Contacts of the helix formed by residues 127 - 138 (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 ASP 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PHE* 5.8 0.3 - - - +
125A VAL* 3.2 4.1 - - - +
126A GLU* 1.3 93.5 - - + +
128A ALA* 1.3 58.4 + - - +
129A GLU* 3.3 19.7 + - - +
130A SER* 3.5 23.3 + - - -
131A ALA* 2.8 29.5 + - - +
154A THR* 5.5 1.2 - - - +
170A SER* 3.7 5.1 + - - -
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Residues in contact with ALA 128 (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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125A VAL* 3.5 9.4 - - - +
127A ASP* 1.3 72.3 - - - +
129A GLU* 1.3 58.1 + - - +
131A ALA* 3.7 1.1 - - - +
132A PHE* 2.9 30.7 + - - +
154A THR* 3.4 28.7 - - + +
155A ILE* 4.3 1.6 - - - +
156A ALA* 4.0 6.3 - - - +
168A TYR* 3.6 26.3 - - + +
170A SER* 2.8 24.0 + - - +
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Residues in contact with GLU 129 (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* 3.2 11.7 + - - +
128A ALA* 1.3 79.0 - - - +
130A SER* 1.3 62.5 + - - +
132A PHE* 3.3 3.1 + - - +
133A SER* 3.0 35.9 + - - +
146A PRO* 3.8 34.9 - - + +
148A VAL* 5.5 6.2 - - - +
154A THR* 3.9 8.6 - - + +
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Residues in contact with SER 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 5.0 2.3 - - - +
126A GLU* 5.9 0.7 - - - -
127A ASP* 3.2 29.0 + - - -
129A GLU* 1.3 77.1 - - - +
131A ALA* 1.3 61.1 + - - +
132A PHE 3.3 0.2 + - - -
133A SER* 3.3 5.0 + - - +
134A ILE* 2.8 56.4 + - - +
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Residues in contact with ALA 131 (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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21A PHE* 3.6 37.5 - - + +
125A VAL* 3.9 8.5 - - + -
127A ASP 2.8 17.7 + - - +
128A ALA 3.7 4.7 - - - +
130A SER* 1.3 76.9 - - - +
132A PHE* 1.3 56.3 + - - +
135A SER* 2.8 34.5 + - - -
168A TYR* 3.8 21.8 - - + -
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Residues in contact with PHE 132 (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 2.9 18.1 + - - +
129A GLU 3.6 0.4 - - - +
131A ALA* 1.3 74.2 - - - +
133A SER* 1.3 68.2 + - - +
135A SER* 3.3 1.6 + - - -
136A VAL* 2.9 46.6 + - + +
142A PRO* 3.7 26.0 - - + -
144A SER 3.3 24.2 - - - -
145A PRO* 4.0 13.5 - - + -
146A PRO* 3.5 31.2 - - + -
156A ALA* 3.7 12.1 - - + -
157A GLU 3.3 13.7 - - - -
158A VAL* 3.8 19.3 - - + -
168A TYR* 3.9 7.8 - + - -
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Residues in contact with SER 133 (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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129A GLU* 3.0 27.3 + - - +
130A SER* 3.9 4.9 - - - -
132A PHE* 1.3 83.0 - - - +
134A ILE* 1.3 64.8 + - - +
136A VAL* 3.3 4.2 + - - +
137A ALA* 2.9 24.8 + - - +
146A PRO* 5.4 0.2 - - - +
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Residues in contact with ILE 134 (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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20A LYS* 3.6 45.5 - - + +
21A PHE* 4.2 9.9 - - + -
130A SER* 2.8 43.9 + - - +
131A ALA 4.2 2.5 - - - +
133A SER* 1.3 74.1 - - - +
135A SER* 1.3 63.4 + - - +
137A ALA* 3.3 5.1 + - - +
138A ASN* 2.8 40.2 + - - +
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Residues in contact with SER 135 (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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21A PHE* 3.1 12.3 - - - -
131A ALA 2.8 21.2 + - - -
132A PHE 3.6 3.4 - - - -
134A ILE* 1.3 77.3 - - - +
136A VAL* 1.3 61.3 + - - +
138A ASN 3.0 8.1 + - - -
140A ALA* 2.9 26.6 + - - -
158A VAL* 4.4 2.7 - - - -
168A TYR* 2.8 28.4 + - - -
223A PHE* 3.2 31.9 + - - +
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Residues in contact with VAL 136 (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* 2.9 41.9 + - + +
133A SER* 3.9 4.0 - - - +
135A SER* 1.3 70.3 - - - +
137A ALA* 1.3 66.7 + - - +
138A ASN 2.9 2.0 - - - -
139A GLY* 3.0 14.0 + - - -
140A ALA 3.6 14.4 + - - +
142A PRO* 3.5 36.1 - - + -
158A VAL* 4.4 7.0 - - + -
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Residues in contact with ALA 137 (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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133A SER 2.9 19.4 + - - +
134A ILE* 3.6 8.7 - - - +
136A VAL* 1.3 77.2 - - - +
138A ASN* 1.3 65.4 + - - +
139A GLY 3.6 2.4 + - - -
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Residues in contact with ASN 138 (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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20A LYS* 3.1 27.6 - - + +
134A ILE* 2.8 39.3 + - - +
135A SER 3.0 9.9 + - - +
136A VAL 2.9 0.8 - - - -
137A ALA* 1.3 84.5 - - - +
139A GLY* 1.3 56.9 + - - -
219A TYR 5.2 0.3 - - - +
222A GLY* 3.6 16.6 - - - +
223A PHE* 3.6 19.5 + - - +
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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