Contacts of the helix formed by residues 132 - 149 (chain A) in PDB entry 1TJY
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 THR 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A GLY* 1.3 75.0 - - - +
133A PRO* 1.3 75.3 - - - +
134A LYS* 3.6 10.0 + - - +
135A GLN* 3.1 38.8 + - - +
136A LEU* 3.0 21.4 + - - +
309A GLU* 3.6 37.2 - - + +
310A GLN* 4.0 3.1 - - - +
323A LEU* 4.0 17.2 - - + +
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Residues in contact with PRO 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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131A GLY 3.8 0.2 - - - -
132A THR* 1.3 87.9 - - - +
134A LYS* 1.3 56.2 + - + +
137A GLY* 2.8 29.1 + - - -
169A GLN* 3.7 23.8 - - + +
170A TRP* 4.0 13.4 - - + -
173A GLU* 3.5 27.3 - - + +
309A GLU 4.0 8.3 - - - +
310A GLN* 3.3 47.1 - - - +
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Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR* 3.2 8.3 + - - +
133A PRO* 1.3 78.5 - - - +
135A GLN* 1.3 55.7 + - + +
138A SER* 2.8 39.0 + - - +
173A GLU* 3.6 33.6 - - - +
309A GLU 6.1 0.4 - - - +
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Residues in contact with GLN 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLY* 3.5 9.2 - - - -
132A THR* 3.1 44.2 + - - +
134A LYS* 1.3 78.8 - - + +
136A LEU* 1.3 58.4 + - - +
138A SER* 3.4 5.0 + - - -
139A MET* 3.0 31.8 + - - +
323A LEU* 4.8 3.7 - - - +
327A ARG* 3.5 40.1 + - - +
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Residues in contact with LEU 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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130A GLN* 3.8 12.8 - - + -
131A GLY* 3.5 23.1 - - - +
132A THR 3.0 10.4 + - - +
135A GLN* 1.3 74.1 - - - +
137A GLY* 1.3 65.9 + - - +
139A MET* 3.3 25.9 + - - +
140A LEU* 3.1 28.9 + - - +
170A TRP* 3.3 50.3 - - + +
245A PHE* 3.6 17.5 - - + -
266A TRP* 4.1 14.1 - - + -
327A ARG* 4.0 15.3 - - + -
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Residues in contact with GLY 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 PRO 2.8 18.2 + - - -
134A LYS 4.1 0.4 - - - -
136A LEU* 1.3 77.2 - - - +
138A SER* 1.3 59.7 + - - +
140A LEU* 3.3 6.8 + - - +
141A VAL* 3.2 28.0 + - - +
170A TRP* 3.8 20.6 + - - +
173A GLU* 4.5 2.0 - - - -
174A ALA* 3.9 14.5 - - - +
177A LYS* 4.7 1.6 - - - -
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Residues in contact with SER 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 2.8 26.6 + - - +
135A GLN* 3.6 6.1 - - - -
136A LEU 3.2 0.2 - - - -
137A GLY* 1.3 73.4 - - - +
139A MET* 1.3 59.5 + - - +
141A VAL* 3.3 1.0 + - - +
142A GLU* 2.8 52.8 + - - +
177A LYS* 3.8 26.7 + - - +
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Residues in contact with MET 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLN 3.0 15.1 + - - +
136A LEU* 3.3 29.4 + - + +
138A SER* 1.3 76.2 - - - +
140A LEU* 1.3 63.2 + - - +
142A GLU* 3.9 12.1 + - - +
143A MET* 3.0 32.4 + - + +
245A PHE* 4.1 11.7 - - + -
264A GLY* 4.0 11.9 - - - -
265A LEU 4.1 9.6 - - - +
327A ARG* 3.8 26.7 - - + -
328A VAL 3.9 15.0 - - - +
329A ILE* 3.6 29.2 - - + -
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Residues in contact with LEU 140 (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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136A LEU 3.1 16.0 + - - +
137A GLY* 3.6 13.5 - - - +
138A SER 3.2 0.2 - - - -
139A MET* 1.3 78.4 - - - +
141A VAL* 1.3 63.7 + - + +
143A MET* 3.5 8.8 + - + +
144A ALA* 3.1 22.2 + - - +
157A PHE* 5.2 1.3 - - + -
170A TRP* 4.6 9.4 - - + +
171A VAL* 5.3 0.4 - - + -
174A ALA* 4.5 13.5 - - + -
218A ILE* 4.0 23.0 - - + +
220A PRO* 3.8 28.3 - - + -
243A VAL* 4.0 5.2 - - - +
244A GLY* 3.9 24.2 - - - +
245A PHE* 3.6 30.5 - - + -
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Residues in contact with VAL 141 (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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137A GLY 3.2 16.8 + - - +
