Contacts of the strand formed by residues 184 - 190 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115D LYS* 2.9 22.7 + - - -
125D VAL* 3.3 26.9 - - + +
127D ILE* 3.8 29.2 - - + -
175D ASN 4.5 4.3 - - - +
176D ILE* 4.8 5.2 - - + -
179D HIS* 3.8 14.6 - - + -
180D GLY 3.5 19.1 - - - +
181D ALA* 3.2 8.6 + - - +
183D ASN* 1.3 77.1 - - - +
185D VAL* 1.3 65.4 + - - +
186D ALA 3.4 19.5 + - - +
187D ILE* 4.4 2.7 - - + -
218D ILE* 3.8 37.6 - - + +
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Residues in contact with VAL 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LEU* 3.6 16.4 - - + +
112D LEU* 3.5 40.2 - - + +
115D LYS* 4.4 14.3 - - + +
121D ALA* 4.6 6.5 - - + -
124D PRO* 3.6 30.7 - - + -
125D VAL 2.9 10.6 + - - +
126D PHE* 3.6 31.9 - - + -
183D ASN 4.2 1.3 - - - +
184D ILE* 1.3 72.9 - - - +
186D ALA* 1.3 61.0 + - - +
219D PHE* 4.0 14.2 + - - +
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Residues in contact with ALA 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LEU* 4.1 17.9 - - + -
125D VAL 4.1 0.6 + - - -
126D PHE* 3.5 26.5 - - + +
127D ILE 3.2 20.6 + - - -
184D ILE* 3.2 4.3 - - - +
185D VAL* 1.3 82.7 - - - +
187D ILE* 1.3 70.1 + - - +
188D VAL* 5.2 0.2 - - + -
218D ILE* 4.0 6.3 - - - -
219D PHE* 3.1 17.3 - - + +
221D VAL* 4.4 4.9 - - + -
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Residues in contact with ILE 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ILE* 3.1 24.2 - - + +
167D PHE* 3.8 27.6 - - + -
172D LEU* 4.2 21.1 - - + -
176D ILE* 5.2 1.6 - - + -
184D ILE* 4.4 3.8 - - + -
186D ALA* 1.3 77.4 - - - +
188D VAL* 1.3 62.9 + - - +
189D SER* 4.4 3.1 - - - +
209D VAL* 3.8 17.0 - - + -
213D ALA* 3.8 30.5 - - + -
218D ILE* 3.9 18.6 - - + -
219D PHE 2.9 6.7 + - - -
220D VAL* 3.4 10.7 - - + +
221D VAL* 2.9 27.9 + - - +
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Residues in contact with VAL 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D PHE* 4.2 17.3 - - + -
126D PHE* 4.1 25.8 - - + -
127D ILE 2.8 9.4 + - - +
128D SER* 2.6 42.0 + - - +
131D HIS* 4.2 12.6 - - + +
135D THR* 4.4 13.0 - - + -
167D PHE* 3.6 5.0 - - - -
186D ALA* 5.2 0.7 - - + -
187D ILE* 1.3 75.9 - - - +
189D SER* 1.3 58.8 + - - +
190D THR* 4.0 8.5 - - - +
221D VAL* 3.2 14.4 - - + +
223D ASP* 3.9 26.7 - - + +
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Residues in contact with SER 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ASN* 5.8 0.2 - - - -
167D PHE* 3.5 27.7 - - - -
187D ILE* 4.0 2.3 + - - +
188D VAL* 1.3 69.8 - - - +
190D THR* 1.3 62.8 + - - +
191D VAL* 3.6 1.3 + - - -
201D VAL* 6.1 0.2 - - - -
206D LEU* 4.0 13.9 - - - +
209D VAL* 4.4 4.3 - - - +
220D VAL* 3.9 17.1 - - - +
221D VAL 2.9 11.6 + - - -
222D MET* 3.4 26.1 - - - +
223D ASP 2.8 24.8 + - - +
256D TYR 5.0 2.0 + - - -
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Residues in contact with THR 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D SER* 3.3 10.0 + - - -
129D ASN* 2.9 33.5 + - - -
130D PHE 3.0 24.3 + - - +
131D HIS* 4.7 1.2 - - - -
132D PHE 4.8 2.8 + - - +
135D THR* 6.1 0.2 - - - +
188D VAL* 4.0 8.5 - - - +
189D SER* 1.3 71.4 - - - +
191D VAL* 1.3 58.7 + - - +
192D THR 3.3 21.5 - - - +
193D CYS* 3.3 2.5 + - - -
194D ASN* 4.2 10.1 - - + +
201D VAL* 3.5 3.5 - - - +
223D ASP* 3.8 11.0 + - - +
266D LLP 3.6 28.9 - - + -
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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