Contacts of the strand formed by residues 184 - 190 (chain B) in PDB entry 1AX4
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 ILE 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LYS* 2.8 26.3 + - - -
125B VAL* 3.3 26.9 - - + +
127B ILE* 3.7 28.9 - - + -
175B ASN 4.5 4.7 - - - +
176B ILE* 4.8 5.2 - - + -
179B HIS* 3.9 13.2 - - + -
180B GLY 3.5 19.5 - - - +
181B ALA* 3.1 8.3 + - - +
182B ASP 3.4 0.2 - - - -
183B ASN* 1.3 76.2 - - - +
185B VAL* 1.3 68.0 - - - +
186B ALA 3.5 19.2 + - - +
187B ILE* 4.4 2.7 - - + -
218B ILE* 3.8 38.3 - - + +
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Residues in contact with VAL 185 (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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111B LEU* 3.6 15.9 - - + +
112B LEU* 3.6 35.4 - - + +
115B LYS* 4.5 13.8 + - + +
121B ALA* 4.6 7.2 - - + -
124B PRO* 3.6 31.2 - - + -
125B VAL 2.8 13.8 + - - +
126B PHE* 3.6 36.1 - - + -
183B ASN 4.3 0.4 - - - +
184B ILE* 1.3 74.8 - - - +
186B ALA* 1.3 61.6 + - - +
219B PHE* 4.0 14.6 + - - +
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Residues in contact with ALA 186 (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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111B LEU* 4.2 16.6 - - + -
125B VAL 4.1 0.6 + - - -
126B PHE* 3.6 27.5 - - + -
127B ILE 3.2 21.1 + - - -
184B ILE* 3.3 6.2 - - - +
185B VAL* 1.3 83.5 - - - +
187B ILE* 1.3 70.2 + - - +
218B ILE* 4.0 3.6 - - - -
219B PHE* 3.2 17.5 - - + +
221B VAL* 4.4 6.3 - - + -
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Residues in contact with ILE 187 (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 ILE* 3.2 22.2 - - + +
167B PHE* 3.7 29.4 - - + -
172B LEU* 4.1 20.9 - - + -
176B ILE* 5.2 1.8 - - + -
184B ILE* 4.4 3.8 - - + -
186B ALA* 1.3 77.6 - - - +
188B VAL* 1.3 63.6 - - - +
189B SER* 4.5 2.9 - - - +
209B VAL* 3.8 15.9 - - + +
213B ALA* 3.8 29.6 - - + +
218B ILE* 3.9 18.1 - - + +
219B PHE 2.9 6.9 + - - -
220B VAL* 3.4 11.9 - - + +
221B VAL* 2.8 27.4 + - - +
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Residues in contact with VAL 188 (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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108B PHE* 4.3 16.4 - - + -
126B PHE* 4.0 26.2 - - + -
127B ILE 2.8 10.0 + - - +
128B SER* 2.4 46.5 + - - +
129B ASN* 3.6 1.2 - - - +
131B HIS* 4.1 13.5 - - + +
135B THR* 4.4 14.1 - - + -
167B PHE* 3.7 3.3 - - - -
186B ALA* 5.1 0.7 - - + -
187B ILE* 1.3 75.3 - - - +
189B SER* 1.3 57.6 - - - +
190B THR* 4.0 3.4 - - - +
221B VAL* 3.2 14.1 - - + +
223B ASP* 3.9 26.7 - - + +
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Residues in contact with SER 189 (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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129B ASN* 4.9 0.2 - - - -
167B PHE* 3.5 28.2 - - - -
187B ILE* 4.0 0.9 - - - +
188B VAL* 1.3 70.1 - - - +
190B THR* 1.3 63.0 + - - +
191B VAL 3.5 1.0 + - - -
201B VAL* 6.3 0.2 - - - -
206B LEU* 4.0 15.1 + - - +
209B VAL* 4.4 5.4 - - - +
220B VAL* 4.0 16.4 - - - +
221B VAL 2.8 11.7 + - - -
222B MET* 3.5 24.5 - - - +
223B ASP 2.9 24.6 + - - +
256B TYR 5.0 2.3 + - - -
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Residues in contact with THR 190 (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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128B SER* 3.2 10.0 + - - -
129B ASN* 2.9 33.1 + - - -
130B PHE 3.0 24.7 + - - +
131B HIS* 4.7 1.0 - - - -
132B PHE 4.9 2.4 + - - +
188B VAL* 3.9 8.7 + - - +
189B SER* 1.3 71.7 - - - +
191B VAL* 1.3 60.5 + - - +
192B THR 3.3 23.2 - - - +
193B CYS* 3.4 2.7 + - - -
194B ASN* 4.2 9.9 - - + +
201B VAL* 3.5 3.6 - - - +
223B ASP* 3.8 9.6 + - - +
266B LLP 3.6 29.8 - - + -
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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
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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