Contacts of the helix formed by residues 124 - 132 (chain C) in PDB entry 1AYZ
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 VAL 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C PRO* 4.2 23.8 - - + +
122C ALA 3.8 4.4 + - - +
123C ASN* 1.3 69.6 + - - +
125C GLU* 1.3 67.8 + - - +
127C ALA* 3.1 6.6 + - - -
128C THR* 2.8 41.3 + - + +
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Residues in contact with GLU 125 (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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77C PHE* 4.2 10.1 - - + -
123C ASN* 3.2 10.5 + - - +
124C VAL* 1.3 77.0 - - - +
126C ALA* 1.3 64.1 + - - +
128C THR* 3.2 7.1 + - - +
129C LEU* 2.9 35.0 + - + +
140C ARG* 3.2 37.0 + - - -
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Residues in contact with ALA 126 (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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77C PHE* 3.3 26.6 - - + -
78C HIS* 3.9 23.1 - - - +
79C PRO* 3.9 3.8 - - + -
123C ASN* 3.2 29.4 + - - +
125C GLU* 1.3 80.8 - - - +
127C ALA* 1.3 57.2 + - - +
129C LEU* 3.8 0.2 - - - +
130C PHE* 2.9 29.3 + - - +
137C TYR* 3.8 6.0 - - + -
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Residues in contact with ALA 127 (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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79C PRO* 4.1 12.3 - - + +
118C PRO* 4.0 16.9 - - + +
121C PRO* 3.5 37.0 - - + -
123C ASN 3.2 2.7 + - - +
124C VAL 3.1 7.4 + - - +
126C ALA* 1.3 76.7 - - - +
128C THR* 1.3 67.0 + - + +
130C PHE* 3.2 4.6 + - - +
131C LYS* 3.1 32.6 + - - +
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Residues in contact with THR 128 (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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124C VAL* 2.8 38.4 + - + +
125C GLU* 3.2 12.3 + - - -
127C ALA* 1.3 72.6 - - + +
129C LEU* 1.3 63.7 + - - +
131C LYS* 3.2 18.1 + - - +
132C ASP* 2.8 45.4 + - - +
133C HIS* 5.8 0.2 - - - -
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Residues in contact with LEU 129 (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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77C PHE* 3.8 17.3 - - + -
125C GLU* 2.9 23.8 + - + +
126C ALA 3.8 3.8 - - - +
128C THR* 1.3 80.6 + - - +
130C PHE* 1.3 59.9 + - - +
133C HIS* 2.8 54.5 + - + +
136C GLN* 4.1 25.1 - - + +
137C TYR* 4.0 25.1 - - + +
140C ARG* 3.7 26.7 - - - +
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Residues in contact with PHE 130 (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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79C PRO* 4.9 1.8 - - + -
116C PRO* 3.6 40.4 - - + -
118C PRO* 3.7 24.7 - - + -
126C ALA 2.9 19.5 + - - +
127C ALA* 3.2 8.5 + - - +
129C LEU* 1.3 77.4 - - - +
131C LYS* 1.3 63.5 + - + +
134C LYS* 3.7 41.2 - - + +
137C TYR* 3.5 45.5 - + + +
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Residues in contact with LYS 131 (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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118C PRO* 4.3 32.2 + - + -
121C PRO* 6.2 0.8 - - - +
127C ALA* 3.1 26.5 + - - +
128C THR* 3.6 15.0 - - - +
130C PHE* 1.3 82.7 - - + +
132C ASP* 1.3 72.2 + - - +
134C LYS* 5.1 1.0 + - - +
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Residues in contact with ASP 132 (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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128C THR* 2.8 29.5 + - - +
131C LYS* 1.3 87.9 - - - +
133C HIS* 1.3 86.5 + - + +
134C LYS 3.7 1.4 + - - -
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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