Contacts of the helix formed by residues 117 - 130 (chain C) in PDB entry 1OY1
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 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C PRO* 4.2 5.8 - - - +
46C LYS* 2.7 33.9 + - - +
81C LEU* 3.5 11.9 - - - +
103C ASN 4.7 0.4 - - - -
104C LEU* 2.8 30.5 + - + +
105C SER* 4.4 0.2 - - - +
116C VAL* 1.3 73.8 - - - +
118C ARG* 1.3 67.9 + - - +
119C GLU* 3.2 20.5 + - - +
120C LEU* 3.2 25.4 + - + -
121C LYS* 2.9 22.5 + - - +
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Residues in contact with ARG 118 (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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116C VAL 3.4 5.2 + - - +
117C ASP* 1.3 74.1 + - - +
119C GLU* 1.3 58.7 + - + +
121C LYS* 3.2 6.3 + - - +
122C ALA* 2.8 35.3 + - - +
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Residues in contact with GLU 119 (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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44C PRO* 4.7 6.6 - - - +
45C ASP 5.6 0.7 + - - -
46C LYS* 6.1 0.2 - - - +
81C LEU* 3.9 22.5 - - + +
82C ALA* 3.1 38.3 + - - +
117C ASP* 3.2 17.8 + - - +
118C ARG* 1.3 77.2 - - + +
120C LEU* 1.3 58.5 + - - +
122C ALA* 3.2 6.5 + - - +
123C LEU* 2.7 37.7 + - - +
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Residues in contact with LEU 120 (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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10C ILE* 4.3 23.8 - - + -
81C LEU* 3.8 11.1 - - + +
92C LEU* 4.7 10.5 - - + -
94C VAL* 4.7 10.3 - - + -
104C LEU* 3.8 32.8 - - + +
116C VAL* 4.2 6.1 - - + -
117C ASP* 3.2 20.6 + - + +
119C GLU* 1.3 78.2 - - - +
121C LYS* 1.3 58.8 + - - +
123C LEU* 3.7 5.3 - - + +
124C ALA* 2.8 35.8 + - + +
136C PHE* 5.1 3.4 - - + -
143C MSE 3.7 33.7 - - + -
147C ILE* 4.8 3.8 - - + -
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Residues in contact with LYS 121 (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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116C VAL* 4.2 17.2 - - + +
117C ASP 2.9 17.0 + - - +
118C ARG* 3.5 6.1 - - - +
120C LEU* 1.3 76.5 - - - +
122C ALA* 1.3 63.5 + - - +
124C ALA* 3.2 5.8 + - - +
125C GLN* 2.9 43.8 + - - +
146C LYS 3.2 25.8 + - - +
147C ILE* 3.7 30.5 - - + -
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Residues in contact with ALA 122 (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 ARG 2.8 17.6 + - - +
119C GLU* 3.5 8.3 - - - +
121C LYS* 1.3 77.6 - - - +
123C LEU* 1.3 63.0 + - - +
125C GLN* 3.2 10.2 + - - +
126C ALA* 2.9 24.2 + - - +
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Residues in contact with LEU 123 (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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10C ILE* 4.3 4.3 - - + -
81C LEU* 4.3 14.8 - - + -
84C ALA* 3.9 34.1 - - + +
85C ASP 4.4 0.2 - - - -
86C ALA* 3.7 35.2 - - + +
89C LEU* 4.5 5.6 - - + -
92C LEU* 3.8 33.0 - - + -
119C GLU 2.7 21.2 + - - +
120C LEU* 3.7 4.9 - - + +
122C ALA* 1.3 72.1 - - - +
124C ALA* 1.3 65.0 + - - +
126C ALA* 3.2 6.0 + - + +
127C MSE 3.0 31.7 + - + +
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Residues in contact with ALA 124 (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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92C LEU* 4.2 16.6 - - + +
120C LEU* 2.8 25.1 + - + +
121C LYS 3.5 4.0 - - - +
123C LEU* 1.3 73.2 - - - +
125C GLN* 1.3 62.4 + - - +
127C MSE 3.3 4.4 + - - +
128C HIS* 3.0 22.3 + - - +
134C LEU* 3.7 16.4 - - + +
136C PHE* 5.0 2.7 - - + -
147C ILE* 3.6 28.9 - - + -
148C PHE* 4.2 2.5 - - - -
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Residues in contact with GLN 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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121C LYS* 2.9 40.2 + - - +
122C ALA* 3.7 6.9 - - - +
124C ALA* 1.3 72.1 - - - +
126C ALA* 1.3 57.4 + - - +
128C HIS* 3.1 2.4 + - - +
129C GLN* 2.7 39.9 + - - +
147C ILE* 2.9 33.7 + - + +
148C PHE* 4.0 16.4 - - + +
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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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86C ALA* 3.7 21.8 - - + +
122C ALA 2.9 17.6 + - - +
123C LEU* 3.6 7.0 - - - +
125C GLN* 1.3 75.3 - - - +
127C MSE 1.3 63.6 + - - +
129C GLN* 3.5 12.3 + - - +
130C ALA* 3.2 23.2 + - - +
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Residues in contact with MSE 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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86C ALA* 2.9 48.9 - - + +
89C LEU* 4.1 22.9 - - - +
91C ALA 4.5 11.9 - - - +
92C LEU* 4.3 4.5 - - + -
123C LEU* 3.0 32.4 + - + +
124C ALA 3.3 7.6 - - - +
125C GLN 3.1 0.2 - - - -
126C ALA* 1.3 76.0 - - - +
128C HIS* 1.3 64.4 + - - +
130C ALA* 3.1 7.9 + - + -
132C LYS* 2.9 62.4 + - + +
134C LEU* 3.8 21.3 - - + -
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Residues in contact with HIS 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 ALA 3.0 8.4 + - - +
125C GLN 3.7 2.8 + - - +
127C MSE 1.3 74.8 - - - +
129C GLN* 1.3 63.8 + - - +
131C GLY* 2.9 19.5 + - - -
132C LYS 4.2 8.7 + - - -
134C LEU* 4.6 4.9 - - + +
148C PHE* 3.5 32.8 - + + -
150C PHE* 3.2 27.9 - + - -
187C ASN* 2.5 55.8 + - + +
189C ILE* 4.8 2.2 - - + -
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Residues in contact with GLN 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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125C GLN* 2.7 22.6 + - - +
126C ALA* 3.7 11.0 - - - +
128C HIS* 1.3 78.2 + - - +
130C ALA* 1.3 57.1 + - - +
131C GLY 3.4 0.6 + - - -
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Residues in contact with ALA 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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126C ALA 3.2 14.4 + - - +
127C MSE 3.1 5.6 + - + +
128C HIS 3.0 0.8 - - - -
129C GLN* 1.3 77.5 - - - +
131C GLY* 1.3 61.8 + - - +
132C LYS* 3.2 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