Contacts of the helix formed by residues 139 - 149 (chain A) in PDB entry 3T2E
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 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A PHE* 4.0 18.4 - - + -
131A ALA* 3.9 26.2 - - + -
136A PRO 3.1 7.8 + - - +
137A GLY 3.0 0.8 - - - -
138A ALA* 1.4 81.6 - - + +
140A ASN* 1.3 64.2 + - - +
141A LEU 3.4 1.1 - - - -
142A PRO* 3.5 4.0 - - - -
143A LEU* 2.9 37.0 + - + +
217A ASN* 3.3 27.1 - - - +
235A PRO* 3.5 36.3 - - + -
236A VAL 4.0 0.4 - - - -
237A LEU* 3.7 20.6 - - + -
255A PHE* 3.7 36.6 - + - -
273A LEU* 5.0 3.1 - - + -
302A VAL* 3.9 11.9 - - + -
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Residues in contact with ASN 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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137A GLY* 3.0 16.7 + - - +
139A PHE* 1.3 77.4 - - - +
141A LEU* 1.4 60.1 + - - +
143A LEU* 4.6 0.2 - - - -
144A TYR* 2.9 32.8 + - - +
194A ILE* 2.9 36.6 + - + +
197A THR* 3.8 15.0 - - + +
200A TYR 2.8 27.6 + - - -
201A ILE* 3.6 9.5 - - - +
202A ILE* 2.9 35.9 + - - +
217A ASN* 4.9 0.5 + - - -
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Residues in contact with LEU 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 4.5 0.8 + - - -
138A ALA 4.3 1.2 + - - -
140A ASN* 1.4 80.1 - - - +
142A PRO* 1.3 72.2 - - + +
144A TYR* 3.7 5.1 - - - +
145A LYS* 2.9 69.4 + - + +
197A THR* 5.8 0.4 - - - +
254A ALA 4.2 2.5 - - - +
257A HIS* 5.1 3.8 - - + +
259A HIS* 3.8 45.5 - - + +
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Residues in contact with PRO 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 ALA 3.3 18.6 - - - +
139A PHE* 3.5 7.2 - - - +
141A LEU* 1.3 95.9 - - + +
143A LEU* 1.3 56.3 + - + +
145A LYS* 3.2 1.1 + - + -
146A MET* 2.8 31.4 + - + +
254A ALA* 3.3 31.7 - - + +
255A PHE* 3.6 42.2 - - + -
259A HIS* 3.6 18.6 - - + -
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Residues in contact with LEU 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 PHE* 2.9 34.1 + - + +
142A PRO* 1.3 73.5 - - - +
144A TYR* 1.3 66.9 + - - +
146A MET* 4.0 9.6 - - - -
147A PHE* 3.2 53.2 + - + +
168A PHE* 3.9 3.6 - - + -
202A ILE* 3.7 37.9 - - + -
205A VAL* 4.7 2.0 - - + -
215A ALA* 3.9 9.4 - - + -
217A ASN* 4.2 11.0 - - + +
237A LEU* 3.8 39.3 - - + -
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Residues in contact with TYR 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 ASN 2.9 18.7 + - - +
141A LEU* 3.7 4.9 - - - +
143A LEU* 1.3 77.6 - - - +
145A LYS* 1.4 67.1 + - + +
148A ALA* 2.8 53.6 + - + +
149A ASP* 4.2 17.7 - - + -
168A PHE* 4.1 7.4 - - - -
183A THR* 4.7 0.2 - - + -
187A ALA* 3.6 20.8 - - + +
188A TYR* 6.0 0.3 - - - -
190A LEU* 3.8 27.1 - - + -
191A LEU* 3.6 49.3 - - + +
194A ILE* 3.9 11.0 - - + -
202A ILE* 4.0 1.0 - - - +
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Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A LEU* 2.9 52.9 + - + +
142A PRO 3.6 3.6 - - - +
144A TYR* 1.4 79.0 - - + +
146A MET* 1.3 64.3 - - - +
149A ASP* 3.0 48.1 + - + +
152A THR* 3.5 23.8 + - - +
153A THR* 3.8 0.5 + - - -
253A GLU 5.1 2.6 + - - -
254A ALA* 4.0 21.0 + - + +
257A HIS* 3.8 30.3 - - - +
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Residues in contact with MET 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 PRO* 2.8 33.8 + - + +
143A LEU* 3.6 15.0 - - + +
145A LYS* 1.3 75.9 - - - +
147A PHE* 1.4 91.7 + - + +
152A THR* 4.2 3.8 - - - -
153A THR* 2.7 28.0 + - - +
162A MET* 5.3 0.2 - - - +
237A LEU* 4.9 0.7 - - + -
239A VAL* 4.1 14.1 - - + -
246A PRO* 3.3 16.7 - - + +
250A GLU 4.1 9.2 - - - +
251A VAL* 3.8 29.4 - - + -
254A ALA* 3.8 10.5 - - + -
255A PHE* 3.8 26.5 - - + -
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Residues in contact with PHE 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 LEU* 3.2 24.9 + - + +
146A MET* 1.4 105.8 - - + +
148A ALA* 1.3 59.0 + - - +
156A LEU* 3.5 13.7 - - - +
165A GLY* 5.4 0.3 - - - -
166A PHE* 3.3 47.1 - + + -
168A PHE* 3.5 20.0 - - + -
183A THR* 4.1 4.2 + - - -
205A VAL* 3.8 17.3 - - + -
214A ALA* 3.7 34.3 - - + -
215A ALA* 3.8 23.1 - - + -
239A VAL* 4.3 7.0 - - + -
240A ARG 5.2 0.2 - - - -
246A PRO* 3.5 28.5 - - + -
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Residues in contact with ALA 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 TYR* 2.8 50.8 + - + +
145A LYS 3.6 0.2 + - - -
147A PHE* 1.3 76.5 - - - +
149A ASP* 1.4 58.8 + - - +
150A PRO* 3.3 11.8 - - - +
156A LEU* 3.5 9.8 - - - +
168A PHE* 4.1 3.6 - - + -
183A THR* 3.9 26.2 - - + +
187A ALA* 5.7 1.0 - - + +
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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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144A TYR* 3.4 12.0 + - + -
145A LYS* 3.0 39.7 + - + +
148A ALA* 1.4 74.7 - - - +
150A PRO* 1.3 66.3 - - - +
151A PHE* 3.0 29.0 + - - +
152A THR* 2.8 35.7 + - - -
153A THR 3.0 11.3 + - - -
156A LEU* 3.7 4.2 - - - +
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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