Contacts of the helix formed by residues 109 - 119 (chain J) in PDB entry 6AHU
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 THR 109 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82J SER* 3.5 19.6 + - - -
84J PRO* 6.6 0.4 - - - -
107J PRO 3.9 0.2 - - - -
108J LYS* 1.3 81.2 + - - +
110J GLU* 1.3 59.1 + - + +
111J LYS* 3.2 24.2 - - + +
112J LEU* 2.9 18.1 + - + +
113J PHE* 2.6 36.4 + - - +
135J PHE* 3.8 3.6 - - - -
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Residues in contact with GLU 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J THR* 1.3 76.4 - - + +
111J LYS* 1.3 71.2 + - + +
113J PHE* 3.9 3.2 - - - +
114J HIS* 3.6 21.0 + - - +
135J PHE* 3.5 27.3 - - + -
136J TYR* 4.9 20.5 + - - +
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Residues in contact with LYS 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J THR* 3.2 13.5 - - + +
110J GLU* 1.3 87.0 - - + +
112J LEU* 1.3 59.3 + - - +
114J HIS* 4.0 4.7 + - - +
115J ILE* 3.6 22.2 + - - +
69T A 6.1 1.3 - - - -
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Residues in contact with LEU 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81J VAL* 3.7 33.9 - - + -
82J SER* 4.1 11.4 - - - +
83J ASP 3.8 23.6 - - - +
84J PRO* 4.1 11.2 - - + -
87J CYS* 5.0 4.7 - - + -
105J VAL* 5.5 3.8 - - + -
107J PRO* 3.8 26.0 - - + -
108J LYS 4.5 2.0 - - - +
109J THR* 2.9 18.4 + - - +
111J LYS* 1.3 78.5 - - - +
113J PHE* 1.3 62.7 + - - +
114J HIS 3.3 1.6 - - - -
115J ILE* 3.3 30.2 - - + +
116J ALA* 3.3 12.4 + - + +
120J LEU* 6.4 0.7 - - + -
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Residues in contact with PHE 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J PRO* 3.6 26.5 - - + -
109J THR 2.6 19.0 + - - +
110J GLU* 4.2 4.3 - - - -
111J LYS 3.5 0.2 - - - -
112J LEU* 1.3 74.9 - - - +
114J HIS* 1.3 62.6 + - + +
116J ALA* 3.6 2.4 + - + +
117J CYS* 3.4 41.6 + - - -
125J VAL* 4.0 18.6 - - + -
127J ILE* 4.7 11.9 - - + -
135J PHE* 3.7 32.1 - + + -
136J TYR 5.6 0.7 - - - -
137J PHE* 5.4 6.3 - + - -
138J LYS* 5.2 5.4 - - + -
141J PRO* 4.0 31.2 - - + -
142J ILE* 4.0 20.9 - - + -
152J PHE* 4.2 6.3 - + - -
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Residues in contact with HIS 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J GLU 3.6 15.1 + - - +
111J LYS* 4.3 6.5 - - - +
112J LEU 3.3 0.6 - - - -
113J PHE* 1.3 78.5 - - + +
115J ILE* 1.3 70.1 + - + +
117J CYS* 3.5 1.6 + - - +
118J THR* 3.2 39.2 + - + -
119J HIS* 5.0 6.8 - - - -
138J LYS* 5.9 0.9 - - + -
140J PRO 5.4 0.4 - - - -
141J PRO* 4.2 29.2 - - + +
67T G 2.9 42.4 + - - -
68T G 3.3 27.5 + - - -
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Residues in contact with ILE 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87J CYS* 4.4 14.6 - - + -
91J ARG* 3.5 25.1 - - - +
111J LYS 3.6 16.4 + - - +
112J LEU* 3.3 34.1 - - + +
114J HIS* 1.3 80.1 - - - +
116J ALA* 1.3 59.5 + - + +
119J HIS* 2.9 30.7 + - + +
120J LEU* 2.5 35.1 + - + -
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Residues in contact with ALA 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J VAL* 4.3 24.7 - - + -
107J PRO* 5.2 6.3 - - + -
112J LEU* 3.3 19.4 + - + +
113J PHE* 3.9 7.6 - - + +
114J HIS 3.3 0.6 - - - -
115J ILE* 1.3 80.5 - - + +
117J CYS* 1.3 58.3 + - - +
120J LEU* 3.3 35.6 - - + +
122J VAL* 3.8 12.3 - - - +
125J VAL* 5.0 4.9 - - + -
148J ARG* 4.2 0.7 + - - -
150J LEU* 4.1 4.4 - - - +
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Residues in contact with CYS 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J PHE* 3.4 45.1 + - - +
114J HIS 3.5 3.3 + - - +
115J ILE 3.3 0.2 - - - -
116J ALA* 1.3 78.3 - - - +
118J THR* 1.3 60.1 + - - +
125J VAL* 4.6 3.4 - - - -
141J PRO* 3.4 31.0 - - + +
144J VAL* 4.4 8.7 - - - +
145J ALA* 4.5 5.2 - - + +
148J ARG* 3.2 21.8 + - - -
150J LEU* 3.7 26.2 - - + +
152J PHE* 4.4 7.6 - - - -
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Residues in contact with THR 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J HIS* 3.2 34.4 + - + -
116J ALA 3.5 0.2 - - - -
117J CYS* 1.3 81.7 + - - +
119J HIS* 1.3 83.0 + - + +
140J PRO 5.3 0.2 + - - -
141J PRO* 5.0 3.3 - - - +
144J VAL* 4.5 23.7 - - + +
148J ARG* 3.0 19.8 + - - +
47T U 4.3 5.7 - - - +
49T C 5.6 4.9 - - - +
67T G 5.5 5.4 - - - +
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Residues in contact with HIS 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J ARG* 4.0 19.1 + - - +
114J HIS* 5.0 8.6 - - - -
115J ILE* 2.9 32.0 + - + +
118J THR* 1.3 94.0 - - + +
120J LEU* 1.3 66.8 + - - +
121J ASP* 3.5 12.0 + - - +
148J ARG* 4.4 0.4 - - - -
7T G 5.9 4.0 + - - -
8T U 5.5 6.5 - - - -
47T U 4.0 13.6 - - - +
49T C 4.4 29.8 + - - -
67T G 5.7 1.2 + - - -
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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