 70.5 - - - +
159A CYS* 1.3 59.7 + - - +
164A ALA* 3.6 0.8 - - - -
165A LYS* 3.1 32.5 + - - +
166A ALA* 2.9 37.2 + - + +
167A VAL 3.9 5.8 - - - +
999A NNA 3.5 38.6 - - + +
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Residues in contact with CYS 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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132A ILE* 3.3 33.4 - - + -
158A VAL* 1.3 74.1 - - - +
160A THR* 1.3 66.8 + - - +
162A GLY* 4.7 3.1 - - - -
163A VAL 3.2 11.0 - - - +
164A ALA* 4.1 0.9 - - + -
165A LYS* 3.0 8.1 - - - +
999A NNA 3.1 71.2 + - - +
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Residues in contact with THR 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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158A VAL* 5.6 1.1 - - + -
159A CYS* 1.3 81.4 - - - +
161A ARG* 1.3 81.7 + - - +
162A GLY 3.0 5.5 + - - +
163A VAL* 3.0 15.9 + - - +
165A LYS* 2.8 30.8 + - - +
999A NNA 4.6 8.5 - - + -
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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