Contacts of the helix formed by residues 141 - 152 (chain A) in PDB entry 3JTC
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 SER 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A VAL* 3.9 5.7 + - - -
140A THR* 1.3 81.3 - - - +
142A GLY* 1.3 66.7 + - - +
143A VAL* 3.3 8.2 + - - +
144A VAL* 3.3 29.1 + - - +
145A THR* 3.1 27.1 + - - -
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Residues in contact with GLY 142 (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 ARG* 4.1 17.6 + - - +
141A SER* 1.3 74.7 - - - +
143A VAL* 1.3 57.9 + - - +
145A THR* 3.8 5.1 - - - -
146A PHE* 2.9 33.2 + - - +
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Residues in contact with VAL 143 (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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83A VAL* 4.0 8.9 - - + +
87A ARG* 4.1 19.7 - - + +
88A THR 3.6 24.7 - - - +
89A LEU* 3.7 26.2 - - + -
123A PHE* 4.2 17.7 - - + -
141A SER* 3.1 7.6 + - - +
142A GLY* 1.3 77.6 - - - +
144A VAL* 1.3 57.8 + - - +
146A PHE* 3.9 1.9 - - - +
147A THR* 2.8 39.3 + - - +
606A PTY 4.5 1.8 - - + -
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Residues in contact with VAL 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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123A PHE* 3.4 31.6 - - + -
124A VAL* 4.4 10.3 - - + -
135A ALA* 4.1 15.9 - - + -
137A THR* 4.2 13.9 - - + -
139A VAL 4.3 8.1 - - - +
140A THR* 5.6 0.2 - - - -
141A SER* 3.3 23.7 + - - +
143A VAL* 1.3 76.7 - - + +
145A THR* 1.3 65.4 + - - +
147A THR* 3.3 1.0 + - - -
148A LEU* 2.9 43.8 + - + +
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Residues in contact with THR 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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140A THR* 5.7 2.1 - - - -
141A SER 3.1 18.9 + - - -
142A GLY* 3.8 6.1 - - - -
144A VAL* 1.3 79.5 - - - +
146A PHE* 1.3 58.8 + - - +
148A LEU* 3.4 6.9 + - - +
149A GLN* 2.9 28.9 + - + +
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Residues in contact with PHE 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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82A LEU* 4.2 8.7 - - + -
83A VAL* 3.8 38.1 - - + -
86A GLU* 3.5 34.1 - - + -
87A ARG* 3.6 43.3 - - + +
142A GLY 2.9 18.6 + - - +
143A VAL 3.9 2.0 - - - +
145A THR* 1.3 77.1 - - - +
147A THR* 1.3 66.9 + - - +
149A GLN* 3.1 14.4 + - + +
150A GLN* 2.9 60.5 + - + +
7C CGU 4.6 4.0 - - - -
25C CGU 5.0 1.8 - - + -
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Residues in contact with THR 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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79A LEU* 5.5 1.8 - - + -
83A VAL* 3.6 24.2 - - + +
123A PHE* 3.9 26.4 - - + -
124A VAL* 4.8 4.3 - - + -
143A VAL* 2.8 24.9 + - - +
144A VAL 3.8 3.1 - - - -
146A PHE* 1.3 80.3 - - - +
148A LEU* 1.3 59.5 + - - +
150A GLN* 3.3 4.9 + - - +
151A LEU* 2.9 46.9 + - + +
606A PTY 4.0 24.0 - - + +
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Residues in contact with LEU 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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124A VAL* 3.7 23.8 - - + -
133A TRP* 3.6 39.7 - - + +
134A GLN* 3.7 4.5 - - - -
135A ALA* 3.6 22.4 - - + +
144A VAL* 2.9 34.8 + - + +
145A THR* 3.8 5.6 - - - +
147A THR* 1.3 74.6 - - - +
149A GLN* 1.4 66.4 + - - +
151A LEU* 3.8 3.3 - - + +
152A ASN* 2.9 36.7 + - - +
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Residues in contact with GLN 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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145A THR* 2.9 17.2 + - + +
146A PHE* 3.1 20.0 + - - +
148A LEU* 1.4 76.6 - - - +
150A GLN* 1.3 90.2 + - - +
152A ASN* 3.4 3.7 + - - +
153A ALA* 3.1 33.5 + - - +
154A TYR* 5.0 1.0 + - - -
2C ASN* 5.3 8.0 + - - +
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Residues in contact with GLN 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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79A LEU* 4.3 17.5 - - + +
82A LEU* 3.6 16.5 - - + +
83A VAL* 5.5 0.2 - - + -
146A PHE* 2.9 48.6 + - + +
147A THR* 3.6 8.3 - - - +
149A GLN* 1.3 97.7 + - - +
151A LEU* 1.4 64.5 + - + +
153A ALA 3.0 10.6 + - - -
154A TYR* 2.7 52.4 + - + -
157A THR* 5.7 0.4 - - - -
2C ASN* 4.8 1.2 - - - +
5C LEU 5.5 0.9 + - - -
7C CGU 2.9 25.1 - - - +
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Residues in contact with LEU 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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79A LEU* 3.5 29.6 - - + -
124A VAL* 4.3 10.1 - - + -
133A TRP* 3.4 49.9 - - + -
147A THR* 2.9 39.5 + - + +
148A LEU* 4.0 4.3 - - + +
150A GLN* 1.4 75.6 - - - +
152A ASN* 1.4 60.0 + - - +
153A ALA 3.2 0.2 - - - -
157A THR* 2.8 33.8 + - + -
158A ARG* 3.5 10.7 - - - +
606A PTY 3.9 25.1 - - + -
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Residues in contact with ASN 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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131A ALA 4.5 0.7 - - - +
132A LEU* 3.4 23.3 - - + +
133A TRP* 2.7 53.5 + - - +
148A LEU* 2.9 28.6 + - - +
149A GLN* 3.7 4.5 - - - +
151A LEU* 1.4 74.2 - - - +
153A ALA* 1.3 58.6 + - - +
154A TYR 3.6 0.9 - - - -
158A ARG* 3.5 22.4 + - - +
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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