Contacts of the helix formed by residues 133 - 141 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C HIS 4.6 0.9 - - - +
132C PHE* 1.3 95.3 - - + +
134C THR* 1.3 59.9 + - + +
136C ALA* 3.9 5.1 - - - +
137C ALA* 3.0 27.0 + - - +
195C SER* 4.5 6.8 + - - -
395C LEU* 4.6 22.2 - - - +
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Residues in contact with THR 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ARG* 3.5 50.3 - - - +
104C GLU* 2.7 23.8 + - - -
132C PHE* 3.4 22.8 - - + -
133C ASP* 1.3 76.2 - - + +
135C THR* 1.3 67.7 + - - +
137C ALA* 3.1 6.9 + - - +
138C HIS* 3.0 29.9 + - - -
266C LLP 3.5 8.2 - - - -
293D VAL* 5.0 4.3 - - + +
294D PRO* 5.3 4.0 - - + -
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Residues in contact with THR 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C GLU* 2.7 25.0 + - - +
108C PHE* 3.4 31.4 - - + -
131C HIS* 4.1 15.9 - - + -
132C PHE* 3.4 32.1 - - - +
134C THR* 1.3 76.7 + - - +
136C ALA* 1.3 62.1 + - - +
138C HIS* 3.3 4.4 + - - +
139C VAL* 3.0 26.2 + - - +
188C VAL* 4.4 9.6 - - + -
223C ASP* 3.5 11.4 + - - +
261C THR* 6.0 0.4 - - - +
266C LLP 3.7 0.9 + - - -
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C HIS* 3.9 20.5 - - + +
132C PHE 2.9 15.1 + - - +
133C ASP* 4.0 5.4 - - - +
135C THR* 1.3 76.6 - - - +
137C ALA* 1.3 62.4 - - - +
139C VAL* 3.2 8.9 + - - +
140C GLU* 3.0 35.5 + - - +
146C ALA* 4.2 12.3 - - + -
148C ASN* 6.2 0.4 - - - +
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Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ASP 3.0 18.4 + - - +
134C THR* 3.1 9.6 + - - +
136C ALA* 1.3 77.9 - - - +
138C HIS* 1.3 55.6 + - - +
140C GLU* 3.4 7.0 + - - +
141C LEU* 2.9 37.8 + - + +
294D PRO* 4.4 19.7 - - + -
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Residues in contact with HIS 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ARG* 3.5 7.3 + - + +
104C GLU* 3.7 24.5 - - + -
105C ASN* 3.7 30.8 + - + -
108C PHE* 4.1 20.2 - - + -
134C THR* 3.0 27.5 + - - +
135C THR 3.8 4.0 - - - +
137C ALA* 1.3 73.7 - - - +
139C VAL* 1.3 66.6 + - - +
141C LEU* 4.3 6.4 - - + +
142C ASN* 2.7 39.3 + - - +
294D PRO* 2.6 37.3 + - + +
295D MET* 3.9 20.8 - - + +
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Residues in contact with VAL 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C PHE* 4.1 12.1 - - + -
126C PHE* 3.6 46.7 - - + -
131C HIS* 4.1 10.8 - - + -
135C THR 3.0 18.7 + - - +
136C ALA* 3.4 9.4 - - - +
138C HIS* 1.3 77.3 - - - +
140C GLU* 1.3 59.5 + - - +
142C ASN* 3.3 7.0 + - - +
143C GLY 3.7 0.2 + - - -
144C CYS* 3.0 27.7 + - + +
145C LYS 3.6 33.4 - - - +
146C ALA* 3.7 9.4 - - + +
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Residues in contact with GLU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ALA* 3.0 25.1 + - - +
137C ALA* 3.9 5.7 - - - +
139C VAL* 1.3 75.8 - - + +
141C LEU* 1.3 59.5 + - - +
142C ASN 3.1 1.8 - - - -
143C GLY* 2.9 21.0 + - - -
144C CYS 3.5 16.3 - - - +
145C LYS* 5.3 0.4 - - - -
146C ALA* 4.3 16.0 + - + +
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ALA* 2.9 28.9 + - + +
138C HIS* 3.4 9.6 + - - +
140C GLU* 1.3 76.0 - - - +
142C ASN* 1.3 63.8 + - - +
143C GLY 3.2 2.9 + - - -
291D ARG* 5.6 5.8 - - - +
294D PRO* 4.0 26.2 - - + -
295D MET* 3.9 27.6 - - + -
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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