Contacts of the helix formed by residues 103 - 123 (chain i) in PDB entry 3J7Y
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 PHE 103 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2X PRO* 3.0 58.3 - - + -
3X LEU* 3.5 21.1 - - - -
4X HIS* 3.7 20.2 - + - -
214Y GLU* 3.3 56.1 - - + +
217Y ALA* 3.9 15.9 - - + -
218Y ARG* 4.3 3.1 - - + -
102i MET* 1.3 74.3 - - - +
104i ALA* 1.3 52.2 + - - +
105i ASP* 3.2 11.4 - - - +
106i ASP* 2.6 43.0 + - - +
107i LEU* 2.7 15.3 + - - -
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Residues in contact with ALA 104 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207Y HIS* 4.9 7.0 - - + -
210Y ARG* 3.3 25.6 - - - +
211Y LEU* 3.7 16.4 - - + -
214Y GLU* 3.1 23.8 + - - +
102i MET 4.4 0.2 - - - -
103i PHE* 1.3 69.8 - - - +
105i ASP* 1.3 61.2 + - - +
107i LEU* 4.0 6.6 - - - +
108i HIS* 3.2 26.3 + - - +
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Residues in contact with ASP 105 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211Y LEU* 4.1 14.6 - - + +
214Y GLU* 3.1 19.6 - - - +
215Y LYS 5.5 0.3 + - - -
218Y ARG* 2.7 33.7 + - - +
103i PHE* 3.5 9.7 - - - +
104i ALA* 1.3 74.8 - - - +
106i ASP* 1.3 82.1 + - - +
108i HIS* 4.2 4.2 + - - +
109i ASN* 3.4 26.9 + - - +
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Residues in contact with ASP 106 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2X PRO* 3.5 25.7 - - - +
218Y ARG* 2.6 28.5 + - - -
102i MET* 4.4 12.6 - - + +
103i PHE* 2.6 27.5 + - + +
105i ASP* 1.3 77.7 - - - +
107i LEU* 1.3 57.5 + - - +
108i HIS 3.2 1.6 - - - -
109i ASN* 3.2 8.6 + - - +
110i LEU* 2.9 28.4 + - - +
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Residues in contact with LEU 107 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210Y ARG* 5.4 4.9 - - - +
95i ARG* 4.4 15.9 - - + -
99i GLY* 3.5 28.3 - - - +
100i SER* 5.6 0.9 - - - +
102i MET* 3.8 27.5 - - + +
103i PHE 2.7 18.7 + - - +
104i ALA* 4.0 6.7 - - - +
106i ASP* 1.3 71.9 - - - +
108i HIS* 1.3 57.1 + - - +
110i LEU* 3.2 3.8 + - + +
111i ASN* 2.9 48.6 + - - +
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Residues in contact with HIS 108 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2008A G 4.1 6.0 + - - -
2009A G 3.2 44.3 - - - -
104i ALA 3.2 15.8 + - - +
105i ASP* 4.2 5.5 + - - +
107i LEU* 1.3 77.9 - - - +
109i ASN* 1.3 62.6 + - - +
111i ASN* 3.2 14.4 + - + +
112i LYS* 2.9 47.0 + - + +
115i ARG* 5.6 4.1 + - - -
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Residues in contact with ASN 109 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F ALA 5.0 1.1 + - - +
119F GLU* 3.6 47.5 + - + +
105i ASP 3.4 15.7 + - - +
106i ASP* 3.2 13.1 + - - +
108i HIS* 1.3 85.7 + - - +
110i LEU* 1.3 56.5 + - - +
112i LYS* 3.2 24.4 + - - +
113i ARG* 2.9 31.8 + - - +
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Residues in contact with LEU 110 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91i CYS* 3.5 41.3 - - + +
94i LYS* 3.9 14.4 - - + -
95i ARG* 3.8 37.5 - - + +