140A LEU* 1.3 73.4 - - + +
142A GLU* 1.3 60.6 + - - +
144A ALA* 3.2 6.7 + - - +
145A ALA* 2.8 28.1 + - - +
174A ALA* 3.5 34.3 - - + +
177A LYS* 3.8 27.6 - - + -
178A ILE* 3.8 16.6 - - + -
182A HIS* 3.6 33.0 - - + +
185A TRP* 4.6 2.5 - - + -
218A ILE* 5.1 2.7 - - + -
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Residues in contact with GLU 142 (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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138A SER* 2.8 38.7 + - - +
139A MET* 3.9 13.3 - - - +
141A VAL* 1.3 77.2 - - - +
143A MET* 1.3 62.1 + - + +
145A ALA* 3.9 5.4 - - - +
146A HIS* 3.1 24.6 + - - +
177A LYS* 4.5 13.6 + - - +
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Residues in contact with MET 143 (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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139A MET 3.0 25.2 + - - +
140A LEU* 3.8 15.0 - - + +
142A GLU* 1.3 76.6 - - + +
144A ALA* 1.3 63.0 + - - +
146A HIS* 3.5 9.1 + - - +
147A GLN* 3.6 12.6 + - - -
243A VAL* 3.9 19.9 - - + +
244A GLY 3.6 28.7 - - - +
245A PHE* 4.2 8.3 - - + -
262A GLU* 3.6 26.3 - - + +
263A PHE* 3.4 34.1 - - - +
264A GLY* 3.5 7.9 - - - +
329A ILE* 3.9 19.3 - - + -
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Residues in contact with ALA 144 (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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140A LEU 3.1 12.5 + - - +
141A VAL 3.5 7.4 - - - +
143A MET* 1.3 78.9 - - - +
145A ALA* 1.3 57.0 + - - +
147A GLN* 3.2 4.7 + - - +
148A VAL* 2.9 32.4 + - - +
185A TRP* 4.0 14.4 - - + -
216A ALA* 4.8 9.9 - - + -
218A ILE* 3.9 24.2 - - + -
241A ALA* 5.5 1.1 - - - -
243A VAL* 4.0 14.9 - - + +
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Residues in contact with ALA 145 (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 VAL 2.8 20.9 + - - +
142A GLU* 3.9 6.1 - - - +
144A ALA* 1.3 73.2 - - - +
146A HIS* 1.3 63.5 + - - +
148A VAL 4.5 0.2 - - - +
149A ASP* 3.0 24.1 + - - +
182A HIS* 3.7 31.0 - - + +
185A TRP* 3.7 12.8 - - + -
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Residues in contact with HIS 146 (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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142A GLU 3.1 17.7 + - - +
143A MET* 3.7 7.4 - - - +
144A ALA 3.3 0.2 - - - -
145A ALA* 1.3 77.7 - - - +
147A GLN* 1.3 69.3 + - + +
149A ASP* 4.1 10.2 - - - +
262A GLU* 4.6 20.1 + - + +
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Residues in contact with GLN 147 (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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143A MET 3.6 5.6 + - - +
144A ALA 3.2 4.5 + - - +
145A ALA 3.2 0.2 - - - -
146A HIS* 1.3 88.6 - - + +
148A VAL* 1.3 66.4 + - - +
149A ASP* 4.4 2.6 - - - +
240A LEU 5.0 0.5 - - - +
241A ALA* 3.6 34.4 - - + +
242A ILE 4.4 2.5 + - - -
243A VAL* 3.5 25.0 - - - +
261A LYS* 3.9 37.4 + - + +
262A GLU* 4.0 17.0 + - - +
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Residues in contact with VAL 148 (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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144A ALA 2.9 21.9 + - - +
147A GLN* 1.3 79.6 - - - +
149A ASP* 1.3 65.7 + - - +
150A LYS* 3.1 27.2 + - + +
153A ALA* 3.6 30.5 - - + -
155A VAL* 5.5 0.9 - - + -
185A TRP* 4.0 21.8 - - + -
215A ASP* 4.1 13.5 - - + +
216A ALA* 3.8 28.3 - - + -
241A ALA* 4.3 4.0 - - + -
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Residues in contact with ASP 149 (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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145A ALA* 3.0 18.5 + - - +
146A HIS 4.1 11.7 - - - +
147A GLN 4.4 2.7 - - - +
148A VAL* 1.3 78.3 - - - +
150A LYS* 1.3 60.5 + - - +
185A TRP* 5.4 0.8 - - - -
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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