Contacts of the helix formed by residues 152 - 161 (chain D) in PDB entry 3TJF
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 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150D VAL 3.8 0.6 + - - -
151D ASP* 1.3 76.9 - - - +
153D GLN* 1.3 59.4 + - - +
154D PHE* 3.1 11.7 + - - +
155D THR* 3.0 27.6 + - - -
156D HIS* 3.0 25.8 + - - -
178D SER* 3.5 7.2 - - - -
180D LEU* 3.9 21.5 - - - +
118E LEU* 4.0 28.7 - - - +
119E ASP 4.7 1.2 + - - -
151E ASP* 4.6 5.5 + - - -
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Residues in contact with GLN 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D THR* 4.0 31.5 + - + +
92D ALA 5.3 0.4 - - - -
93D VAL* 3.5 6.6 - - + +
98D PHE* 3.4 46.8 - - + +
152D SER* 1.3 79.0 - - - +
154D PHE* 1.3 81.5 + - + +
156D HIS* 4.1 11.0 - - + -
157D LEU* 2.9 23.2 + - - +
178D SER* 3.7 14.6 + - - -
180D LEU* 4.6 7.6 - - - +
118E LEU* 5.4 0.2 - - - +
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Residues in contact with PHE 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D PHE* 3.5 32.8 - + - -
152D SER* 3.1 5.8 + - - +
153D GLN* 1.3 98.1 - - + +
155D THR* 1.3 57.4 + - - +
157D LEU* 3.4 4.6 + - + +
158D ALA* 3.0 27.0 + - - +
118E LEU* 3.7 24.9 - - + -
119E ASP 4.0 7.9 - - - +
120E PHE* 3.7 24.0 - - - +
121E THR* 3.7 19.1 - - + -
122E PHE* 3.5 35.4 - + - -
462E SO4 4.2 10.1 - - - -
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Residues in contact with THR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ASP* 3.5 22.2 - - + +
120D PHE* 4.0 7.4 - - + -
151D ASP* 4.0 10.5 - - - +
152D SER* 3.0 19.8 + - - -
154D PHE* 1.3 74.6 - - - +
156D HIS* 1.3 64.9 + - - +
158D ALA* 3.3 1.9 + - - +
159D TRP* 2.9 22.7 + - - +
119E ASP 4.4 2.8 + - - -
120E PHE* 4.0 11.1 - - - -
151E ASP* 3.6 8.7 + - - -
155E THR* 3.3 44.5 - - + +
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Residues in contact with HIS 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D VAL* 3.6 11.2 - - + -
116D TYR* 3.1 17.0 + - - -
119D ASP* 2.6 27.7 + - - -
149D SER* 3.1 27.1 + - - -
151D ASP* 3.6 13.5 + - + -
152D SER 3.0 15.1 + - - -
153D GLN* 3.5 10.1 - - - +
155D THR* 1.3 76.5 - - - +
157D LEU* 1.3 56.9 + - - +
159D TRP* 3.3 4.4 + - - +
160D ILE* 3.0 33.9 + - - +
176D LEU* 3.4 38.0 - - + +
177D LEU 3.0 25.5 + - - -
178D SER* 4.0 6.5 - - - -
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D VAL* 4.0 10.9 - - + +
96D GLY* 3.8 34.1 - - - +
98D PHE* 4.2 24.5 - - + -
153D GLN 2.9 17.6 + - - +
154D PHE* 3.8 4.7 - - - +
155D THR 3.2 0.2 - - - -
156D HIS* 1.3 74.5 - - - +
158D ALA* 1.3 59.5 + - - +
160D ILE* 3.3 9.3 + - + +
161D ASN* 2.9 54.8 + - - +
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Residues in contact with ALA 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D PHE* 4.0 3.1 - - + -
154D PHE 3.0 15.2 + - - +
155D THR 3.3 3.8 + - - +
157D LEU* 1.3 75.2 - - - +
159D TRP* 1.3 55.6 + - - +
161D ASN* 3.3 11.1 + - - +
162D THR* 2.7 31.6 + - - -
120E PHE* 3.5 46.9 - - + -
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Residues in contact with TRP 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D TYR* 3.5 9.4 - + - -
118D LEU 4.3 0.2 - - - -
119D ASP* 3.3 34.8 - - + +
120D PHE* 3.3 53.2 - + + +
121D THR 4.4 0.2 - - - -
124D CYS* 4.1 2.2 - - + -
125D PRO* 3.6 40.2 - - + -
128D ILE* 3.4 34.5 - - + -
155D THR 2.9 14.2 + - - +
156D HIS 3.4 8.3 - - - +
158D ALA* 1.3 72.7 - - - +
160D ILE* 1.3 64.1 + - - +
162D THR* 3.1 11.5 + - - -
167D GLY 3.0 18.4 + - - -
168D GLY* 3.6 7.8 - - - -
169D LEU* 3.0 42.7 + - + -
176D LEU* 4.5 2.2 - - + -
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Residues in contact with ILE 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D VAL* 3.7 32.5 - - + +
96D GLY* 5.7 7.2 - - - +
156D HIS 3.0 19.8 + - - +
157D LEU* 3.6 10.8 - - + +
158D ALA 3.3 0.2 - - - -
159D TRP* 1.3 76.1 - - - +
161D ASN* 1.3 64.1 + - - +
162D THR 3.1 5.5 + - - -
169D LEU* 4.1 5.8 - - + -
170D GLY* 3.2 36.0 - - - +
171D PRO* 3.8 15.6 - - + +
172D ILE* 3.6 28.0 - - + +
176D LEU* 3.8 20.0 - - + -
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Residues in contact with ASN 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 2.9 45.8 + - - +
158D ALA* 3.3 11.5 + - - +
160D ILE* 1.3 79.1 - - - +
162D THR* 1.3 57.2 + - - +
163D PRO* 3.8 6.8 - - - +
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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