Contacts of the helix formed by residues 122 - 134 (chain C) in PDB entry 3TJK
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 PHE 122 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B PHE* 3.6 36.6 - + - -
120C PHE 4.8 1.6 - - - -
121C THR* 1.3 96.6 + - + +
123C VAL* 1.3 67.4 + - - +
124C CYS* 3.3 0.6 - - - -
125C PRO* 3.1 11.1 - - - +
126C THR* 3.7 1.0 - - - +
244D VAL* 3.8 18.2 - - + -
256D ILE* 3.4 15.8 - - + +
258D PRO* 3.4 41.1 - - + -
259D ASP 3.4 28.0 - - - -
260D PRO* 4.0 1.3 - - + -
263D LYS* 3.7 26.0 - - + -
267D PHE* 3.3 20.0 - - - -
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Residues in contact with VAL 123 (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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122C PHE* 1.3 74.4 - - - +
124C CYS* 1.3 64.7 + - - +
126C THR* 2.8 28.0 + - - -
127C GLU* 3.2 11.9 + - + +
200C ARG* 3.4 34.0 - - - +
219C LEU 4.3 2.0 - - - +
220C PRO 4.0 4.9 - - - +
222C GLY* 3.6 20.2 - - - -
244D VAL* 3.4 31.4 - - + -
245D ALA 3.3 31.9 - - - +
246D PRO* 4.2 4.3 - - + -
256D ILE* 4.6 2.2 - - + -
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Residues in contact with CYS 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C TYR* 3.6 19.6 - - + -
117C PRO* 3.6 22.7 - - - -
118C LEU 3.6 18.2 - - - +
121C THR* 3.2 19.1 - - - +
122C PHE 4.8 0.4 - - - -
123C VAL* 1.3 74.9 - - - +
125C PRO* 1.4 67.8 - - + +
127C GLU* 3.4 7.0 + - - +
128C ILE* 3.1 27.2 + - - +
159C TRP* 4.1 4.7 - - + -
200C ARG* 3.4 28.0 - - - +
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Residues in contact with PRO 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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121C THR 3.5 17.9 - - - +
122C PHE 3.1 24.2 - - - +
124C CYS* 1.4 88.5 - - + +
126C THR* 1.3 54.4 + - - -
128C ILE* 3.3 0.5 + - - -
129C ILE* 2.9 36.8 + - + +
159C TRP* 3.6 19.2 - - + -
167C GLY 3.8 14.6 - - - +
168C GLY 4.3 4.7 - - - +
169C LEU* 3.7 18.5 - - + +
267D PHE* 3.5 22.4 - - + -
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Residues in contact with THR 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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122C PHE 3.7 18.6 - - - +
123C VAL 2.8 12.4 + - - -
125C PRO* 1.3 76.0 - - - +
127C GLU* 1.3 56.1 + - - +
129C ILE* 4.0 6.1 - - - +
130C ALA* 2.8 32.2 + - - +
246D PRO* 3.4 10.2 - - + +
247D ALA* 3.0 25.4 + - - +
256D ILE* 3.7 15.3 - - + -
266D TYR* 3.6 28.3 - - + +
267D PHE* 3.9 5.4 - - + -
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Residues in contact with GLU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C PHE* 4.5 11.0 - - + -
116C TYR* 4.4 1.6 - - - +
123C VAL* 3.2 17.1 + - + +
124C CYS* 3.8 7.9 - - - +
126C THR* 1.3 78.2 + - - +
128C ILE* 1.3 66.8 + - - +
130C ALA* 3.7 0.3 - - - +
131C PHE* 3.1 36.5 + - + -
200C ARG* 2.8 26.3 + - - -
222C GLY* 3.3 3.5 - - - -
223C ARG* 2.7 67.4 + - + +
247D ALA* 3.7 23.1 - - + -
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Residues in contact with ILE 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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114C PHE* 4.1 23.3 - - + -
