Contacts of the helix formed by residues 110 - 126 (chain C) in PDB entry 2JG1
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C LYS* 3.4 30.7 - - - +
108C GLU 4.0 2.0 + - - -
109C ILE* 1.3 75.5 - - - +
111C ASN* 1.3 67.5 + - - +
112C GLN* 3.1 11.9 + - - +
113C GLU* 2.7 52.8 + - - +
114C ALA* 3.0 22.8 + - - +
140C GLY 5.7 0.4 - - - -
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Residues in contact with ASN 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ILE 5.2 1.0 + - - -
110C ASP* 1.3 77.1 - - - +
112C GLN* 1.3 59.0 + - + +
114C ALA* 3.5 5.8 + - - +
115C ALA* 3.0 29.6 + - - +
140C GLY 5.5 4.2 + - - -
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Residues in contact with GLN 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C TYR* 3.9 4.2 + - - -
84C LYS* 6.1 0.7 - - - -
110C ASP* 3.1 10.6 + - - +
111C ASN* 1.3 77.9 - - + +
113C GLU* 1.3 62.3 - - + +
115C ALA* 3.9 4.8 - - - +
116C GLY* 2.9 25.6 + - - -
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Residues in contact with GLU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C PHE* 3.7 3.0 - - + -
81C TYR* 3.8 28.3 - - + +
82C ASN 4.4 1.7 - - - +
83C ILE* 3.3 19.5 - - + +
84C LYS* 2.9 42.5 + - - +
85C GLY 5.4 0.2 + - - -
108C GLU 4.3 2.6 - - - +
109C ILE* 3.6 19.9 - - + +
110C ASP* 2.7 45.0 + - - +
112C GLN* 1.3 73.0 - - + +
114C ALA* 1.3 58.7 + - - +
116C GLY* 3.4 0.3 + - - -
117C PHE* 2.9 30.7 + - - +
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C PHE* 4.4 0.9 - - - -
109C ILE* 3.7 6.0 - - + +
110C ASP 3.0 16.8 + - - +
111C ASN* 3.8 6.7 - - - +
113C GLU* 1.3 74.7 - - - +
115C ALA* 1.3 63.2 + - - +
118C ILE* 3.5 11.4 + - - +
140C GLY 5.7 1.6 - - - +
141C LEU* 3.6 28.7 - - + -
145C TYR* 2.6 32.7 + - + -
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Residues in contact with ALA 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C ASN 3.0 18.6 + - - +
112C GLN* 3.9 6.1 - - - +
114C ALA* 1.3 74.9 - - - +
116C GLY* 1.3 65.2 + - - +
118C ILE* 3.4 17.1 + - - +
119C LYS* 3.4 18.4 + - - +
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Residues in contact with GLY 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C TYR* 3.6 19.8 - - - -
112C GLN 2.9 18.5 + - - -
113C GLU 3.8 1.3 - - - -
115C ALA* 1.3 77.8 - - - +
117C PHE* 1.3 59.4 + - - +
119C LYS* 3.4 10.0 + - - +
120C HIS* 3.0 21.8 + - - +
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Residues in contact with PHE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 3.9 21.8 - - + -
7C LEU* 3.6 24.2 - - + -
56C SER* 3.6 20.0 - - - -
57C GLY* 4.0 14.1 - - - -
58C PHE* 3.5 30.1 - + + -
81C TYR* 3.8 25.9 - - + -
113C GLU 2.9 9.3 + - - +
115C ALA 3.3 0.6 - - - -
116C GLY* 1.3 74.4 - - - +
118C ILE* 1.3 58.2 + - + +
120C HIS* 3.1 8.9 + + - +
121C PHE* 2.6 51.6 + - + +
124C MSE 4.8 0.9 - - + -
145C TYR* 3.6 20.9 - + - +
149C ILE* 4.3 14.4 - - + -
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Residues in contact with ILE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ALA 3.5 6.7 + - - +
115C ALA* 3.4 9.6 + - - +
116C GLY 3.4 0.6 - - - -
117C PHE* 1.3 78.0 - - + +
119C LYS* 1.3 63.6 + - + +
121C PHE* 3.4 6.5 + - + +
122C GLU* 2.9 33.7 + - - +
145C TYR* 3.5 35.2 - - + +
