Contacts of the helix formed by residues 99 - 111 (chain C) in PDB entry 1Y3A
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 ALA 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97C ASP* 2.9 18.9 + - - +
98C SER* 1.3 78.4 - - - +
100C ARG* 1.3 82.1 + - - +
101C ALA 3.1 1.0 + - - -
102C ASP* 3.1 20.4 + - - +
103C ASP* 3.8 3.3 + - - +
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Residues in contact with ARG 100 (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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95C PHE* 3.5 22.2 - - + -
97C ASP* 2.8 35.9 + - - +
99C ALA* 1.3 91.7 + - - +
101C ALA* 1.3 62.6 + - - +
103C ASP* 2.8 46.0 + - - +
104C ALA* 2.8 13.9 + - - +
129C ARG* 3.4 48.0 + - - +
130C LEU* 3.8 6.7 - - + +
133C ASP* 3.3 31.6 + - + +
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Residues in contact with ALA 101 (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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95C PHE* 3.8 22.6 - - + -
98C SER* 3.0 17.0 + - - +
100C ARG* 1.3 77.8 - - - +
102C ASP* 1.3 61.1 + - - +
104C ALA* 3.3 3.7 + - - +
105C ARG* 3.0 22.3 + - - +
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Residues in contact with ASP 102 (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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98C SER 4.4 0.2 + - - -
99C ALA* 3.1 11.2 + - - +
100C ARG 3.1 0.6 - - - -
101C ALA* 1.3 77.8 - - - +
103C ASP* 1.3 65.7 + - - +
105C ARG* 3.4 21.6 + - - +
106C GLN* 2.9 34.4 + - - +
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Residues in contact with ASP 103 (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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99C ALA 3.8 2.7 + - - -
100C ARG* 2.8 45.9 + - - +
102C ASP* 1.3 79.7 - - - +
104C ALA* 1.3 56.7 + - - +
106C GLN* 3.2 5.2 + - - +
107C LEU 2.7 30.1 + - - -
126C VAL* 3.3 18.6 - - + +
129C ARG* 2.9 39.6 + - - +
130C LEU* 4.0 18.4 - - + -
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Residues in contact with ALA 104 (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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85C ILE* 4.4 16.2 - - + -
95C PHE* 3.7 30.1 - - + -
100C ARG 2.8 4.9 + - - -
101C ALA 3.5 9.6 - - - +
103C ASP* 1.3 75.1 - - - +
105C ARG* 1.3 64.7 + - - +
107C LEU* 3.1 19.4 + - - +
108C PHE* 3.2 17.7 - - + -
130C LEU* 4.0 14.3 - - + +
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Residues in contact with ARG 105 (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 ALA 3.0 13.5 + - - +
102C ASP* 3.4 26.1 + - - +
104C ALA* 1.3 79.2 - - - +
106C GLN* 1.3 62.9 + - - +
107C LEU 3.4 0.2 + - - -
108C PHE* 3.4 9.3 + - - +
109C VAL* 3.4 26.7 + - + +
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Residues in contact with GLN 106 (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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102C ASP* 2.9 24.1 + - - +
103C ASP* 3.2 7.8 + - - +
105C ARG* 1.3 76.7 - - - +
107C LEU* 1.3 64.0 + - - +
109C VAL* 3.3 19.6 + - - +
110C LEU* 3.0 42.9 + - + +
122C GLU* 4.4 13.9 + - + +
126C VAL* 3.9 21.3 - - + -
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Residues in contact with LEU 107 (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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78C ILE* 5.1 2.2 - - + -
81C ILE* 4.2 28.9 - - + +
82C ILE* 4.0 32.3 - - + -
85C ILE* 4.6 9.4 - - + -
103C ASP 2.7 16.5 + - - +
104C ALA 3.2 11.2 - - - +
106C GLN* 1.3 73.5 - - - +
108C PHE* 1.3 66.7 + - + +
110C LEU* 3.4 1.9 + - - +
111C ALA* 3.0 24.5 + - + +
123C LEU* 3.9 22.2 - - + -
126C VAL* 3.8 12.3 - - + +
127C ILE* 4.3 9.2 - - + -
130C LEU* 3.9 17.9 - - + -
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Residues in contact with PHE 108 (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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82C ILE* 3.7 37.0 - - + -
85C ILE* 3.7 33.7 - - + -
86C ARG* 3.7 33.7 - - + -
104C ALA* 3.2 24.9 + - + -
105C ARG* 3.9 7.4 - - - +
106C GLN 3.3 0.2 - - - -
107C LEU* 1.3 81.2 - - + +
109C VAL* 1.3 64.0 + - + +
111C ALA* 3.4 20.8 - - - +
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Residues in contact with VAL 109 (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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105C ARG* 3.4 20.6 + - + +
106C GLN* 3.3 24.8 + - - +
108C PHE* 1.3 80.3 - - + +
110C LEU* 1.3 65.1 + - + +
111C ALA 3.4 4.5 + - - +
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Residues in contact with LEU 110 (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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106C GLN* 3.0 39.4 + - + +
109C VAL* 1.3 79.8 - - + +
111C ALA* 1.3 58.1 + - - +
120C THR* 5.5 1.8 - - - +
122C GLU* 3.2 52.0 - - + +
123C LEU* 3.8 42.6 - - + +
126C VAL* 4.6 2.5 - - + -
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Residues in contact with ALA 111 (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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78C ILE* 3.8 33.2 - - + -
82C ILE* 4.2 13.9 - - + -
107C LEU* 3.0 19.0 + - + +
108C PHE 3.4 14.8 - - - +
109C VAL 3.3 3.8 - - - +
110C LEU* 1.3 79.8 - - - +
123C LEU* 5.0 4.7 - - + -
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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