Contacts of the helix formed by residues 163 - 168 (chain A) in PDB entry 3LIO
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 TYR 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A THR* 5.4 0.9 - - - -
158A LEU* 3.6 22.4 - - - -
159A TRP 3.7 10.8 - - - -
160A GLU* 3.1 23.2 + - + +
162A ALA* 1.3 79.8 - - + +
164A TYR* 1.3 67.8 + + - +
165A ILE* 3.2 3.4 - - - -
166A ASP* 3.1 6.7 + - - +
167A TYR* 2.8 42.9 + - + +
168A ARG 3.2 28.0 - - - -
169A ASN* 4.6 7.9 + - - -
171A ARG* 2.9 43.0 + - + +
174A TYR* 3.5 50.5 - + + -
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Residues in contact with TYR 164 (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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160A GLU* 2.8 32.3 + - + +
161A HIS 4.3 1.4 + - - -
162A ALA 4.0 0.2 - - - -
163A TYR* 1.3 81.0 - + - +
165A ILE* 1.3 58.2 - - - +
168A ARG* 2.9 75.0 + - - +
169A ASN* 3.6 2.0 + - - -
25B PHE* 3.7 15.6 - - - +
26B HIS 5.1 0.2 + - - -
30B HIS* 2.7 38.9 + + - -
161B HIS* 3.7 24.6 + - + +
164B TYR* 4.2 28.5 - + + -
165B ILE* 3.7 34.8 - - + -
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Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 4.3 4.0 - - - +
21A GLU* 3.7 23.1 - - + +
22A THR* 3.5 24.5 - - - +
25A PHE* 4.0 17.9 - - + -
161A HIS 5.3 3.6 - - - +
163A TYR 3.2 0.4 - - - -
164A TYR* 1.3 77.3 - - - +
166A ASP* 1.3 71.8 + - - +
168A ARG* 3.2 18.7 + - - +
164B TYR* 3.7 27.8 - - + -
168B ARG* 3.6 33.4 - - - +
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Residues in contact with ASP 166 (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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16A PRO 6.1 0.9 - - - +
17A HIS 4.5 1.1 - - - +
18A ILE* 3.7 8.6 - - - +
19A SER* 2.7 46.0 + - - -
22A THR* 2.8 22.5 + - - +
162A ALA 5.1 2.1 - - - +
163A TYR* 3.1 3.5 + - - +
165A ILE* 1.3 83.3 - - - +
167A TYR* 1.3 89.8 + - + +
168A ARG* 3.9 1.3 - - - -
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Residues in contact with TYR 167 (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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16A PRO 3.9 4.8 + - - -
17A HIS* 2.5 39.1 + - - -
18A ILE* 5.3 1.1 - - + -
163A TYR* 2.8 24.0 + - + +
166A ASP* 1.3 98.3 - - + +
168A ARG* 1.3 71.4 + - - +
170A VAL* 3.0 33.6 + - - +
173A ASP* 3.5 38.7 + - + -
174A TYR* 3.6 34.5 - + + +
177A GLY* 4.2 5.2 - - - -
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Residues in contact with ARG 168 (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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163A TYR* 3.2 17.4 + - - -
164A TYR* 2.9 72.7 + - + -
165A ILE* 3.2 23.2 + - - +
166A ASP 5.5 0.7 - - - -
167A TYR* 1.3 80.5 - - - +
169A ASN* 1.3 62.9 + - - +
170A VAL* 5.5 0.4 - - + -
21B GLU* 2.7 35.3 + - - -
25B PHE* 3.6 35.6 - - + -
165B ILE* 3.7 22.6 - - - +
168B ARG* 5.7 6.7 - - - +
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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