102i MET* 3.8 26.7 - - + -
106i ASP 2.9 12.9 + - - +
107i LEU* 3.3 11.4 - - + +
109i ASN* 1.3 74.9 - - - +
111i ASN* 1.3 58.3 + - - +
113i ARG* 3.2 6.7 + - - +
114i ILE* 2.9 31.9 + - + +
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Residues in contact with ASN 111 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1732A C 4.6 7.7 + - - +
95i ARG* 3.0 38.3 + - - +
107i LEU* 2.9 36.9 + - - +
108i HIS* 3.4 13.8 - - + +
110i LEU* 1.3 76.4 - - - +
112i LYS* 1.3 59.6 + - + +
114i ILE* 3.2 8.8 + - - +
115i ARG* 2.9 49.7 + - - +
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Residues in contact with LYS 112 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2009A G 2.8 28.3 + - - +
2010A U 4.2 22.2 + - - +
2011A G 2.7 30.1 + - - +
3312A MG 3.8 8.5 - - - -
118F ALA* 3.9 22.4 + - + +
108i HIS* 2.9 38.5 + - + +
109i ASN* 3.2 23.7 + - - +
111i ASN* 1.3 77.5 - - - +
113i ARG* 1.3 56.7 + - - +
115i ARG* 3.2 15.6 + - - +
116i TYR* 2.9 29.7 + - - +
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Residues in contact with ARG 113 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1869A A 4.5 2.2 + - - -
2011A G 2.4 36.6 + - - -
116F THR* 4.0 8.8 + - + +
119F GLU* 3.6 22.0 - - + +
156F ARG* 3.2 38.6 - - - +
87i GLU* 2.6 30.9 + - - -
91i CYS* 4.6 12.1 - - - -
109i ASN 2.9 11.8 + - - +
110i LEU* 3.2 13.5 - - - +
112i LYS* 1.3 74.4 - - - +
114i ILE* 1.3 54.2 + - - +
116i TYR* 3.2 28.7 + - - +
117i LEU* 2.7 58.5 + - - +
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Residues in contact with ILE 114 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993 ALA* 5.2 3.6 - - - +
1731A A 4.8 12.8 - - + -
88i LEU* 3.9 17.1 - - + +
91i CYS* 3.6 33.2 - - + +
92i ILE* 4.0 9.6 - - + +
95i ARG* 3.4 49.8 - - + +
110i LEU* 2.9 32.8 + - + +
111i ASN 3.5 7.2 - - - +
113i ARG* 1.3 77.6 - - - +
115i ARG* 1.3 57.3 + - - +
117i LEU* 3.2 2.3 + - - +
118i TYR* 2.9 30.2 + - + +
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Residues in contact with ARG 115 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1731A A 4.3 19.9 - - - +
1732A C 3.2 53.9 + - + +
2009A G 3.2 29.5 + - - -
2010A U 3.3 21.3 + - - +
108i HIS* 5.6 4.4 + - - -
111i ASN* 2.9 32.0 + - - +
112i LYS* 3.3 16.4 - - - +
114i ILE* 1.3 77.1 - - - +
116i TYR* 1.3 63.9 + - - +
118i TYR* 3.6 3.1 + - - +
119i LYS* 3.3 36.4 + - + +
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Residues in contact with TYR 116 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1869A A 2.8 36.6 + - - -
1904A C 3.7 3.6 + - - -
2011A G 3.0 67.7 + + + +
2013A U 5.9 1.6 - - - -
112i LYS 2.9 13.2 + - - +
113i ARG* 3.2 41.3 - - - +
115i ARG* 1.3 77.3 - - - +
117i LEU* 1.3 63.4 + - + +
119i LYS* 3.2 20.3 + - + +
120i HIS* 2.9 36.2 + - + +
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Residues in contact with LEU 117 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1869A A 3.7 20.6 - - + +
87i GLU* 3.5 30.5 - - + +
88i LEU* 3.7 40.8 - - + +
91i CYS* 4.0 11.9 - - + -
113i ARG* 2.7 48.2 + - - +
114i ILE 3.2 0.4 + - - +
