Contacts of the helix formed by residues 133 - 141 (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 ASP 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B HIS 4.6 1.6 - - - +
132B PHE* 1.3 95.3 - - + +
134B THR* 1.3 68.2 + - + +
136B ALA* 3.5 5.0 + - - +
137B ALA* 2.9 22.9 + - - +
195B SER* 4.5 6.4 + - - -
391B ILE* 5.7 1.6 - - - +
395B LEU* 3.9 31.9 - - - +
458B HIS* 4.7 6.1 - - - -
459B PHE* 6.1 0.6 - - + -
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Residues in contact with THR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A VAL* 5.1 3.4 - - + +
294A PRO* 5.3 4.3 - - + -
101B ARG* 3.5 49.4 - - - +
104B GLU* 2.6 23.7 + - - -
132B PHE* 3.4 22.8 - - + -
133B ASP* 1.3 79.7 - - + +
135B THR* 1.3 64.3 + - - +
137B ALA* 3.1 7.2 + - - +
138B HIS* 2.9 29.9 + - - -
266B LLP 3.5 8.6 - - - -
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLU* 2.6 27.2 + - - +
108B PHE* 3.4 30.1 - - + -
131B HIS* 4.1 15.3 - - + -
132B PHE* 3.3 31.4 - - - +
134B THR* 1.3 78.7 + - - +
136B ALA* 1.3 61.0 + - - +
138B HIS* 3.3 3.9 + - - +
139B VAL* 3.1 25.7 + - - +
188B VAL* 4.4 9.9 - - + -
223B ASP* 3.5 11.2 + - + +
266B LLP 3.7 0.7 + - - -
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Residues in contact with ALA 136 (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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131B HIS* 3.9 19.4 - - + +
132B PHE 2.9 16.0 + - - +
133B ASP* 3.9 5.4 - - - +
135B THR* 1.3 72.5 - - - +
137B ALA* 1.4 65.5 + - - +
139B VAL* 3.2 8.6 + - - +
140B GLU* 2.9 36.3 + - - +
146B ALA* 4.2 11.9 - - + -
148B ASN* 6.2 0.9 - - - +
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Residues in contact with ALA 137 (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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294A PRO* 4.5 18.4 - - + -
133B ASP 2.9 14.9 + - - +
134B THR* 3.1 12.5 + - - +
136B ALA* 1.4 77.2 - - - +
138B HIS* 1.3 55.9 + - - +
140B GLU* 3.4 7.9 + - - +
141B LEU* 2.9 36.8 + - + +
456B LEU* 6.3 2.7 - - + -
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Residues in contact with HIS 138 (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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294A PRO* 2.8 35.2 + - + +
295A MET* 3.9 21.2 - - + +
101B ARG* 3.5 8.3 + - + -
104B GLU* 3.8 24.2 - - + -
105B ASN* 3.6 31.7 + - + -
108B PHE* 4.1 19.9 - - + +
134B THR* 2.9 25.7 + - - +
135B THR 3.8 6.5 - - - +
137B ALA* 1.3 73.0 - - - +
139B VAL* 1.3 64.6 + - - +
141B LEU* 4.3 7.5 - - + +
142B ASN* 2.7 39.2 + - - +
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Residues in contact with VAL 139 (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* 4.1 11.9 - - + -
126B PHE* 3.5 45.1 - - + -
131B HIS* 4.2 10.5 - - + +
135B THR 3.1 17.7 + - - +
136B ALA* 3.2 9.4 + - - +
138B HIS* 1.3 76.1 - - - +
140B GLU* 1.3 60.7 + - - +
142B ASN* 3.3 7.2 + - - +
144B CYS* 3.0 27.1 + - + +
145B LYS 3.5 34.8 - - - +
146B ALA* 3.7 9.0 - - + +
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Residues in contact with GLU 140 (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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136B ALA* 2.9 25.4 + - - +
137B ALA* 3.8 6.7 - - - +
139B VAL* 1.3 77.1 - - + +
141B LEU* 1.3 58.4 + - - +
143B GLY* 2.9 20.3 + - - -
144B CYS 3.6 16.1 - - - +
145B LYS* 5.4 0.2 - - - -
146B ALA* 4.2 17.0 + - + +
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Residues in contact with LEU 141 (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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291A ARG* 5.7 5.8 - - - +
294A PRO* 4.1 25.4 - - + -
295A MET* 3.9 28.3 - - + -
137B ALA* 2.9 27.9 + - + +
138B HIS* 4.0 9.9 - - - +
139B VAL 3.4 0.2 - - - -
140B GLU* 1.3 74.9 - - + +
142B ASN* 1.3 63.4 + - - +
143B GLY 3.2 3.2 + - - -
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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