Contacts of the helix formed by residues 149 - 160 (chain A) in PDB entry 3TR6
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 ASN 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LYS* 5.4 6.9 - - - +
146A ASP* 2.8 22.6 + - - +
147A LYS 3.1 1.0 - - - -
148A ALA* 1.3 83.6 - - - +
150A THR* 1.3 57.5 + - - +
151A ASP 3.3 3.1 - - - -
152A LEU* 3.3 25.7 + - + +
153A TYR* 2.9 58.5 + - + -
224A SAH 5.0 3.0 + - - -
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Residues in contact with THR 150 (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 ILE* 4.6 16.8 - - + +
145A ALA 5.6 0.7 - - - +
146A ASP 4.1 2.5 - - - +
147A LYS* 2.9 50.5 + - + +
148A ALA 3.5 1.0 - - - -
149A ASN* 1.3 76.8 - - - +
151A ASP* 1.3 60.6 + - - +
153A TYR* 3.7 8.9 - - + +
154A TYR* 2.8 31.4 + - - +
169A VAL* 5.1 9.9 - - + -
170A ASP 6.0 0.9 - - - +
191A ILE* 4.0 14.4 - - + +
194A PHE* 3.8 26.0 - - - +
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Residues in contact with ASP 151 (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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148A ALA 4.9 2.6 + - - +
149A ASN 3.3 0.6 - - - -
150A THR* 1.3 78.0 + - - +
152A LEU* 1.3 60.3 + - - +
154A TYR* 3.2 4.0 + - - +
155A GLU* 2.8 37.2 + - - +
194A PHE* 4.0 19.0 - - + +
197A LYS* 2.7 39.2 + - - +
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Residues in contact with LEU 152 (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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123A LYS* 3.7 42.8 - - + -
149A ASN* 3.3 30.6 + - - +
151A ASP* 1.3 79.6 + - - +
153A TYR* 1.3 64.1 + - + +
155A GLU* 3.1 8.6 + - + +
156A GLU* 2.9 52.6 + - + +
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Residues in contact with TYR 153 (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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68A ILE* 4.2 13.9 - - + -
122A ALA* 3.7 13.9 - - + +
123A LYS* 3.7 27.3 + - + +
126A LEU* 4.0 20.0 - - + +
143A ILE* 3.8 29.6 - - + -
145A ALA* 4.2 10.3 - - + -
146A ASP* 2.8 39.1 + - - -
149A ASN* 2.9 46.6 + - + +
150A THR* 3.8 4.3 - - + +
152A LEU* 1.3 80.5 - - + +
154A TYR* 1.3 54.6 + - - +
156A GLU* 3.8 1.2 - - - +
157A SER* 2.7 38.4 + - - -
224A SAH 3.7 10.9 + - - -
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Residues in contact with TYR 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 3.7 10.5 - - + +
150A THR 2.8 22.8 + - - +
151A ASP 3.4 3.8 - - - +
153A TYR* 1.3 73.2 - - - +
155A GLU* 1.3 75.6 + - - +
157A SER* 3.1 4.3 + - - -
158A LEU* 3.0 31.5 + - + +
167A ILE* 3.7 33.1 - - + +
169A VAL* 4.7 2.5 - - + -
194A PHE* 3.8 24.7 - + + -
197A LYS* 4.0 20.4 - - + -
198A VAL* 3.8 19.3 - - + +
201A ASP* 2.8 28.8 + - - -
203A ARG* 4.0 6.1 - - - -
204A VAL* 3.7 21.5 - - - +
216A THR* 6.4 0.7 - - + -
218A ALA* 4.3 11.6 - - + +
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Residues in contact with GLU 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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151A ASP* 2.8 21.8 + - - +
152A LEU* 3.5 8.5 - - + +
154A TYR* 1.3 82.1 - - - +
156A GLU* 1.3 62.3 + - + +
158A LEU* 3.5 12.8 + - - +
159A LYS* 3.6 33.3 + - - +
197A LYS* 3.2 30.7 + - - -
203A ARG* 2.7 39.8 + - - -
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Residues in contact with GLU 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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123A LYS* 5.0 2.3 - - - +
126A LEU* 3.7 28.4 - - + +
127A ALA* 4.2 19.6 + - - +
130A ILE* 3.4 20.6 - - + +
152A LEU* 2.9 38.8 + - + +
153A TYR 3.9 0.2 - - - +
155A GLU* 1.3 74.7 - - + +
157A SER* 1.3 65.1 + - - +
159A LYS* 3.2 30.4 + - - +
160A LEU* 3.2 25.8 + - - +
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Residues in contact with SER 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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68A ILE* 4.2 4.5 - - - +
126A LEU* 4.7 2.3 - - - +
141A ILE* 3.2 40.5 - - - +
143A ILE* 3.9 6.1 - - - +
153A TYR 2.7 24.4 + - - -
154A TYR* 3.1 6.7 + - - -
156A GLU* 1.3 73.8 - - - +
158A LEU* 1.3 65.6 + - - +
160A LEU* 3.4 2.1 + - - -
161A LEU* 3.0 31.1 + - - +
167A ILE* 3.9 18.2 - - - -
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Residues in contact with LEU 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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154A TYR* 3.0 21.7 + - + +
155A GLU* 3.6 11.0 - - - +
156A GLU 3.2 0.4 - - - -
157A SER* 1.3 74.7 - - - +
159A LYS* 1.3 62.1 + - + +
161A LEU* 3.3 8.0 + - + -
167A ILE* 4.1 15.0 - - + +
201A ASP* 4.0 7.4 - - - +
203A ARG* 3.4 51.8 - - + +
204A VAL* 3.9 21.1 - - + -
218A ALA 5.9 0.2 - - - +
220A LYS* 2.9 56.5 + - + +
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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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130A ILE* 3.8 31.0 - - + -
135A ALA* 3.4 14.2 - - + +
136A TRP* 3.1 22.2 + - - +
155A GLU* 3.6 29.8 + - - +
156A GLU* 3.2 22.4 + - - +
158A LEU* 1.3 78.8 - - + +
160A LEU* 1.3 58.4 + - - +
161A LEU 3.5 1.0 + - - +
220A LYS* 4.1 5.6 + - - +
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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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66A ILE* 4.4 8.7 - - + -
126A LEU* 3.8 39.7 - - + +
129A LEU* 3.8 24.2 - - + -
130A ILE* 3.9 17.9 - - + -
134A GLN* 3.7 21.8 - - + +
135A ALA 4.3 0.2 - - - +
136A TRP 3.6 4.3 - - - +
137A GLN 3.1 7.1 + - - -
138A TYR* 2.9 42.0 + - + +
141A ILE* 4.1 8.7 - - + -
156A GLU 3.2 20.5 + - - +
157A SER* 3.8 4.5 - - - +
158A LEU 3.2 0.8 - - - -
159A LYS* 1.3 76.2 - - - +
161A LEU* 1.3 59.5 + - - +
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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