Contacts of the helix formed by residues 158 - 167 (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 ARG 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A PHE* 3.4 12.4 - - - -
130A ARG* 2.8 30.5 + - - +
131A ALA* 2.7 27.2 + - + +
132A LEU* 3.5 20.0 - - - +
133A TRP* 5.1 0.9 - - + -
151A LEU 3.5 17.3 - - - +
152A ASN* 3.5 27.4 + - - +
153A ALA 5.1 0.4 - - - -
154A TYR 3.2 18.5 + - - +
157A THR* 1.4 78.0 - - - +
159A TYR* 1.3 97.3 + - + +
160A GLU 3.6 0.4 - - - -
161A LEU* 3.5 0.9 + - - +
162A ARG* 2.9 23.9 + - - +
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Residues in contact with TYR 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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130A ARG 4.4 1.8 + - - -
131A ALA* 4.2 6.3 - - + -
155A ASN* 2.9 31.8 + - + +
158A ARG* 1.3 117.9 + - + +
160A GLU* 1.3 60.8 + - + +
162A ARG* 3.2 37.3 + - - +
163A GLU* 2.8 50.6 + - - +
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Residues in contact with GLU 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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155A ASN* 2.9 18.3 + - + +
156A ARG* 2.8 61.1 + - - +
159A TYR* 1.3 75.9 - - + +
161A LEU* 1.3 57.0 + - - +
163A GLU* 3.3 11.2 + - - +
164A PHE 2.9 24.4 + - - -
606A PTY 3.4 34.4 + - - +
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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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72A TYR* 5.8 0.2 - - + -
114A PHE* 4.1 27.8 - - + -
126A PHE* 3.7 26.9 - - + -
133A TRP* 3.6 35.4 - - + -
156A ARG 3.3 6.2 + - - +
157A THR 3.6 17.9 - - - +
158A ARG 3.5 2.7 + - - +
159A TYR 3.2 0.4 - - - -
160A GLU* 1.3 75.8 - - - +
162A ARG* 1.3 63.9 + - - +
164A PHE* 3.2 6.6 + - + +
165A LEU* 3.2 28.3 + - + +
606A PTY 3.8 46.0 - - + +
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Residues in contact with ARG 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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109A ARG* 5.8 2.9 - - - +
126A PHE* 3.9 15.9 - - + -
128A PRO* 2.9 31.8 + - + -
129A GLU 3.1 19.2 + - - -
130A ARG* 4.1 1.8 - - - +
131A ALA* 3.7 20.4 - - - +
158A ARG 2.9 18.4 + - - +
159A TYR* 3.5 30.4 - - - +
161A LEU* 1.3 74.8 - - - +
163A GLU* 1.3 58.7 + - + +
165A LEU* 3.0 6.1 + - - +
166A GLU* 2.7 61.4 + - + +
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Residues in contact with GLU 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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159A TYR* 2.8 44.0 + - - +
160A GLU* 3.5 11.5 - - - +
162A ARG* 1.3 75.9 + - + +
164A PHE* 1.3 60.7 + - - +
166A GLU* 5.0 0.7 - - - -
167A ASP* 2.9 56.1 + - + +
168A THR* 3.0 3.0 + - - -
606A PTY 3.7 18.9 + - - -
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Residues in contact with PHE 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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13A MET* 3.9 19.1 - - + -
69A LEU* 5.2 4.7 - - + -
99A LEU* 3.9 20.0 - - + -
114A PHE* 6.0 0.4 - + - -
160A GLU 2.9 10.5 + - - +
161A LEU* 3.2 8.7 + - + +
163A GLU* 1.3 73.4 - - - +
165A LEU* 1.3 71.3 + - + +
168A THR* 3.4 17.2 + - + -
169A CYS* 2.8 30.5 + - - +
606A PTY 3.3 113.2 - - + +
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Residues in contact with LEU 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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13A MET* 5.1 1.1 - - + -
99A LEU* 4.0 24.7 - - + -
100A GLY* 4.0 13.2 - - - +
101A CYS* 3.4 14.2 - - - +
112A VAL* 3.5 29.1 - - + +
113A PHE 3.8 26.5 - - - +
114A PHE* 4.2 5.6 - - + -
126A PHE* 4.0 23.8 - - + -
161A LEU* 3.2 22.6 + - + +
162A ARG 3.0 6.7 + - - +
164A PHE* 1.3 88.6 - - + +
166A GLU* 1.3 61.6 + - - +
169A CYS* 3.2 20.1 - - + +
170A VAL* 3.7 1.7 - - - +
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Residues in contact with GLU 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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109A ARG* 2.9 40.1 + - + +
110A ALA* 5.1 7.4 - - + +
112A VAL* 3.9 22.1 - - + +
128A PRO* 3.6 23.7 - - - +
162A ARG* 2.7 42.6 + - + +
163A GLU* 6.2 0.2 - - + -
165A LEU* 1.3 75.6 - - - +
167A ASP* 1.3 68.9 + - - +
170A VAL* 3.2 25.6 - - - +
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Residues in contact with ASP 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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109A ARG* 5.7 1.6 + - - -
163A GLU* 2.9 38.9 + - + +
166A GLU* 1.3 92.0 - - - +
168A THR* 1.3 65.2 + - - +
169A CYS 3.4 0.7 - - - -
170A VAL* 3.9 1.0 - - - +
171A GLN* 3.0 43.9 + - - +
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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