Contacts of the helix formed by residues 101 - 113 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B GLN 5.1 1.7 + - - -
100B PRO* 1.3 74.6 - - - +
102B GLY* 1.3 67.1 + - - +
103B GLU 3.6 1.4 + - - -
104B LEU* 3.7 7.6 + - - +
105B LEU* 3.6 20.9 + - - -
201B ASP* 5.7 0.7 + - - -
204B SER* 4.1 7.5 + - - -
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Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B SER* 1.3 79.0 + - - +
103B GLU* 1.3 62.7 + - - -
105B LEU* 3.9 3.6 - - - +
106B ASP* 3.2 30.9 + - - +
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Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B SER 3.6 0.6 + - - -
102B GLY* 1.3 69.4 - - - -
104B LEU* 1.3 61.3 + - - +
106B ASP* 3.4 16.9 + - - +
107B ALA* 3.0 27.4 + - - +
207B TYR* 4.2 17.0 - - + -
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PRO* 4.2 4.5 - - + -
101B SER 3.7 3.0 + - - +
102B GLY 3.3 1.0 - - - -
103B GLU* 1.3 76.3 - - - +
105B LEU* 1.3 60.1 + - - +
107B ALA* 3.1 4.4 + - - +
108B ILE* 2.8 46.0 + - + +
137B LEU* 4.9 1.1 - - + -
144B LEU* 4.3 5.2 - - + -
169B ILE* 4.0 11.2 - - + -
200B TRP* 4.0 17.3 - - + -
203B VAL* 3.6 26.9 - - + -
204B SER* 3.4 37.4 + - - +
207B TYR* 3.9 36.5 - - + -
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLN* 5.4 7.4 - - - +
100B PRO* 3.5 36.0 - - + +
101B SER* 3.6 27.8 + - - -
102B GLY 3.6 3.7 + - - +
103B GLU 3.4 0.4 - - - -
104B LEU* 1.3 78.1 - - - +
106B ASP* 1.3 55.3 + - - +
108B ILE* 3.2 6.6 + - + +
109B ASN* 2.8 60.6 + - - +
115B PHE* 4.3 16.4 - - + -
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Residues in contact with ASP 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLY 3.2 17.1 + - - +
103B GLU* 3.4 22.9 - - - +
104B LEU 3.2 0.4 - - - -
105B LEU* 1.3 81.3 - - - +
107B ALA* 1.3 56.3 + - - +
109B ASN* 3.4 12.1 + - - +
110B SER* 3.0 29.1 + - - -
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLU 3.0 9.3 + - - +
104B LEU 3.1 7.6 + - - +
106B ASP* 1.3 72.5 - - - +
108B ILE* 1.3 61.0 + - - +
110B SER* 2.7 22.7 + - - -
111B ALA* 2.9 19.2 + - - +
144B LEU* 3.7 15.9 - - + +
207B TYR* 3.2 37.5 - - + +
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PRO* 3.8 27.4 - - + -
104B LEU* 2.8 31.4 + - + +
105B LEU* 3.5 6.3 - - + +
107B ALA* 1.3 73.6 - - - +
109B ASN* 1.3 61.5 + - - +
112B PHE* 2.9 36.5 + - + +
113B GLY 3.7 0.2 + - - -
114B SER 4.0 0.8 - - - +
115B PHE* 3.8 37.5 - - + +
118B PHE* 3.8 23.8 - - + -
137B LEU* 4.8 6.1 - - + -
144B LEU* 3.7 18.6 - - + -
200B TRP* 4.4 10.8 - - + -
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Residues in contact with ASN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU* 2.8 45.6 + - - +
106B ASP* 3.7 11.5 + - - +
108B ILE* 1.3 74.5 - - - +
110B SER* 1.3 57.5 + - - +
113B GLY* 2.7 43.5 + - - +
114B SER* 3.5 17.7 - - - -
115B PHE 3.7 6.9 + - - -
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Residues in contact with SER 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ASP 3.0 11.9 + - - -
107B ALA* 2.7 26.2 + - - -
109B ASN* 1.3 79.3 - - - +
111B ALA* 1.3 64.0 + - - +
113B GLY* 4.3 1.4 + - - -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ALA 2.9 13.2 + - - +
110B SER* 1.3 82.6 + - - +
112B PHE* 1.3 82.0 + - + +
143B LYS* 5.9 1.8 - - + -
144B LEU* 3.8 30.1 - - + +
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Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ILE* 2.9 20.9 + - + +
111B ALA* 1.3 84.0 - - + +
113B GLY* 1.3 58.8 + - - +
114B SER 3.3 3.4 - - - +
117B ALA* 3.3 21.3 - - - +
118B PHE* 3.8 44.4 - + + +
121B LYS* 3.1 44.6 - - + -
137B LEU* 3.9 11.0 - - + -
144B LEU* 3.7 27.1 - - + -
145B ASP* 3.9 14.4 - - - -
146B VAL* 3.7 21.3 - - + -
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Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ASN* 2.7 35.1 + - - +
110B SER 4.3 1.2 + - - -
111B ALA 3.8 1.0 - - - -
112B PHE* 1.3 70.3 - - - +
114B SER* 1.3 60.5 + - - +
117B ALA* 5.1 0.4 - - - -
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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