Contacts of the strand formed by residues 184 - 190 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A LYS* 2.9 24.9 + - - -
125A VAL* 3.3 27.4 - - + +
127A ILE* 3.7 27.8 - - + -
175A ASN 4.5 4.5 - - - +
176A ILE* 4.7 5.6 - - + -
179A HIS* 3.9 13.9 - - + -
180A GLY 3.5 18.2 - - - +
181A ALA* 3.1 10.7 + - - +
182A ASP 3.4 0.2 - - - -
183A ASN* 1.3 74.5 - - - +
185A VAL* 1.3 67.6 + - - +
186A ALA 3.8 18.8 - - - +
187A ILE* 4.4 3.6 - - + -
218A ILE* 3.8 36.4 - - + +
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 3.6 15.8 - - + +
112A LEU* 3.6 36.3 - - + +
115A LYS* 4.5 12.7 - - + +
121A ALA* 4.6 7.0 - - + -
124A PRO* 3.6 32.1 - - + -
125A VAL 2.8 17.8 + - - +
126A PHE* 3.5 32.5 - - + -
183A ASN 4.2 0.9 - - - +
184A ILE* 1.3 74.3 - - - +
186A ALA* 1.3 59.3 + - - +
218A ILE* 4.9 0.2 - - - -
219A PHE* 4.1 14.0 + - - +
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 4.1 17.3 - - + -
125A VAL 4.0 0.6 + - - -
126A PHE* 3.5 28.8 - - + -
127A ILE 3.2 21.1 + - - +
184A ILE* 3.3 6.1 - - - +
185A VAL* 1.3 82.2 - - - +
187A ILE* 1.3 69.6 + - - +
188A VAL* 5.0 0.2 - - + -
218A ILE* 4.0 3.4 - - - -
219A PHE* 3.2 17.3 - - + +
221A VAL* 4.3 5.6 - - + -
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Residues in contact with ILE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ILE* 3.2 22.2 - - + +
167A PHE* 3.8 27.1 - - + -
172A LEU* 4.1 21.8 - - + -
176A ILE* 5.0 1.6 - - + -
184A ILE* 4.4 3.6 - - + -
186A ALA* 1.3 77.7 - - - +
188A VAL* 1.3 64.1 + - - +
189A SER* 4.5 3.4 - - - +
209A VAL* 3.8 17.7 - - + -
213A ALA* 3.8 29.8 - - + -
218A ILE* 3.9 19.0 - - + +
219A PHE 2.8 6.9 + - - +
220A VAL* 3.4 11.8 - - + +
221A VAL* 2.9 26.3 + - - +
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 4.2 18.2 - - + -
126A PHE* 4.0 26.5 - - + -
127A ILE 2.7 10.5 + - - +
128A SER* 2.5 42.3 + - - +
129A ASN* 3.6 1.4 - - - +
131A HIS* 4.2 11.9 - - + +
135A THR* 4.4 13.7 - - + -
167A PHE* 3.7 3.2 - - - -
186A ALA* 5.0 0.7 - - + -
187A ILE* 1.3 76.6 - - - +
189A SER* 1.3 59.7 + - - +
190A THR* 3.5 7.8 + - - +
221A VAL* 3.2 14.4 - - + +
223A ASP* 3.9 26.9 - - + +
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Residues in contact with SER 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ASN* 4.9 0.2 - - - -
167A PHE* 3.5 28.1 - - - -
187A ILE* 4.0 0.8 + - - +
188A VAL* 1.3 71.3 - - - +
190A THR* 1.3 61.4 + - - +
191A VAL* 3.7 1.1 + - - -
201A VAL* 6.4 0.2 - - - -
206A LEU* 4.0 23.8 + - - +
209A VAL* 4.4 5.9 - - - +
220A VAL* 3.9 16.2 - - - +
221A VAL 2.8 12.0 + - - -
222A MET* 3.4 15.4 - - - +
223A ASP 2.9 25.1 + - - +
256A TYR 5.0 2.2 + - - -
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Residues in contact with THR 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A SER* 3.3 10.6 + - - -
129A ASN* 2.9 34.6 + - - -
130A PHE 3.2 23.0 + - - +
131A HIS* 4.8 1.4 - - - -
132A PHE 4.9 2.1 + - - +
135A THR* 6.0 0.2 - - - +
188A VAL* 3.9 9.7 + - - +
189A SER* 1.3 71.2 - - - +
191A VAL* 1.3 59.0 + - - +
192A THR 3.3 22.9 - - - +
193A CYS* 3.4 1.9 + - - -
194A ASN* 4.2 9.2 - - + +
201A VAL* 3.5 4.2 - - - +
223A ASP* 3.7 10.8 + - - +
266A LLP 3.6 28.7 - - + -
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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