Contacts of the helix formed by residues 122 - 134 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154D PHE* 3.5 39.9 - + - -
120E PHE 4.6 3.4 - - - -
121E THR* 1.3 97.6 + - + +
123E VAL* 1.3 70.1 + - + +
124E CYS 3.2 0.4 - - - -
125E PRO* 3.2 15.1 - - - +
126E THR* 3.9 9.4 - - - +
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Residues in contact with VAL 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E PHE* 1.3 79.3 - - + +
124E CYS* 1.3 62.9 + - - +
126E THR* 2.8 33.3 + - - +
127E GLU* 3.4 10.2 + - + +
200E ARG* 3.3 29.9 - - - +
219E LEU 4.4 0.7 - - - +
220E PRO* 3.9 24.7 - - + +
222E GLY* 3.6 32.3 - - - +
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Residues in contact with CYS 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E TYR* 3.6 18.5 - - + -
117E PRO* 3.5 34.5 - - - -
118E LEU 3.6 17.0 - - - +
121E THR* 3.1 22.0 - - - +
122E PHE 4.6 0.2 - - - -
123E VAL* 1.3 76.7 - - - +
125E PRO* 1.4 69.6 - - + +
127E GLU* 3.5 5.4 + - - +
128E ILE* 3.1 28.7 + - - +
159E TRP* 4.1 2.0 - - + -
200E ARG* 3.5 15.2 - - - +
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Residues in contact with PRO 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E THR 3.5 20.0 - - - +
122E PHE 3.2 15.7 - - - +
124E CYS* 1.4 94.9 - - + +
126E THR* 1.3 57.9 + - + +
128E ILE* 3.3 1.0 + - - +
129E ILE* 2.9 40.3 + - + +
159E TRP* 3.7 18.8 - - + -
167E GLY* 3.8 21.5 - - - +
168E GLY 4.3 5.2 - - - +
169E LEU* 3.9 18.4 - - + -
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Residues in contact with THR 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E PHE 3.9 12.6 - - - +
123E VAL* 2.8 29.0 + - - +
125E PRO* 1.3 76.9 - - + +
127E GLU* 1.3 54.4 + - - +
129E ILE* 3.8 6.7 - - - +
130E ALA* 2.8 34.4 + - - +
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Residues in contact with GLU 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E PHE* 4.6 11.0 - - + -
116E TYR* 4.4 1.0 - - - +
123E VAL* 3.4 14.3 + - + +
124E CYS* 3.9 7.0 - - - +
125E PRO 3.3 0.4 - - - -
126E THR* 1.3 78.1 + - - +
128E ILE* 1.3 67.8 + - - +
129E ILE 3.2 0.2 - - - -
130E ALA* 3.4 4.9 + - - -
131E PHE* 3.1 37.3 + - + -
200E ARG* 2.9 25.8 + - - -
222E GLY* 3.2 8.2 - - - -
223E ARG* 2.7 74.2 + - + +
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Residues in contact with ILE 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E PHE* 4.1 24.0 - - + -
116E TYR* 3.7 25.4 - - + -
124E CYS 3.1 22.6 + - - +
125E PRO* 3.9 3.4 - - + +
127E GLU* 1.3 77.6 - - - +
129E ILE* 1.3 58.2 + - - +
132E GLY* 2.9 26.9 + - - -
147E ALA* 4.4 2.2 - - + -
159E TRP* 3.6 32.3 - - + -
169E LEU* 4.0 13.5 - - + -
172E ILE* 3.8 25.4 - - + +
174E ILE* 4.0 11.2 - - + +
176E LEU* 4.3 9.9 - - + -
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Residues in contact with ILE 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E PRO* 2.9 27.5 + - + +
126E THR* 3.9 5.8 - - - +
128E ILE* 1.3 75.6 - - - +
130E ALA* 1.3 59.1 + - - +
133E ASP* 2.7 42.3 + - - +
164E ARG* 3.7 58.3 - - + +
168E GLY 4.2 10.5 - - - +
169E LEU* 4.1 14.4 - - + +
172E ILE* 4.3 7.4 - - + -
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Residues in contact with ALA 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E THR 2.8 20.7 + - - +
127E GLU* 3.8 6.1 - - - +
129E ILE* 1.3 79.5 - - - +
131E PHE* 1.3 60.8 + - - +
133E ASP* 3.7 2.8 + - - +
134E ARG* 3.3 29.7 + - - +
225E VAL* 3.7 19.7 - - + +
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Residues in contact with PHE 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E VAL* 4.1 7.9 - - + -
114E PHE* 3.9 21.5 - + + -
127E GLU* 3.1 32.2 + - + +
128E ILE 4.0 0.2 - - - +
130E ALA* 1.3 73.0 - - - +
132E GLY* 1.3 66.8 + - - +
134E ARG* 3.0 13.2 + - - +
135E LEU* 3.0 15.8 + - - +
138E PHE* 3.6 35.4 - + - -
145E VAL* 4.2 13.5 - - + -
174E ILE* 3.6 17.9 - - + +
202E LEU* 3.8 17.0 - - + -
223E ARG* 5.1 11.7 - - + -
224E SER 4.5 0.9 - - - -
225E VAL* 3.8 24.0 - - + -
228E THR* 3.6 30.1 - - + -
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Residues in contact with GLY 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E ILE 2.9 16.8 + - - -
129E ILE 3.7 0.7 - - - -
131E PHE* 1.3 77.1 - - - +
133E ASP* 1.3 62.2 + - - +
134E ARG 3.2 0.9 + - - -
135E LEU* 3.3 9.9 + - - +
172E ILE* 4.5 11.4 - - - -
173E ARG* 3.1 27.9 + - - -
174E ILE* 3.2 18.5 - - - +
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Residues in contact with ASP 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E ILE* 2.7 28.7 + - - +
130E ALA* 4.3 4.0 - - - +
132E GLY* 1.3 73.6 - - - -
134E ARG* 1.3 64.3 + - + +
135E LEU 3.5 0.6 + - - -
164E ARG* 3.0 39.7 + - - -
172E ILE* 5.5 0.3 - - - +
173E ARG* 4.9 4.9 + - - +
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Residues in contact with ARG 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ALA* 3.3 18.9 + - - +
131E PHE 3.0 7.2 + - - +
133E ASP* 1.3 84.5 - - + +
135E LEU* 1.3 64.6 + - - +
136E GLU 3.1 2.7 - - - -
137E GLU* 2.7 65.2 + - + +
138E PHE* 3.6 5.7 - - - -
225E VAL* 3.8 32.1 - - + +
226E ASP* 2.9 33.5 + - - +
229E LEU* 3.5 11.7 - - - +
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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