Contacts of the strand formed by residues 156 - 160 (chain A) in PDB entry 6PAU
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 PHE 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A LEU* 3.9 16.8 - - + +
153A PRO* 3.3 41.4 + - + +
154A GLN 3.7 11.2 - - - -
155A GLY* 1.3 83.1 + - - +
157A MET* 1.3 62.2 + - - +
214A VAL* 3.9 23.8 - - + -
215A ARG 3.4 6.7 - - - +
216A VAL* 4.6 2.5 - - + -
217A SER* 3.3 7.9 + - - -
223A VAL* 4.0 13.2 - - + -
254A LEU* 3.2 37.7 - - + -
257A LYS* 3.8 28.5 - - + -
259A VAL* 4.1 19.5 - - + -
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Residues in contact with MET 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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152A LEU* 3.5 8.7 - - - -
156A PHE* 1.3 76.0 - - - +
158A TRP* 1.3 74.3 + - - +
159A ASP* 4.9 5.4 - - + -
214A VAL* 3.4 4.7 - - - -
215A ARG* 2.9 58.4 + - + +
216A VAL 4.7 0.4 - - - +
217A SER* 3.8 18.2 - - - +
220A LYS* 3.9 36.6 - - + -
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Residues in contact with TRP 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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149A PRO* 3.7 22.0 - - + +
150A TYR 2.8 23.7 + - - -
152A LEU* 3.6 21.0 - - + +
157A MET* 1.3 87.8 - - - +
159A ASP* 1.3 63.7 + - - +
212A CYS* 3.4 33.2 - - - -
213A GLY 3.7 7.9 - - - -
214A VAL* 3.5 20.0 - - + -
262A VAL* 3.5 37.5 - - + -
263A LEU* 3.9 5.4 - - + -
266A GLU* 3.4 29.4 - - + -
270A ARG* 4.3 15.0 - - - +
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Residues in contact with ASP 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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157A MET* 4.9 5.4 - - + -
158A TRP* 1.3 78.1 - - - +
160A THR* 1.3 76.4 + - - +
161A LEU* 3.5 7.9 + - + +
212A CYS* 5.3 0.4 - - - -
213A GLY* 2.9 36.0 + - - +
215A ARG* 2.5 51.1 + - + +
270A ARG* 5.6 1.6 - - - -
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Residues in contact with THR 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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159A ASP* 1.3 83.0 + - - +
161A LEU* 1.3 62.4 + - - +
162A ASP* 3.6 3.6 + - - +
208A LEU* 2.9 50.3 - - + +
209A GLN* 3.8 7.7 - - + +
211A HIS 3.7 6.1 - - - +
270A ARG* 3.2 24.1 + - - +
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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