Contacts of the helix formed by residues 110 - 122 (chain B) in PDB entry 1JG0
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 ASP 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B TRP 3.6 1.2 - - - +
99B ARG* 2.9 53.2 + - - +
108B HIS 4.2 1.4 + - - -
109B ILE* 1.3 70.5 - - - +
111B GLN* 1.3 57.3 + - - +
112B ILE 3.2 5.0 + - - -
113B THR* 2.6 38.9 + - - -
114B THR* 2.9 29.8 + - - -
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Residues in contact with GLN 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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133A TRP* 4.9 0.9 + - - -
135A VAL* 3.6 30.7 - - + +
97B GLN 3.0 23.5 + - - +
98B TRP 3.1 10.8 + - - +
101B TRP* 3.5 12.3 - - + +
109B ILE* 3.3 7.5 + - + +
110B ASP* 1.3 69.8 - - - +
112B ILE* 1.3 67.0 + - - +
114B THR* 3.6 7.1 - - - -
115B VAL* 3.0 29.1 + - - +
129B ILE 3.7 7.4 - - - +
130B VAL* 3.2 21.5 - - + +
131B SER 2.8 48.5 + - - +
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Residues in contact with ILE 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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63B LEU* 4.2 12.8 - - + -
98B TRP* 3.2 47.4 + - + +
99B ARG* 3.7 16.8 - - - -
110B ASP* 3.2 6.8 + - - +
111B GLN* 1.3 76.9 - - - +
113B THR* 1.3 58.7 + - - +
115B VAL* 3.4 4.3 + - + +
116B LEU* 2.9 48.3 + - + +
130B VAL* 4.2 17.7 - - + -
150B PHE* 4.6 4.9 - - + -
184B LEU* 5.7 3.8 - - + -
188B MET* 5.0 4.3 - - - -
239B ILE* 4.1 7.6 - - + -
240B PHE* 3.8 19.5 - - + -
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Residues in contact with THR 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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110B ASP* 2.6 34.2 + - - -
112B ILE* 1.3 75.8 - - - +
114B THR* 1.3 66.6 + - - +
116B LEU* 3.1 9.1 + - + +
117B ASN* 3.0 38.5 + - - +
240B PHE* 3.4 20.4 - - - -
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Residues in contact with THR 114 (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 ILE* 4.5 8.5 - - - +
110B ASP 2.9 21.8 + - - -
111B GLN* 3.6 11.8 - - - -
112B ILE 3.3 0.2 - - - -
113B THR* 1.3 77.5 - - - +
115B VAL* 1.3 61.1 + - + +
117B ASN* 3.2 7.7 + - - +
118B GLN* 2.9 51.6 + - + +
127B ARG* 4.9 10.3 - - - +
129B ILE 6.1 0.9 - - - +
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Residues in contact with VAL 115 (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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111B GLN 3.0 16.4 + - - +
112B ILE* 3.7 4.0 - - - +
114B THR* 1.3 80.2 - - - +
116B LEU* 1.3 65.1 + - - +
118B GLN* 3.2 17.3 + - - +
119B LEU* 3.0 24.6 + - + +
128B ILE* 3.4 20.4 - - + -
129B ILE 3.7 15.7 - - - +
130B VAL* 3.7 22.2 - - + -
152B PHE* 3.6 21.8 - - + -
188B MET* 3.7 17.3 - - + -
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Residues in contact with LEU 116 (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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112B ILE* 2.9 42.0 + - + +
113B THR* 3.1 13.7 + - + +
115B VAL* 1.3 75.9 - - - +
117B ASN* 1.3 68.2 + - - +
119B LEU* 3.3 2.4 + - - +
120B LYS* 3.2 41.7 + - - +
188B MET* 3.3 39.0 - - + -
191B GLN* 4.1 18.6 - - + -
192B CYS* 3.9 19.4 - - - -
239B ILE* 4.1 15.9 - - + +
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Residues in contact with ASN 117 (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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113B THR* 3.0 31.3 + - - +
114B THR* 3.5 9.3 - - - +
116B LEU* 1.3 79.0 - - - +
118B GLN* 1.3 61.1 + - - +
120B LYS* 4.6 12.0 - - - +
121B ASN* 2.8 50.0 + - - +
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Residues in contact with GLN 118 (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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114B THR* 2.9 31.6 + - + +
115B VAL* 3.5 26.8 - - - +
117B ASN* 1.3 78.0 - - + +
119B LEU* 1.3 59.8 + - - +
122B ASP* 2.7 46.8 + - + +
123B PRO 3.0 0.2 - - - -
125B SER* 3.8 13.3 + - - +
127B ARG* 3.3 29.7 + - - +
128B ILE* 3.6 32.5 - - + +
129B ILE 4.4 1.2 + - - +
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Residues in contact with LEU 119 (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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115B VAL* 3.0 20.0 + - + +
116B LEU 3.3 4.9 + - - +
118B GLN* 1.3 77.0 - - - +
120B LYS* 1.3 58.6 + - - +
123B PRO* 3.4 21.7 - - + +
128B ILE* 3.7 22.9 - - + -
152B PHE* 4.2 9.6 - - + -
153B TYR 5.1 0.2 - - - +
154B VAL* 3.5 30.1 - - + -
159B LEU* 3.7 27.8 - - + -
188B MET* 3.3 33.7 - - + -
192B CYS* 3.8 16.2 - - + +
194B LEU* 4.8 9.8 - - + +
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Residues in contact with LYS 120 (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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116B LEU* 3.2 31.7 + - - +
117B ASN* 4.0 10.7 - - - +
119B LEU* 1.3 79.9 - - - +
121B ASN* 1.3 73.6 + - - +
123B PRO* 4.1 5.4 - - - +
191B GLN* 3.3 29.7 + - - +
192B CYS* 3.8 22.7 - - + +
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Residues in contact with ASN 121 (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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117B ASN* 2.8 37.1 + - - +
118B GLN* 5.1 0.2 - - - -
120B LYS* 1.3 88.8 + - - +
122B ASP* 1.3 58.9 + - + +
123B PRO* 3.5 5.2 - - - +
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Residues in contact with ASP 122 (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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118B GLN* 2.7 25.3 + - + +
121B ASN* 1.3 78.9 - - + +
123B PRO* 1.3 57.3 - - - +
124B ASP* 3.0 15.1 + - - +
125B SER* 3.1 37.3 + - - -
128B ILE* 4.1 0.5 - - - +
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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