Contacts of the helix formed by residues 156 - 163 (chain A) in PDB entry 3A46
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 PRO 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A LYS 4.8 0.4 - - - +
155A GLN* 1.3 88.8 - - + +
157A ILE* 1.3 57.2 + - - +
158A VAL* 3.1 11.9 - - + -
159A ALA* 2.7 34.0 + - + +
160A LEU* 3.2 9.0 + - - +
187A PRO 3.7 13.0 - - - +
188A HIS* 3.8 18.2 - - + +
189A LYS 3.7 6.1 - - - +
190A LEU* 4.3 7.0 - - + -
269A ILE* 4.4 13.9 - - + -
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Residues in contact with ILE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 3.8 26.0 - - + -
155A GLN 3.2 3.2 + - - -
156A PRO* 1.3 70.4 - - - +
158A VAL* 1.3 66.1 + - - +
160A LEU* 3.3 5.9 + - + -
161A LEU* 3.1 29.0 + - + +
180A LEU* 3.9 27.4 - - + -
185A ILE* 4.4 5.8 - - + -
186A ASP 3.6 14.8 - - - +
187A PRO* 3.2 17.7 - - + +
189A LYS 2.7 21.1 + - - +
191A GLY 4.8 0.2 - - - +
194A LEU* 3.5 30.5 - - + -
202A LEU* 3.8 16.8 - - + -
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PRO* 4.2 2.7 - - + -
157A ILE* 1.3 82.8 - - - +
159A ALA* 1.3 63.2 + - - +
161A LEU* 3.6 1.4 + - - +
162A MET* 3.0 34.0 + - + +
173A ASN* 6.0 0.7 - - - +
176A VAL* 3.5 23.1 - - + -
180A LEU* 3.9 14.4 - - + -
187A PRO* 3.6 20.6 - - + +
269A ILE* 4.1 19.3 - - + -
270A ILE* 3.8 28.0 - - + -
279A THR* 3.9 22.2 - - + +
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Residues in contact with ALA 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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155A GLN* 4.9 9.6 - - + +
156A PRO* 2.7 32.4 + - + +
158A VAL* 1.3 74.0 - - - +
160A LEU* 1.3 64.3 + - + +
162A MET* 3.2 3.3 + - - +
163A ASP* 3.0 23.6 + - - +
270A ILE* 4.0 22.9 - - + -
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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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139A PHE* 5.9 0.2 - - - -
150A ILE* 4.0 26.9 - - + +
153A TYR* 3.4 44.6 - - + -
155A GLN* 3.6 31.6 - - + +
156A PRO 3.2 7.5 + - - +
157A ILE* 3.3 8.7 + - - +
159A ALA* 1.3 77.1 - - - +
161A LEU* 1.3 61.6 + - - +
163A ASP* 3.4 20.6 + - - +
166A LYS* 3.6 19.0 - - + +
167A ILE* 3.8 16.3 + - + +
191A GLY* 3.9 18.4 - - - +
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PHE* 4.2 25.9 - - + -
150A ILE* 4.5 16.6 - - + -
157A ILE* 3.1 26.9 + - + +
158A VAL 4.1 1.6 - - - +
160A LEU* 1.3 77.2 - - - +
162A MET* 1.3 64.5 + - - +
163A ASP 3.2 6.9 + - - +
164A GLN* 4.4 0.3 + - - -
167A ILE* 5.0 1.8 - - + -
171A LEU* 3.6 32.4 - - + +
176A VAL* 3.8 23.8 - - + -
179A ILE* 4.9 5.8 - - + -
180A LEU* 4.0 26.2 - - + -
202A LEU* 4.1 14.8 - - + -
206A ILE* 4.3 11.2 - - + -
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Residues in contact with MET 162 (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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60A LYS* 4.8 2.3 + - - +
158A VAL* 3.0 28.5 + - + +
159A ALA* 3.2 4.7 + - - +
161A LEU* 1.3 76.4 - - - +
163A ASP* 1.3 58.3 + - - +
164A GLN* 2.7 25.5 + - - +
171A LEU 4.1 2.3 - - - +
172A GLY* 3.4 29.8 - - - +
173A ASN* 3.5 35.0 - - - +
176A VAL* 3.7 11.7 - - + -
270A ILE* 3.6 22.2 - - + -
277A ARG* 3.6 31.2 - - + +
21D G 4.5 1.1 - - - +
22D T 4.9 1.6 + - - -
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Residues in contact with ASP 163 (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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159A ALA 3.0 11.8 + - - +
160A LEU* 3.4 19.3 - - - +
161A LEU 3.5 6.8 - - - +
162A MET* 1.3 79.5 - - - +
164A GLN* 1.3 59.6 + - - +
165A LYS* 2.7 31.9 + - - +
166A LYS* 2.8 46.2 + - + +
168A GLY 3.1 15.8 + - - +
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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