148C GLN* 4.4 19.5 - - + +
149C ILE* 4.0 23.6 - - + -
152C ARG* 3.5 38.4 - - - +
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Residues in contact with LYS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ALA 3.4 17.5 - - - +
116C GLY* 3.4 8.7 + - - +
117C PHE 3.2 0.2 - - - -
118C ILE* 1.3 77.9 - - - +
120C HIS* 1.3 65.6 + - - +
122C GLU* 2.3 40.2 + - - +
123C GLN* 3.4 25.5 + - - +
152C ARG* 5.2 1.6 - - - +
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Residues in contact with HIS 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C SER* 3.9 4.3 - - - -
79C ALA* 2.9 36.6 + - + -
80C PHE 4.6 2.4 + - - -
81C TYR* 4.3 18.2 - + + -
116C GLY 3.0 14.7 + - - +
117C PHE* 3.4 20.2 - + - +
119C LYS* 1.3 75.6 - - - +
121C PHE* 1.3 62.6 + - - +
123C GLN* 3.1 33.9 + - - +
124C MSE 3.3 43.4 + - + +
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Residues in contact with PHE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 3.7 29.6 - - + -
5C LEU* 3.7 29.2 - - + -
117C PHE* 2.6 34.5 + + + +
118C ILE* 3.5 9.6 - - + +
120C HIS* 1.3 73.3 - - - +
122C GLU* 1.3 60.9 + - + +
124C MSE 3.1 11.3 + - + +
125C MSE 2.7 65.2 + - + +
131C VAL* 4.4 3.8 - - + -
149C ILE* 3.4 39.9 - - + -
152C ARG* 4.4 6.3 - - + -
153C CYS* 3.6 13.9 - - - -
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Residues in contact with GLU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ILE* 2.9 18.4 + - - +
119C LYS* 2.3 39.7 + - - +
120C HIS 3.4 0.6 - - - -
121C PHE* 1.3 80.4 - - + +
123C GLN* 1.3 61.3 + - - +
125C MSE 4.4 9.4 - - + +
126C GLU* 3.1 27.7 + - - +
152C ARG* 2.3 57.3 + - + +
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Residues in contact with GLN 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C LYS 3.4 12.7 + - - +
120C HIS* 3.1 34.9 + - - +
122C GLU* 1.3 79.4 - - - +
124C MSE 1.3 65.8 + - + +
126C GLU* 3.9 10.8 - - - +
127C LYS* 3.7 28.2 - - - +
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Residues in contact with MSE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 4.2 16.8 - - + -
54C LEU* 3.8 29.4 - - + -
56C SER* 3.3 34.5 - - - +
79C ALA* 4.1 5.6 - - + -
117C PHE* 4.8 2.5 - - + -
120C HIS* 3.3 39.0 + - + +
121C PHE* 3.1 29.0 + - + +
123C GLN* 1.3 79.4 - - + +
125C MSE 1.3 64.1 + - - +
127C LYS* 3.1 17.0 + - - +
128C VAL* 3.6 14.6 - - - +
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Residues in contact with MSE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 4.3 2.9 - - + +
121C PHE* 2.7 51.1 + - + +
122C GLU* 4.5 12.8 - - + +
124C MSE 1.3 67.7 - - - +
126C GLU* 1.3 68.2 + - - +
127C LYS 2.8 6.4 + - - -
128C VAL* 3.0 26.7 + - + +
131C VAL* 3.9 12.3 - - + -
152C ARG* 3.5 36.8 - - + +
153C CYS* 3.9 16.2 - - - -
156C LYS* 3.8 33.2 - - + -
158C VAL* 4.0 10.4 - - + +
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Residues in contact with GLU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C GLU 3.1 21.0 + - - +
123C GLN* 3.9 13.0 - - - +
125C MSE 1.3 84.7 - - - +
127C LYS* 1.3 77.4 + - - +
128C VAL 3.9 2.9 + - - +
156C LYS* 4.9 25.3 - - + +
158C VAL* 5.3 2.8 - - - +
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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