Contacts of the strand formed by residues 185 - 189 (chain B) in PDB entry 2AY5
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 MET 185 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ALA 4.2 3.8 - - - +
116B LEU* 4.0 16.2 - - - -
119B ALA* 3.5 29.2 - - + -
126B LEU* 3.6 14.1 - - + +
129B ARG 2.8 9.1 + - - +
133B VAL* 3.4 11.7 - - + -
134B PHE* 2.9 29.0 + - - -
184B ASP* 1.3 74.8 - - - +
186B VAL* 1.3 67.0 + - - +
187B LEU 4.1 0.2 - - - -
218B LEU* 3.2 31.9 - - + +
220B LEU* 3.6 40.2 - - + -
251B LEU* 3.9 15.7 - - + -
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Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PHE* 4.0 13.2 - - + -
158B TYR* 4.0 12.3 - - + -
177B LEU* 3.6 33.9 - - + -
180B ALA* 4.7 4.5 - - + -
184B ASP 5.3 0.2 - - - -
185B MET* 1.3 79.7 - - - +
187B LEU* 1.3 56.5 + - - +
188B LEU* 3.4 28.5 - - + +
212B LEU* 4.0 13.5 - - + -
217B ALA* 3.8 25.4 - - + -
218B LEU 2.9 8.2 + - - +
219B PRO* 3.5 0.3 - - - +
220B LEU 2.7 32.4 + - - +
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 4.3 2.7 - - + -
133B VAL* 4.5 6.7 - - + +
134B PHE 3.0 19.1 + - - +
135B VAL* 4.3 9.4 - - + -
136B SER 4.6 1.0 + - - -
139B THR* 5.3 0.7 - - - +
143B HIS* 3.4 42.0 - - + +
147B MET* 3.6 21.3 - - + -
158B TYR* 2.8 23.2 + - - -
185B MET* 4.1 1.0 - - - +
186B VAL* 1.3 70.0 - - - +
188B LEU* 1.3 62.7 + - - +
189B HIS* 4.7 5.9 - - + +
220B LEU* 3.3 39.3 - - + +
222B ASP* 3.9 24.9 - - + -
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B TYR* 3.4 22.9 - - + +
160B TYR* 6.2 0.4 - - + -
173B MET* 3.9 23.1 - - + -
177B LEU* 5.0 0.7 - - + -
186B VAL* 3.4 36.6 - - + +
187B LEU* 1.3 74.2 - - - +
189B HIS* 1.3 63.4 + - - +
200B LEU* 5.6 0.9 - - + -
205B TRP* 4.2 27.1 - - + -
208B ILE* 4.8 9.9 - - + -
212B LEU* 4.8 8.1 - - + -
219B PRO* 4.3 16.8 - - + -
220B LEU 2.9 7.8 + - - +
221B ILE* 3.2 10.9 - - + -
222B ASP* 2.8 26.9 + - - +
243B ILE* 6.5 0.2 - - + -
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Residues in contact with HIS 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B SER* 3.9 4.6 + - - -
139B THR* 2.9 24.2 + - - -
140B TRP 4.2 0.9 - - - -
143B HIS* 3.9 18.4 - + - -
158B TYR* 5.1 2.0 + - - -
187B LEU* 4.7 5.8 - - + +
188B LEU* 1.3 79.7 - - - +
190B GLY* 1.3 65.8 + - - +
191B CYS* 3.3 14.2 + - - +
192B CYS 4.8 1.6 + - - -
193B HIS* 3.5 32.0 + + + -
194B ASN 3.3 38.7 + - - -
205B TRP* 3.5 17.5 - - - -
222B ASP* 3.5 12.5 + - + +
413B PLP 4.5 12.8 - - + +
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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
------------------------------------------------------------
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