Contacts of the helix formed by residues 133 - 141 (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 ASP 133 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D HIS 4.6 1.7 - - - +
132D PHE* 1.3 91.1 - - + +
134D THR* 1.3 67.9 + - + +
136D ALA* 3.5 4.8 + - - +
137D ALA* 3.0 23.0 + - - +
194D ASN* 5.4 0.3 + - - -
195D SER* 4.5 6.2 + - - -
391D ILE* 5.9 0.5 - - - +
395D LEU* 4.5 20.3 - - - +
458D HIS* 6.0 0.9 - - - -
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Residues in contact with THR 134 (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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293C VAL* 5.1 2.7 - - + +
294C PRO* 5.2 4.9 - - + -
101D ARG* 3.5 49.6 - - - +
104D GLU* 2.7 24.5 + - - -
132D PHE* 3.5 14.7 - - + -
133D ASP* 1.3 78.6 - - + +
135D THR* 1.3 66.4 + - - +
137D ALA* 3.1 8.0 + - - +
138D HIS* 3.0 28.6 + - - -
266D LLP 3.5 15.3 - - - -
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Residues in contact with THR 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D GLU* 2.6 26.3 + - - +
108D PHE* 3.5 30.5 - - + -
131D HIS* 4.0 16.2 - - + -
132D PHE* 3.3 32.7 - - - +
134D THR* 1.3 79.3 + - - +
136D ALA* 1.3 61.5 + - - +
138D HIS* 3.3 3.2 + - - +
139D VAL* 3.1 26.8 + - - +
188D VAL* 4.4 9.4 - - + -
223D ASP* 3.5 10.1 + - + +
261D THR* 6.1 0.2 - - - +
266D LLP 3.7 0.3 + - - -
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Residues in contact with ALA 136 (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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131D HIS* 3.8 19.2 - - + +
132D PHE 3.0 14.8 + - - +
133D ASP* 3.9 5.8 - - - +
135D THR* 1.3 74.6 - - - +
137D ALA* 1.3 61.6 + - - +
139D VAL* 3.2 9.0 + - - +
140D GLU* 2.9 40.2 + - - +
146D ALA* 4.3 11.7 - - + -
148D ASN* 6.2 0.4 - - - +
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Residues in contact with ALA 137 (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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294C PRO* 4.6 17.9 - - + -
133D ASP 3.0 14.5 + - - +
134D THR* 3.1 11.9 + - - +
136D ALA* 1.3 77.2 - - - +
138D HIS* 1.3 56.3 + - - +
140D GLU* 3.4 8.4 + - - +
141D LEU* 2.8 38.8 + - + +
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Residues in contact with HIS 138 (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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294C PRO* 2.7 36.5 + - + +
295C MET* 3.9 19.4 - - + +
101D ARG* 3.5 8.3 + - + +
104D GLU* 3.7 25.1 - - + -
105D ASN* 3.6 31.5 + - + +
108D PHE* 4.1 19.6 - - + +
134D THR* 3.0 29.1 + - - +
135D THR 3.9 4.0 - - - +
137D ALA* 1.3 71.4 - - - +
139D VAL* 1.3 67.7 + - - +
141D LEU* 4.3 7.0 - - + +
142D ASN* 2.7 37.6 + - - +
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Residues in contact with VAL 139 (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* 4.1 10.5 - - + -
126D PHE* 3.6 46.9 - - + -
131D HIS* 4.1 12.8 - - + -
135D THR 3.1 15.0 + - - +
136D ALA* 3.4 9.2 - - - +
138D HIS* 1.3 78.6 - - - +
140D GLU* 1.3 59.1 + - - +
142D ASN* 3.3 7.0 + - - +
143D GLY 3.7 0.2 + - - -
144D CYS* 3.0 26.6 + - + +
145D LYS 3.6 33.7 - - - +
146D ALA* 3.7 9.0 - - + +
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Residues in contact with GLU 140 (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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136D ALA* 2.9 26.6 + - - +
137D ALA* 3.8 5.9 - - - +
139D VAL* 1.3 75.3 - - + +
141D LEU* 1.3 60.2 + - + +
143D GLY* 3.0 20.6 + - - -
144D CYS 3.5 16.3 - - - +
145D LYS* 5.3 0.7 - - - -
146D ALA* 4.3 16.5 + - + +
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Residues in contact with LEU 141 (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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291C ARG* 5.7 5.6 - - - +
294C PRO* 4.1 24.2 - - + -
295C MET* 4.0 27.8 - - + -
137D ALA* 2.8 32.8 + - + +
138D HIS* 4.0 10.3 - - - +
139D VAL 3.4 0.2 - - - -
140D GLU* 1.3 73.4 - - + +
142D ASN* 1.3 64.5 + - - +
143D GLY 3.2 2.9 + - - -
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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