Contacts of the helix formed by residues 101 - 113 (chain A) in PDB entry 1Y67
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 SER 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A GLN 5.3 0.4 - - - -
100A PRO* 1.3 74.7 - - - +
102A GLY* 1.3 69.3 + - - +
103A GLU 3.6 1.0 + - - -
104A LEU* 3.7 7.6 + - - +
105A LEU* 3.4 21.0 + - - -
204A SER* 4.4 5.9 + - - -
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Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A SER* 1.3 77.8 + - - +
103A GLU* 1.3 63.9 + - - -
105A LEU* 3.1 5.5 + - - +
106A ASP* 3.0 30.5 + - - +
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Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A SER 3.6 0.6 + - - -
102A GLY* 1.3 71.1 - - - -
104A LEU* 1.3 63.1 + - - +
106A ASP* 3.4 16.3 + - - +
107A ALA* 3.0 23.2 + - - +
207A TYR* 4.0 15.9 + - + -
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PRO* 3.7 8.7 - - + -
101A SER 3.7 4.0 + - - +
102A GLY 3.3 0.6 - - - -
103A GLU* 1.3 80.5 - - - +
105A LEU* 1.3 56.5 + - - +
107A ALA* 3.2 2.1 + - - +
108A ILE* 2.9 39.2 + - + +
137A LEU* 5.0 1.6 - - + -
144A LEU* 4.4 6.3 - - + -
169A ILE* 4.2 11.2 - - + -
200A TRP* 3.6 31.6 - - + -
203A VAL* 3.7 14.8 - - + -
204A SER* 3.4 32.6 + - - +
207A TYR* 3.9 37.7 - - + -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLN* 4.2 13.9 - - - +
100A PRO* 3.6 28.7 - - + +
101A SER* 3.4 21.7 + - - +
102A GLY 3.1 9.4 + - - +
104A LEU* 1.3 79.3 - - - +
106A ASP* 1.3 59.4 + - - +
108A ILE* 3.2 7.1 + - + +
109A ASN* 2.8 52.0 + - - +
115A PHE* 4.1 24.2 - - + -
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Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLY* 3.0 22.0 + - - +
103A GLU* 3.5 19.8 - - - +
105A LEU* 1.3 78.7 - - - +
107A ALA* 1.3 56.8 + - - +
109A ASN* 3.3 14.1 + - - +
110A SER* 2.9 28.1 + - - -
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU 3.0 11.6 + - - +
104A LEU 3.5 7.9 - - - +
106A ASP* 1.3 74.1 - - - +
108A ILE* 1.3 59.0 + - - +
110A SER* 3.3 7.8 + - - -
111A ALA* 2.8 31.7 + - - +
144A LEU* 3.7 15.1 - - + +
207A TYR* 3.2 33.7 - - + +
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PRO* 3.8 27.8 - - + -
104A LEU* 2.9 25.2 + - + +
105A LEU* 3.6 8.5 - - + +
107A ALA* 1.3 73.1 - - - +
109A ASN* 1.3 60.0 + - - +
112A PHE* 2.8 38.9 + - + +
113A GLY 3.5 0.5 + - - -
114A SER 3.7 10.3 - - - +
115A PHE* 3.8 21.8 - - + +
118A PHE* 3.6 36.3 - - + -
137A LEU* 4.8 4.9 - - + -
144A LEU* 3.8 18.2 - - + -
200A TRP* 4.5 7.6 - - + -
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Residues in contact with ASN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 2.8 41.0 + - - +
106A ASP* 3.6 14.8 + - - +
108A ILE* 1.3 71.6 - - - +
110A SER* 1.3 58.6 + - - +
113A GLY* 2.9 36.6 + - - +
114A SER* 3.4 20.2 - - - -
115A PHE 3.7 5.9 + - - -
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ASP 2.9 14.5 + - - -
107A ALA* 3.4 11.4 - - - -
108A ILE 3.2 0.2 - - - -
109A ASN* 1.3 78.8 - - - +
111A ALA* 1.3 60.7 + - - +
113A GLY 4.6 0.9 + - - -
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ALA 2.8 19.5 + - - +
110A SER* 1.3 75.5 - - - +
112A PHE* 1.3 86.8 + - + +
143A LYS* 6.2 0.4 - - + -
144A LEU* 3.9 25.4 - - + +
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Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ILE* 2.8 23.0 + - + +
111A ALA* 1.3 90.3 - - + +
113A GLY* 1.3 58.5 + - - +
114A SER 3.4 3.1 - - - +
117A ALA* 3.3 18.2 - - - +
118A PHE* 3.8 43.5 - + + +
121A LYS* 4.4 23.8 - - + -
137A LEU* 3.8 20.0 - - + -
144A LEU* 3.8 25.6 - - + -
145A ASP* 4.0 10.8 - - - -
146A VAL* 3.8 26.2 - - + -
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ILE 3.5 0.4 + - - -
109A ASN* 2.9 28.2 + - - +
110A SER 4.6 0.6 + - - -
111A ALA 3.8 0.6 - - - -
112A PHE* 1.3 76.5 - - - +
114A SER* 1.3 62.9 + - - +
117A ALA* 4.9 0.7 - - - -
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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