Contacts of the strand formed by residues 133 - 137 (chain B) in PDB entry 2AY6
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 VAL 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 4.3 14.1 - - + -
126B LEU* 3.7 25.1 - - + -
129B ARG* 1.3 78.8 - - - +
134B PHE* 1.3 68.2 - - - +
135B VAL* 4.2 0.2 - - + -
147B MET* 3.6 37.9 - - + -
152B LEU* 4.8 8.1 - - + -
154B PRO 2.9 13.5 + - - +
155B VAL* 3.3 6.8 - - + +
156B GLN* 2.8 31.7 + - - +
185B MET* 3.4 21.1 - - + +
187B LEU* 4.6 6.3 - - + -
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Residues in contact with PHE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 4.6 3.6 - - + -
133B VAL* 1.3 76.0 - - - +
135B VAL* 1.3 65.9 + - - +
156B GLN* 3.2 46.4 - - + -
157B THR 4.8 2.0 - - - -
158B TYR* 4.1 22.9 - - + -
176B ASP* 4.3 15.5 - - + -
177B LEU* 4.7 9.6 - - + -
179B ALA* 4.8 4.5 - - + -
180B ALA* 3.6 37.9 - - + -
184B ASP* 3.8 22.7 - - + -
185B MET 2.9 18.2 + - - +
186B VAL* 4.3 13.7 - - + -
187B LEU* 3.0 26.6 + - - +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL* 4.2 1.1 - - + -
134B PHE* 1.3 80.6 - - - +
136B SER* 1.3 66.2 + - - +
139B THR* 4.2 20.0 - - + +
143B HIS* 4.9 2.0 - - + -
144B VAL* 4.4 7.9 - - + -
147B MET* 3.7 36.6 - - + -
155B VAL* 3.7 12.3 - - + -
156B GLN 2.9 17.1 + - - +
157B THR* 3.2 21.9 - - + -
158B TYR* 2.9 29.3 + - - -
187B LEU* 4.2 13.0 - - + -
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Residues in contact with SER 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B VAL* 1.3 80.2 - - - +
137B ASP* 1.3 58.7 + - - +
138B PRO* 2.8 32.9 + - - +
139B THR* 3.3 22.3 + - - +
157B THR* 4.9 2.0 - - - +
158B TYR* 3.3 36.3 + - - -
160B TYR* 3.9 7.4 - - - -
187B LEU* 4.6 1.6 + - - +
189B HIS* 3.4 4.3 + - - -
193B HIS* 3.0 21.2 + - - -
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Residues in contact with ASP 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B SER* 1.3 74.1 - - - +
138B PRO* 1.3 66.6 - - - +
157B THR* 4.6 14.2 - - - +
158B TYR 3.1 20.6 + - - +
159B ARG* 4.4 9.5 - - + +
160B TYR* 3.6 3.8 + - - +
161B PHE* 3.0 29.0 + - - +
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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