116C TYR* 3.5 33.0 - - + +
124C CYS 3.1 18.3 + - - +
125C PRO 3.3 3.1 + - - +
127C GLU* 1.3 77.2 - - - +
129C ILE* 1.3 51.2 + - - +
131C PHE* 3.5 1.6 + - - +
132C GLY* 2.8 32.7 + - - -
147C ALA* 4.5 1.1 - - + -
159C TRP* 3.6 25.4 - - + -
169C LEU* 4.0 22.4 - - + -
172C ILE* 4.2 19.1 - - + +
174C ILE* 4.1 12.0 - - + +
176C LEU* 4.2 8.5 - - + -
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Residues in contact with ILE 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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125C PRO* 2.9 25.9 + - + +
126C THR* 4.0 5.6 - - - +
128C ILE* 1.3 73.2 - - - +
130C ALA* 1.3 61.0 + - - +
132C GLY* 4.3 2.0 - - - +
133C ASP* 2.7 42.0 + - - +
164C ARG* 3.5 61.0 - - + +
168C GLY 4.0 12.8 - - - +
169C LEU* 4.1 13.9 - - + +
172C ILE* 5.2 3.8 - - + -
267D PHE* 5.7 5.4 - - + -
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Residues in contact with ALA 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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126C THR 2.8 22.8 + - - +
127C GLU 3.7 4.3 - - - +
129C ILE* 1.3 77.5 - - - +
131C PHE* 1.3 62.0 + - - +
133C ASP* 3.7 2.2 + - - +
134C ARG* 3.3 27.3 + - - +
225C VAL* 3.8 20.0 - - + +
247D ALA* 3.9 18.2 - - + +
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Residues in contact with PHE 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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112C VAL* 4.2 8.7 - - + -
114C PHE* 3.9 24.0 - + + -
127C GLU* 3.1 31.7 + - + +
128C ILE 4.0 0.2 - - - +
130C ALA* 1.3 78.3 - - - +
132C GLY* 1.3 62.8 + - - +
134C ARG 3.2 2.8 + - - -
135C LEU* 3.0 26.0 + - - +
138C PHE* 3.7 34.9 - + - -
145C VAL* 4.3 13.5 - - + -
174C ILE* 3.6 18.9 - - + +
202C LEU* 3.8 17.5 - - + -
223C ARG* 5.2 11.2 - - + -
224C SER 4.6 1.1 - - - -
225C VAL* 3.9 24.5 - - + -
228C THR* 3.6 28.9 - - + -
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Residues in contact with GLY 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 ILE 2.8 22.5 + - - -
129C ILE* 3.5 1.8 - - - -
131C PHE* 1.3 75.5 - - - +
133C ASP* 1.3 65.3 + - - +
135C LEU* 3.2 17.1 + - - +
164C ARG* 6.1 0.2 - - - -
172C ILE* 5.2 10.8 - - - -
173C ARG* 5.5 7.0 + - - +
174C ILE* 3.3 15.7 - - - +
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Residues in contact with ASP 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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129C ILE* 2.7 26.9 + - - +
130C ALA* 4.3 3.1 - - - +
132C GLY* 1.3 73.0 - - - -
134C ARG* 1.3 62.5 + - + +
135C LEU 3.4 1.2 + - - -
164C ARG* 3.0 42.1 + - - -
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Residues in contact with ARG 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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130C ALA* 3.3 15.9 + - - +
131C PHE 3.2 5.7 + - - +
132C GLY 3.2 1.2 - - - -
133C ASP* 1.3 81.4 - - + +
135C LEU* 1.3 65.1 + - - +
136C GLU 3.3 2.5 - - - -
137C GLU* 2.9 63.6 + - - +
138C PHE* 3.6 5.5 - - - -
225C VAL* 3.7 35.4 - - + +
226C ASP* 2.8 33.9 + - - +
229C LEU* 3.6 10.3 - - - +
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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