Contacts of the helix formed by residues 145 - 157 (chain A) in PDB entry 3C5C
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 THR 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A TYR* 4.6 0.5 + - - -
142A ARG* 3.8 5.4 - - - -
144A VAL* 1.3 81.6 - - - +
146A LYS* 1.3 65.8 + - - +
147A ALA* 3.4 11.1 + - - +
148A GLU* 2.7 46.6 + - - +
149A GLY* 3.2 15.8 + - - -
162A GLU* 4.1 2.1 - - - +
204A UNX 3.4 15.3 - - - -
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Residues in contact with LYS 146 (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 ARG* 3.5 3.9 - - - +
145A THR* 1.3 72.8 - - - +
147A ALA* 1.4 67.3 + - + +
149A GLY* 3.1 11.4 + - - -
150A VAL* 3.1 19.2 + - + +
160A PHE* 3.6 9.3 - - + -
162A GLU* 3.4 30.3 - - + +
204A UNX 3.2 14.4 - - - -
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Residues in contact with ALA 147 (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 THR* 3.2 9.9 + - - +
146A LYS* 1.4 84.1 - - + +
148A GLU* 1.3 55.6 + - + +
150A VAL* 3.4 10.3 + - - +
151A ALA* 3.0 27.3 + - - +
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Residues in contact with GLU 148 (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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103A ARG* 2.9 33.3 + - - +
106A PHE* 3.5 17.6 - - + -
143A GLN 4.8 0.2 - - - +
144A VAL* 3.8 10.1 - - + -
145A THR* 2.7 49.3 + - - +
146A LYS 3.2 0.2 - - - -
147A ALA* 1.3 74.7 - - + +
149A GLY* 1.3 61.2 + - - +
151A ALA* 3.4 8.1 + - + +
152A LEU 2.9 23.9 + - - -
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Residues in contact with GLY 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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98A TYR* 3.6 22.2 - - - -
106A PHE* 4.0 9.7 - - - -
131A LEU* 3.4 8.3 - - - +
145A THR 3.2 4.8 + - - -
146A LYS 3.1 8.0 + - - -
148A GLU* 1.3 78.6 - - - +
150A VAL* 1.3 57.0 + - - +
152A LEU 3.3 0.5 + - - -
153A ALA* 2.9 28.6 + - - +
160A PHE* 3.6 12.3 - - - -
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Residues in contact with VAL 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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146A LYS* 3.1 17.8 + - + +
147A ALA* 3.5 10.1 - - - +
149A GLY* 1.3 75.4 - - - +
151A ALA* 1.3 51.5 + - - +
153A ALA* 3.5 4.8 + - - +
154A GLY* 2.8 30.7 + - - -
160A PHE* 3.5 25.3 - - + -
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Residues in contact with ALA 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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147A ALA 3.0 14.7 + - - +
148A GLU* 3.6 12.6 - - + +
150A VAL* 1.3 72.2 - - - +
152A LEU* 1.3 65.5 + - - +
154A GLY* 3.1 11.9 + - - +
155A ARG* 3.1 20.2 + - - +
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Residues in contact with LEU 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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106A PHE* 3.5 31.2 - - + +
109A SER* 3.4 25.8 - - - +
110A SER* 3.8 11.0 - - - +
113A LEU* 4.0 8.7 - - + -
131A LEU* 3.9 13.7 - - + -
148A GLU 2.9 17.1 + - - +
149A GLY 3.8 3.4 - - - +
151A ALA* 1.3 75.7 - - - +
153A ALA* 1.3 64.1 + - - +
155A ARG* 3.0 50.6 + - - +
156A PHE* 3.4 35.6 + - + -
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Residues in contact with ALA 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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131A LEU* 3.7 4.9 - - + +
149A GLY 2.9 17.4 + - - +
150A VAL* 3.6 4.3 - - - +
152A LEU* 1.3 74.7 - - - +
154A GLY* 1.3 57.6 + - - +
156A PHE 3.1 1.6 + - - -
157A GLY* 2.8 27.7 + - - -
158A CYS* 3.2 45.8 + - - +
159A LEU 4.0 0.4 - - - +
160A PHE* 3.9 19.5 - - + -
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Residues in contact with GLY 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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150A VAL 2.8 15.2 + - - -
151A ALA* 3.1 7.5 + - - -
153A ALA* 1.3 77.4 - - - +
155A ARG* 1.3 58.0 - - - +
156A PHE 3.6 0.3 + - - -
157A GLY* 3.8 7.4 + - - -
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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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106A PHE* 6.3 0.8 - - - -
110A SER* 4.5 8.5 + - - -
114A GLU* 4.6 9.7 + - - -
151A ALA* 3.1 17.3 + - - +
152A LEU* 3.0 38.3 + - - +
154A GLY* 1.3 75.8 - - - +
156A PHE* 1.3 88.1 + - + +
157A GLY 3.7 0.2 - - - -
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Residues in contact with PHE 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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110A SER* 3.8 7.0 - - - -
113A LEU* 3.6 45.5 - - + -
114A GLU* 3.6 42.2 - - + -
117A ALA* 4.6 11.2 - - + -
152A LEU* 3.4 34.5 - - + +
153A ALA 3.1 4.7 + - - +
155A ARG* 1.3 104.3 - - + +
157A GLY* 1.3 63.5 + - - +
158A CYS* 3.3 6.8 + - + +
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Residues in contact with GLY 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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153A ALA 2.8 9.5 + - - -
154A GLY* 3.8 7.7 + - - -
155A ARG 3.7 1.6 - - - -
156A PHE* 1.3 79.5 - - - +
158A CYS* 1.3 57.6 + - - -
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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