Contacts of the helix formed by residues 139 - 147 (chain A) in PDB entry 3RGZ
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 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A PRO* 2.9 22.5 - - + +
138A VAL* 1.3 76.4 - - + +
140A THR* 1.3 64.0 + - - +
141A LEU 3.1 0.4 - - - -
142A THR* 3.2 22.5 + - - -
143A SER* 4.5 0.3 + - - -
162A PHE* 4.6 17.3 - - + -
163A PRO* 5.4 3.4 - - + -
167A SER 5.4 2.5 - - - +
193A TRP* 3.8 30.5 - - + +
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Residues in contact with THR 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER* 4.6 13.2 - - - -
115A VAL* 3.2 45.2 + - - +
135A SER 4.7 0.7 + - - -
136A GLY 4.7 0.7 - - - -
137A PRO* 2.8 42.4 + - + +
138A VAL 4.2 0.9 + - - -
139A THR* 1.3 79.5 + - - +
141A LEU* 1.3 66.1 + - - +
142A THR 3.1 0.4 - - - -
143A SER* 3.0 22.6 + - - -
160A LEU* 4.4 8.1 - - - +
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Residues in contact with LEU 141 (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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115A VAL* 3.8 26.5 - - + -
134A LEU* 5.9 0.4 - - + -
138A VAL* 3.1 22.9 + - + +
140A THR* 1.3 76.1 + - - +
142A THR* 1.3 64.0 + - - +
143A SER 3.0 0.2 - - - -
144A LEU* 2.9 39.0 + - + +
153A LEU* 4.9 4.7 - - + -
155A VAL* 3.9 16.2 - - + -
160A LEU* 3.8 28.3 - - + -
170A LEU* 3.8 16.6 - - + -
172A LEU* 3.6 9.8 - - + +
180A LEU* 3.7 30.1 - - + -
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Residues in contact with THR 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A THR* 3.2 21.0 + - - -
140A THR 3.1 0.8 - - - -
141A LEU* 1.3 78.8 - - - +
143A SER* 1.3 61.2 + - - +
145A GLY* 3.0 16.8 + - - -
169A GLY 3.8 5.8 + - - +
170A LEU* 3.0 36.2 + - - +
171A LYS* 4.4 20.5 - - + +
172A LEU* 4.2 2.7 - - - +
193A TRP* 4.5 0.9 - - - -
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 4.0 4.6 + - - -
116A SER* 3.5 37.2 - - - -
117A GLY* 3.5 10.2 + - - -
118A PHE* 4.5 3.8 - - - -
139A THR 4.5 0.4 + - - -
140A THR* 3.0 18.1 + - - -
141A LEU 3.0 0.2 - - - -
142A THR* 1.3 74.6 - - - +
144A LEU* 1.3 58.4 + - - +
145A GLY 2.8 11.7 + - - -
146A SER* 3.1 19.8 + - - -
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Residues in contact with LEU 144 (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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88A PHE* 4.5 9.4 - - + -
115A VAL* 4.4 7.6 - - + -
118A PHE* 3.6 30.3 - - + -
127A LEU* 3.9 21.8 - - + -
129A LEU* 5.3 2.7 - - + -
141A LEU* 2.9 33.0 + - + +
143A SER* 1.3 75.1 - - - +
145A GLY* 1.3 55.0 + - - +
146A SER 3.0 2.2 - - - -
147A CYS* 2.9 34.8 + - - +
150A LEU* 4.2 14.6 - - + +
153A LEU* 3.7 38.6 - - + -
155A VAL* 5.3 0.9 - - + -
172A LEU* 3.9 6.8 - - + +
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Residues in contact with GLY 145 (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 THR 3.0 12.9 + - - -
143A SER 2.8 3.6 + - - -
144A LEU* 1.3 77.2 - - - +
146A SER* 1.3 58.5 + - - +
147A CYS 3.1 7.9 + - - +
148A SER* 4.4 4.0 + - - -
171A LYS 5.0 3.6 - - - -
172A LEU* 3.4 16.7 - - - +
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Residues in contact with SER 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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117A GLY* 6.4 0.2 - - - -
118A PHE* 2.9 31.6 + - - -
120A CYS* 3.7 25.6 + - - +
143A SER 3.1 13.8 + - - -
144A LEU 3.0 1.6 - - - -
145A GLY* 1.3 75.7 - - - +
147A CYS* 1.3 59.2 + - - +
148A SER* 3.2 8.2 + - - -
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Residues in contact with CYS 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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96A LEU* 5.4 0.2 - - - -
118A PHE* 4.0 16.4 - - - -
120A CYS* 2.1 47.6 - - - -
121A SER 4.8 2.9 - - - -
124A LEU* 3.9 15.5 - - + +
127A LEU* 5.8 0.2 - - - -
144A LEU* 2.9 23.9 + - - +
145A GLY 4.1 3.4 - - - +
146A SER* 1.3 73.4 - - - +
148A SER* 1.3 65.0 + - - +
149A GLY 3.1 2.7 - - - -
150A LEU* 2.9 33.7 + - + +
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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