Contacts of the helix formed by residues 159 - 162 (chain A) in PDB entry 4L2A
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 TRP 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A TYR* 3.6 17.3 - - - -
69A GLN* 3.3 18.0 - - - +
120A SER* 3.3 30.2 - - - +
121A SER 3.5 17.1 - - - +
122A TRP* 3.5 8.2 - + - +
140A ASN* 3.1 32.5 + - - -
157A ASP* 3.2 23.4 + - - +
158A LEU* 1.3 81.1 - - - +
160A GLU* 1.3 58.4 + - - +
161A HIS* 3.6 34.5 - + + +
162A ALA* 2.9 24.4 + - - +
163A TYR* 3.5 2.8 - - - -
118B PHE* 3.9 17.3 - + - -
119B GLY* 3.7 29.8 - - - -
160B GLU* 4.0 13.5 - - + -
171B ARG* 5.8 2.5 - - - -
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Residues in contact with GLU 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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119A GLY 6.0 2.5 - - - +
120A SER* 5.1 3.2 + - - +
158A LEU 3.3 2.0 + - - +
159A TRP* 1.3 71.9 - - - +
161A HIS* 1.4 58.2 + - - +
162A ALA 3.1 0.3 + - - -
163A TYR* 3.2 26.5 + - + +
164A TYR* 2.8 45.4 + - + +
171A ARG* 5.3 2.9 - - - +
30B HIS* 3.6 11.1 - - - -
120B SER* 5.1 0.6 + - - -
159B TRP* 4.0 18.5 - - + -
160B GLU* 3.3 24.2 + - + +
161B HIS* 2.7 57.7 + - - +
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Residues in contact with HIS 161 (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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22A THR* 4.4 9.5 - - - +
26A HIS* 3.1 26.5 + + - +
30A HIS* 3.4 38.3 + + + +
34A TYR* 4.3 9.9 - - - -
73A HIS* 3.6 1.3 + - - -
157A ASP* 3.6 1.0 + - - -
159A TRP* 3.6 31.0 - + + +
160A GLU* 1.4 71.4 - - - +
162A ALA* 1.3 77.2 + - - +
163A TYR 3.3 0.6 + - - -
164A TYR 4.3 2.7 + - - -
165A ILE* 5.2 3.1 + - - +
5000A FE 2.1 32.1 - - - -
160B GLU* 2.7 36.9 + - - +
164B TYR* 3.5 29.1 + - + +
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Residues in contact with ALA 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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18A ILE* 5.1 3.3 - - - +
22A THR* 3.5 18.2 - - - +
26A HIS* 3.5 30.5 + - + -
76A TYR* 4.3 2.9 + - - +
157A ASP* 3.6 25.8 - - - +
159A TRP 2.9 17.3 + - - +
161A HIS* 1.3 81.4 - - - +
163A TYR* 1.3 59.5 + - + +
166A ASP* 5.0 0.7 - - - +
174A TYR* 3.8 16.6 - - + +
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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