116i TYR* 1.3 75.4 - - + +
118i TYR* 1.3 56.0 + - - +
120i HIS* 3.2 3.3 + - + +
121i PHE* 2.9 53.4 + - + -
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Residues in contact with TYR 118 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953 THR* 4.7 1.2 + - - -
973 PHE 4.3 7.2 - - - -
983 SER 4.9 0.4 - - - -
993 ALA* 4.3 11.9 - - + -
1730A U 4.6 3.3 + - - -
1731A A 3.3 62.0 + + + +
1752A U 3.4 10.9 + - - -
1753A A 2.6 30.9 + - - -
88i LEU* 4.3 12.0 - - + +
114i ILE* 2.9 18.2 + - + +
115i ARG 3.7 3.6 - - - +
117i LEU* 1.3 76.1 - - - +
119i LYS* 1.3 61.1 + - + +
121i PHE* 4.9 1.3 - - - -
122i ASN* 2.7 66.4 + - + +
123i ARG* 4.3 22.7 + - - -
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Residues in contact with LYS 119 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1721A C 4.9 10.8 - - - +
1731A A 4.9 5.4 - - - +
2010A U 6.2 2.6 - - - -
2011A G 4.5 11.7 + - - -
2012A A 3.5 14.5 + - - -
2013A U 3.1 29.2 + - - -
115i ARG* 3.3 27.6 + - + +
116i TYR* 3.2 17.3 + - + +
118i TYR* 1.3 88.6 - - + +
120i HIS* 1.3 62.8 + - - +
123i ARG* 3.1 53.2 + - - +
124i HIS* 3.3 10.2 + - + -
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Residues in contact with HIS 120 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1869A A 3.4 36.5 + + - +
1870A A 4.6 3.6 + - - +
1903A C 3.2 45.4 + - - -
1904A C 5.0 4.3 + - - -
116i TYR* 2.9 32.8 + - + +
117i LEU* 3.2 5.6 + - - +
119i LYS* 1.3 76.7 - - - +
121i PHE* 1.3 84.6 + + - +
124i HIS* 3.0 42.2 + - + +
125i GLY* 3.7 7.2 + - - -
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Residues in contact with PHE 121 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963 TYR* 4.2 4.7 - - - -
973 PHE* 3.8 24.9 - + + -
1869A A 4.2 13.2 - - - -
1870A A 2.8 69.1 + + + +
86i ASN* 3.5 23.1 - - - -
87i GLU* 4.6 5.6 - - + -
88i LEU* 3.5 34.3 - - + -
117i LEU* 2.9 29.1 + - + +
118i TYR* 4.1 1.3 - - - +
120i HIS* 1.3 98.8 - + - +
122i ASN* 1.3 67.1 + - - +
123i ARG* 3.1 8.0 + - - -
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Residues in contact with ASN 122 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943 LEU 4.8 5.9 + - - -
953 THR* 3.7 16.4 + - - +
963 TYR* 3.5 24.7 + - - -
973 PHE* 2.7 50.2 + - - +
1752A U 5.3 1.9 + - - -
118i TYR* 2.7 60.8 + - + +
121i PHE* 1.3 74.8 - - - +
123i ARG* 1.3 63.8 + - + +
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Residues in contact with ARG 123 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1721A C 3.5 15.4 + - - -
1722A A 2.8 60.5 + - - +
1730A U 4.8 10.1 + - - -
1731A A 5.4 3.8 + - - +
61M THR* 4.9 2.3 + - - -
62M ARG 4.3 13.0 - - - +
118i TYR* 4.3 23.5 + - - -
119i LYS* 3.1 36.9 + - - +
120i HIS 4.0 0.2 - - - -
121i PHE 3.1 2.2 + - - -
122i ASN* 1.3 86.7 - - + +
124i HIS* 1.3 76.8 + - + +
125i GLY 3.4 6.1 + - - +
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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
------------------------------------------------------------
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