Contacts of the helix formed by residues 123 - 135 (chain C) in PDB entry 2J3T
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 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B MET 4.0 7.6 + - - -
111B GLN* 3.2 8.5 - - - -
112B TYR* 3.5 13.3 + - - -
108C PHE 3.8 8.9 + - - -
112C ASN* 4.6 2.5 - - - -
115C CYS* 3.9 17.4 - - - -
121C VAL* 3.6 3.5 - - - +
122C GLN* 1.3 75.4 - - - +
124C GLU* 1.3 61.4 + - - +
125C LEU* 3.4 10.9 + - - +
126C PHE* 3.2 28.1 + - - +
127C ARG* 3.1 24.7 + - - +
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Residues in contact with GLU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ALA* 6.3 0.9 - - + -
110B LEU* 5.7 4.5 + - - +
111B GLN* 2.7 51.7 + - + +
122C GLN 3.1 5.9 + - - +
123C SER* 1.3 71.7 - - - +
125C LEU* 1.3 49.8 + - - +
127C ARG* 3.4 11.7 + - - +
128C SER* 2.8 42.8 + - - +
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LEU 3.3 26.5 - - - +
105B PRO 3.7 7.9 - - - +
106B MET 4.2 6.3 - - - +
107B ALA* 3.8 20.9 - - - +
108B SER* 3.9 16.1 - - - +
111B GLN* 4.5 0.6 + - - -
108C PHE* 3.4 24.0 - - + -
123C SER* 3.2 9.3 + - - +
124C GLU* 1.3 75.6 - - - +
126C PHE* 1.3 67.5 + - - +
128C SER* 2.9 7.3 + - - -
129C ARG* 2.8 73.3 + - - +
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Residues in contact with PHE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 4.5 20.4 - - + -
17C HIS* 3.9 31.4 - + + -
100C ILE* 4.9 1.6 - - + -
104C LEU* 3.1 44.6 - - + -
105C TYR* 3.7 12.1 - + + -
108C PHE* 3.9 19.8 - - + +
109C VAL* 3.7 10.8 - - + -
121C VAL* 3.5 22.9 - - + -
123C SER* 3.2 20.7 + - - +
125C LEU* 1.3 78.2 - - - +
127C ARG* 1.3 65.4 + - + +
129C ARG* 3.5 2.6 + - - +
130C LEU* 2.9 48.3 + - + +
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Residues in contact with ARG 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C HIS* 4.1 26.8 - - + +
120C THR* 5.6 2.9 - - - +
121C VAL 3.0 25.8 + - - -
122C GLN* 3.3 29.5 + - - +
123C SER 3.1 20.1 + - - +
124C GLU* 3.6 11.4 - - - +
125C LEU 3.1 0.4 - - - -
126C PHE* 1.3 86.3 - - + +
128C SER* 1.3 60.8 + - - +
130C LEU* 3.8 5.2 - - - +
131C ASP* 3.2 25.1 + - - +
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Residues in contact with SER 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C GLU* 2.8 29.4 + - - +
125C LEU* 3.4 8.6 - - - -
127C ARG* 1.3 71.6 - - - +
129C ARG* 1.3 65.5 + - - +
131C ASP* 3.4 4.1 + - - +
132C SER* 2.9 32.1 + - - -
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Residues in contact with ARG 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LEU* 6.0 4.2 - - - +
108B SER* 4.6 10.3 + - - -
104C LEU* 3.4 17.9 - - + +
108C PHE* 3.4 32.8 - - + -
125C LEU* 2.8 46.9 + - - +
126C PHE 3.8 2.2 - - - +
128C SER* 1.3 78.3 - - - +
130C LEU* 1.3 57.6 + - - +
132C SER* 3.5 7.5 + - - +
133C TYR* 2.8 30.8 + - - +
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Residues in contact with LEU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 3.8 28.9 - - + -
8C LEU* 5.2 0.2 - - + -
17C HIS* 3.1 42.8 - - + +
19C SER* 4.4 8.1 - - - +
21C TRP* 5.1 1.3 - - + -
100C ILE* 4.2 17.0 - - + -
104C LEU* 3.6 25.0 - - + +
126C PHE* 2.9 32.0 + - + +
127C ARG 3.8 3.8 - - - +
129C ARG* 1.3 73.6 - - - +
131C ASP* 1.3 63.3 + - + +
133C TYR* 2.9 4.2 + - - +
134C VAL* 2.8 35.4 + - + +
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Residues in contact with ASP 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C SER* 4.3 6.1 + - - +
21C TRP* 3.2 30.1 + - - -
127C ARG 3.2 15.9 + - - +
128C SER* 3.7 4.7 - - - +
130C LEU* 1.3 80.7 - - + +
132C SER* 1.3 63.8 + - - +
134C VAL* 3.5 0.9 + - - +
135C ARG* 2.6 67.5 + - - +
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Residues in contact with SER 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C SER 2.9 19.1 + - - -
129C ARG* 3.7 8.0 + - - +
131C ASP* 1.3 80.2 + - - +
133C TYR* 1.3 63.7 + - - +
135C ARG* 3.5 8.5 + - - +
136C SER* 3.1 23.1 + - - -
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Residues in contact with TYR 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C VAL* 3.4 30.4 - - + +
99C HIS* 3.2 37.0 - + - +
100C ILE* 4.0 21.1 - - + -
104C LEU* 3.6 24.0 - - + -
129C ARG 2.8 21.4 + - - +
130C LEU 2.9 3.3 + - - +
132C SER* 1.3 75.7 + - - +
134C VAL* 1.3 63.7 + - + +
136C SER* 2.9 33.4 + - - -
137C LEU* 3.4 32.5 + - + +
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C VAL* 4.0 14.6 - - + -
6C LEU* 4.3 7.6 - - + -
21C TRP* 3.7 39.3 - - + -
84C MET* 4.4 10.5 - - + -
100C ILE* 4.7 0.9 - - + -
130C LEU* 2.8 34.4 + - + +
131C ASP 4.0 0.4 - - - +
133C TYR* 1.3 74.9 - - + +
135C ARG* 1.3 60.0 + - - +
136C SER 2.9 10.1 + - - -
137C LEU* 3.1 29.8 + - + +
140C PHE* 3.5 22.8 - - + +
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Residues in contact with ARG 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP* 4.0 18.8 - - - +
131C ASP* 2.6 45.2 + - - +
132C SER* 3.9 7.6 - - - +
133C TYR 3.3 0.2 - - - -
134C VAL* 1.3 74.0 - - - +
136C SER* 1.3 59.5 + - - +
137C LEU 4.4 0.5 - - - +
140C PHE* 3.6 49.3 - - + +
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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