Contacts of the helix formed by residues 146 - 157 (chain A) in PDB entry 3U81
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 ARG 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A GLN* 3.4 52.1 + - - +
142A HIS* 3.6 17.5 - - + +
143A TRP* 2.9 27.2 + - + +
145A ASP* 1.3 80.9 + - + +
147A TYR* 1.3 64.7 + - - +
148A LEU 3.3 2.0 - - - -
149A PRO* 3.5 33.4 + - - +
150A ASP* 2.8 53.9 + - - +
153A LEU* 4.8 4.6 - - - +
222A SAH 4.2 5.6 - - - -
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Residues in contact with TYR 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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140A LEU* 3.2 36.4 + - + +
141A ASP* 3.4 2.8 - - - -
142A HIS* 3.6 39.3 - + - -
143A TRP 3.6 9.0 - - - -
144A LYS* 2.8 43.7 + - + +
146A ARG* 1.3 76.7 - - - +
148A LEU* 1.3 58.6 + - - +
151A THR* 2.8 32.7 + - - -
168A ALA* 3.8 20.9 - - + -
169A ASP 2.7 29.9 + - - -
176A THR* 3.6 20.4 - - + -
179A PHE* 3.9 19.3 - + + -
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Residues in contact with LEU 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 LYS 4.8 0.6 + - - -
145A ASP 5.0 0.2 - - - -
147A TYR* 1.3 75.8 - - - +
149A PRO* 1.3 75.3 - - + +
151A THR* 3.1 3.2 + - - -
152A LEU* 3.0 40.6 + - + +
178A ASP* 3.8 31.6 - - + +
179A PHE* 4.0 21.0 - - + +
182A TYR* 3.4 42.4 - - + -
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Residues in contact with PRO 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 ASP 3.3 26.5 - - - +
146A ARG* 3.5 32.7 + - - +
148A LEU* 1.3 95.8 - - + +
150A ASP* 1.3 58.0 + - - +
152A LEU* 3.3 10.6 + - + +
153A LEU* 2.9 27.4 + - - +
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Residues in contact with ASP 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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65A LEU* 4.3 8.3 - - + -
119A SER* 2.7 28.9 + - - -
120A GLN* 4.0 8.7 - - - -
123A ILE* 4.0 15.9 - - + +
140A LEU* 5.4 0.4 - - + -
142A HIS* 2.7 20.7 + - + +
146A ARG* 2.8 50.5 + - - +
147A TYR 4.3 0.7 - - - +
149A PRO* 1.3 69.9 - - - +
151A THR* 1.3 60.7 + - - +
153A LEU* 3.6 8.3 - - - +
154A LEU* 2.8 35.7 + - - +
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Residues in contact with THR 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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140A LEU* 3.7 9.4 - - - +
147A TYR 2.8 22.6 + - - -
148A LEU* 3.5 5.8 - - - -
150A ASP* 1.3 77.2 - - - +
152A LEU* 1.3 63.0 + - - +
154A LEU* 3.3 11.4 + - - +
155A GLU* 3.0 37.5 + - + +
160A LEU* 4.5 1.5 - - + +
166A LEU* 3.8 23.3 - - + +
179A PHE* 3.4 22.0 - - + -
182A TYR* 4.3 8.7 - - + -
183A VAL* 4.9 0.2 - - + -
189A PHE* 3.9 12.6 - - + -
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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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148A LEU* 3.0 37.8 + - + +
149A PRO* 3.6 10.1 - - + +
151A THR* 1.3 75.8 - - - +
153A LEU* 1.3 57.1 + - - +
155A GLU* 3.4 10.8 + - + +
156A LYS* 3.0 29.2 + - - +
182A TYR* 3.5 38.4 - - + +
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Residues in contact with LEU 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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120A GLN* 3.8 34.3 - - + +
123A ILE* 3.9 25.8 - - + -
124A PRO* 4.1 9.0 - - + -
146A ARG* 4.8 3.8 - - - +
149A PRO 2.9 15.3 + - - +
150A ASP* 3.6 13.0 - - - +
151A THR 3.2 0.2 - - - -
152A LEU* 1.3 73.9 - - - +
154A LEU* 1.3 66.0 + - - +
156A LYS* 3.2 8.8 + - + +
157A CYS* 2.9 43.1 + - - -
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Residues in contact with LEU 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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63A LEU* 4.0 11.9 - - + -
65A LEU* 5.0 4.9 - - + -
123A ILE* 3.8 30.1 - - + -
135A LEU* 3.9 20.9 - - + -
138A VAL* 4.2 30.1 - - + -
140A LEU* 5.7 1.6 - - + -
150A ASP 2.8 24.8 + - - +
151A THR* 3.6 11.2 - - - +
153A LEU* 1.3 76.9 - - - +
155A GLU* 1.3 64.1 + - - +
157A CYS 3.5 0.3 + - - -
158A GLY 3.3 2.9 + - - -
159A LEU* 3.1 41.3 + - + +
160A LEU* 4.0 17.2 + - + -
166A LEU* 5.7 3.4 - - + -
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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 THR* 3.0 16.3 + - - +
152A LEU* 3.4 17.6 - - - +
154A LEU* 1.3 76.7 - - - +
156A LYS* 1.3 63.4 + - - +
158A GLY* 3.0 14.6 + - - -
160A LEU* 3.6 25.5 - - + +
182A TYR* 2.6 39.7 + - - -
188A SER* 5.0 3.5 + - - -
189A PHE* 3.6 14.0 - - - -
212A TYR* 4.0 23.6 + - + +
215A PRO* 5.9 0.5 - - - +
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Residues in contact with LYS 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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152A LEU 3.0 17.0 + - - +
153A LEU* 3.2 11.2 + - + +
155A GLU* 1.3 77.2 - - - +
157A CYS* 1.3 64.3 + - - +
158A GLY* 3.3 1.0 + - - -
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Residues in contact with CYS 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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123A ILE* 4.5 1.3 - - - +
124A PRO* 4.0 30.1 - - + -
127A LYS* 3.2 23.2 - - + +
153A LEU* 2.9 37.3 + - - +
154A LEU 3.5 0.4 + - - +
155A GLU 3.2 0.2 - - - -
156A LYS* 1.3 78.7 - - - +
158A GLY* 1.3 61.7 + - - +
159A LEU* 3.3 21.0 + - + +
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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