Contacts of the strand formed by residues 153 - 161 (chain A) in PDB entry 1TFZ
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 VAL 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A ILE 3.7 0.3 - - - +
148A VAL* 3.4 2.6 - - - -
149A LEU* 2.7 41.5 + - + +
152A ALA* 1.3 88.2 - - + +
154A THR* 1.3 67.8 + - - +
155A ILE* 5.5 0.4 - - + -
169A VAL* 3.9 23.3 - - + -
170A SER 3.3 11.2 - - - +
171A TYR* 3.6 25.4 - - + -
172A LYS* 5.6 0.4 - - - -
181A PHE 5.5 1.1 - - - +
182A LEU* 3.9 17.3 - - + -
183A PRO* 3.6 29.2 - - + -
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Residues in contact with THR 154 (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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127A ASP* 5.5 1.1 - - - +
128A ALA* 3.4 18.6 - - + +
129A GLU* 3.9 16.4 - - + +
146A PRO* 4.3 16.6 - - + -
147A ILE 3.4 11.0 - - - +
148A VAL* 3.4 25.2 - - + +
153A VAL* 1.3 76.7 - - - +
155A ILE* 1.3 63.6 + - - +
169A VAL* 3.3 5.2 - - - -
170A SER* 2.9 43.7 + - - -
172A LYS* 4.5 10.3 - - - +
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Residues in contact with ILE 155 (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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99A ILE* 4.5 14.1 - - + -
100A PRO* 4.2 16.6 - - + -
101A SER* 4.9 2.2 - - - +
145A PRO 3.6 2.6 - - - +
146A PRO* 3.3 3.0 - - - +
147A ILE* 3.0 36.4 + - + +
149A LEU* 3.7 23.3 - - + -
153A VAL* 5.5 2.0 - - + -
154A THR* 1.3 76.9 - - - +
156A ALA* 1.3 63.5 + - - +
157A GLU* 4.2 7.4 - - - +
167A ARG* 3.4 44.0 - - + +
168A TYR 3.2 4.3 - - - +
169A VAL* 4.6 7.0 - - + -
182A LEU* 4.6 17.0 - - + -
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Residues in contact with ALA 156 (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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128A ALA* 4.0 9.2 - - + +
132A PHE* 3.7 33.7 - - + -
144A SER* 3.7 6.5 - - - +
145A PRO 4.2 1.3 - - - -
146A PRO* 3.8 14.6 - - + -
155A ILE* 1.3 77.7 - - - +
157A GLU* 1.3 67.6 + - - +
167A ARG* 3.3 0.7 - - - +
168A TYR* 2.7 42.7 + - + +
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Residues in contact with GLU 157 (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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101A SER* 2.6 40.2 + - - -
119A ARG* 4.7 8.7 + - - -
132A PHE* 3.3 5.7 - - - -
143A SER* 2.9 12.3 + - - -
144A SER* 2.8 45.0 + - - +
155A ILE* 4.2 4.3 - - + +
156A ALA* 1.3 81.2 - - - +
158A VAL* 1.3 63.7 + - - +
165A VAL* 3.6 21.2 - - + +
166A LEU 3.4 5.2 - - - +
167A ARG* 2.7 43.4 + - + -
168A TYR* 5.4 0.2 - - - -
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Residues in contact with VAL 158 (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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132A PHE* 3.8 22.0 - - + -
135A SER* 4.4 5.4 - - - -
136A VAL* 4.4 4.5 - - + -
140A ALA* 4.0 20.0 - - + -
141A ILE 3.4 11.2 - - - +
143A SER* 4.0 5.6 - - - +
157A GLU* 1.3 78.8 - - - +
159A LYS* 1.3 59.1 + - - +
165A VAL* 3.2 4.3 - - - +
166A LEU* 2.8 40.4 + - + +
168A TYR* 3.9 18.4 - - + +
223A PHE* 3.6 33.4 - - + -
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Residues in contact with LYS 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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141A ILE* 2.8 51.9 + - + +
142A PRO 4.1 8.3 - - - -
143A SER* 4.3 16.2 - - - +
158A VAL* 1.3 75.4 - - - +
160A LEU* 1.3 61.3 + - - +
161A TYR* 5.1 1.3 - - - +
162A GLY 5.3 10.1 - - - +
164A VAL 4.2 3.8 - - - +
165A VAL* 4.4 5.4 - - + +
219A TYR* 2.9 31.0 + - + +
223A PHE* 3.8 9.5 - - - -
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Residues in contact with LEU 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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121A VAL* 4.4 25.1 - - + -
158A VAL 3.5 0.6 + - - -
159A LYS* 1.3 73.7 - - - +
161A TYR* 1.3 105.9 + - + +
164A VAL* 2.9 21.6 + - + +
165A VAL 4.6 2.0 - - - +
166A LEU* 4.1 26.2 - - + +
216A ALA* 6.0 0.7 - - - +
219A TYR* 3.7 18.7 - - - -
220A VAL* 3.8 41.0 - - + +
223A PHE* 4.6 2.0 - - + -
258A LEU* 4.5 18.4 - - + -
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Residues in contact with TYR 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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159A LYS* 5.1 1.1 - - - +
160A LEU* 1.3 110.5 - - + +
162A GLY* 1.3 70.7 + - - +
163A ASP 3.1 0.2 + - - -
164A VAL* 2.9 41.9 + - + +
206A ALA 4.3 4.2 + - - -
207A VAL 3.9 0.3 - - - -
208A GLY* 3.3 28.8 + - - -
210A VAL* 3.9 23.1 - - + -
216A ALA* 5.6 4.0 - - + -
220A VAL* 5.1 0.2 - - + -
258A LEU* 5.7 4.5 - - + +
259A PRO 4.7 0.8 + - - -
260A ILE* 4.2 29.4 - - + -
283A ALA* 4.6 0.4 - - + -
284A GLY* 4.0 14.8 - - - -
285A LEU* 2.9 26.2 - - - +
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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