Contacts of the strand formed by residues 146 - 151 (chain B) in PDB entry 2ARE
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 HIS 146 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLU* 3.4 8.9 - - - +
129B PHE* 3.7 1.7 - - - -
130B ASP* 3.0 46.4 + - + +
133B TYR* 4.5 3.1 - - + -
141B ASP* 3.1 18.3 + - + -
142B PRO* 3.4 16.8 - - + +
144B TYR* 2.7 27.1 + - + +
145B PRO* 1.3 74.1 - - - +
147B ILE* 1.3 65.4 + - - +
159B THR* 3.8 25.4 - - + -
160B VAL 3.3 16.2 - - - +
162B TRP* 3.7 11.4 - - - +
282B MN 2.2 35.7 + - - -
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Residues in contact with ILE 147 (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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127B VAL* 4.2 17.5 - - + -
128B GLU 3.3 9.4 - - - +
129B PHE* 3.7 31.9 - - + -
146B HIS* 1.3 76.4 - - - +
148B GLY* 1.3 64.0 + - - +
159B THR* 3.2 4.2 - - - -
160B VAL* 3.0 40.7 + - + +
162B TRP* 3.9 24.0 - - + -
185B VAL* 4.5 5.6 - - + -
187B ALA* 4.2 9.4 - - + -
195B TYR* 3.8 29.2 - - + -
197B VAL* 4.1 21.1 - - + +
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 3.4 8.1 - - - +
128B GLU* 2.9 47.7 + - - +
146B HIS* 4.5 0.2 - - - -
147B ILE* 1.3 77.1 - - - +
149B ILE* 1.3 64.3 + - - -
150B ASP* 4.0 0.4 - - - -
156B SER* 3.8 7.2 - - - -
158B LYS 3.2 10.3 - - - -
159B THR* 4.1 4.0 - - - -
197B VAL* 5.9 0.4 - - - -
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Residues in contact with ILE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 5.3 0.4 - - + -
126B ALA 3.6 6.1 - - - +
127B VAL* 4.8 2.9 - - + -
148B GLY* 1.3 74.6 - - - +
150B ASP* 1.3 66.3 + - - +
151B VAL* 4.3 11.4 - - + -
156B SER* 3.4 0.3 - - - -
157B VAL* 2.9 46.1 + - + +
158B LYS* 3.0 10.5 + - + +
183B LEU* 4.0 30.3 - - + +
185B VAL* 4.4 13.0 - - + -
197B VAL* 4.1 37.0 - - + +
198B SER 4.1 0.9 - - - -
199B TYR* 3.7 32.8 - - + +
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Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 5.0 1.2 - - - +
110B LEU* 5.1 1.2 - - - +
111B PHE* 4.6 8.7 - - + -
124B VAL 3.7 1.1 - - - +
125B ILE* 3.3 5.7 - - - +
126B ALA* 2.7 53.4 + - + +
128B GLU* 2.6 35.6 - - - +
149B ILE* 1.3 74.1 - - - +
151B VAL* 1.3 63.1 + - - +
152B ASN 4.0 0.7 - - - -
153B SER 3.4 21.1 - - - +
154B ILE* 4.1 10.5 - - - +
156B SER* 2.6 31.8 + - - +
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B THR* 4.1 6.4 - - - +
124B VAL 3.6 2.9 - - - -
125B ILE* 4.6 10.3 - - + -
149B ILE* 4.1 8.8 + - + -
150B ASP* 1.3 76.2 - - - +
152B ASN* 1.3 68.7 + - - +
153B SER* 3.1 13.8 + - - +
155B ARG 5.6 0.4 + - - -
157B VAL* 4.0 24.9 - - + +
183B LEU* 6.1 0.2 - - + -
199B TYR* 4.1 27.4 - - + +
201B VAL* 4.6 11.9 - - + -
206B VAL* 4.0 34.3 - - + -
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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