Contacts of the helix formed by residues 60 - 74 (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 GLY 60 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ILE* 1.3 78.7 - - - +
61C GLY* 1.3 68.0 + - - +
63C LEU 4.4 0.3 + - - -
64C GLY* 3.3 7.0 + - - -
83C ILE* 4.0 7.9 - - - +
85C GLY 3.4 21.5 - - - -
87C THR* 2.9 31.2 + - - +
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Residues in contact with GLY 61 (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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69B LYS* 5.5 0.9 - - - -
60C GLY* 1.3 72.6 - - - -
62C GLU* 1.3 71.6 + - - -
63C LEU 3.3 0.7 - - - -
64C GLY* 3.2 9.5 + - - -
65C GLN* 3.2 11.4 + - - +
83C ILE 5.0 1.2 + - - -
85C GLY 3.9 3.2 + - - -
86C GLU* 4.3 15.9 - - - -
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Residues in contact with GLU 62 (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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62B GLU* 3.4 39.2 - - + +
63B LEU* 5.8 0.7 - - + -
65B GLN* 3.8 23.9 - - + +
66B PHE* 3.8 23.5 - - + +
69B LYS* 3.1 44.5 + - - +
61C GLY* 1.3 73.4 - - - -
63C LEU* 1.3 63.1 + - + +
65C GLN* 3.2 11.2 + - - +
66C PHE 3.0 21.8 + - - -
86C GLU* 3.9 5.8 - - - +
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Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LYS* 4.1 7.0 - - + +
62B GLU* 5.6 1.1 - - + -
63B LEU* 4.0 26.7 - - + -
11C VAL* 3.5 23.9 - - + +
60C GLY 5.0 0.2 - - - +
61C GLY 3.3 0.8 - - - -
62C GLU* 1.3 78.1 - - + +
64C GLY* 1.3 65.6 + - - +
66C PHE* 3.3 9.2 + - + +
67C ILE* 3.1 28.1 + - - +
87C THR* 3.3 33.0 - - + +
88C ARG 3.7 8.1 - - - +
89C ASN* 3.4 36.6 - - - +
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Residues in contact with GLY 64 (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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59C ILE* 3.5 32.4 - - - +
60C GLY* 3.3 15.5 + - - -
61C GLY 3.2 8.6 + - - -
63C LEU* 1.3 77.2 - - - +
65C GLN* 1.3 59.7 + - - +
67C ILE* 3.4 4.7 + - - +
68C ALA* 3.1 23.3 + - - +
87C THR* 3.7 4.3 - - - -
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Residues in contact with GLN 65 (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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20A LEU 5.8 0.3 - - - +
22A LEU* 5.4 8.1 - - + +
96A GLU* 5.4 1.0 - - - +
98A GLN* 3.7 15.1 + - - +
62B GLU* 3.0 23.1 + - + +
65B GLN* 2.7 42.8 + - - -
61C GLY 3.2 10.7 + - - +
62C GLU* 3.2 10.7 + - - +
64C GLY* 1.3 72.4 - - - +
66C PHE* 1.3 65.9 + - - +
68C ALA* 3.5 5.9 + - + +
69C LYS* 3.0 25.5 + - - +
22D LEU* 3.5 30.2 - - + +
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Residues in contact with PHE 66 (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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62B GLU* 3.6 29.8 - - + +
63B LEU* 6.4 2.0 - - + -
86B GLU* 3.7 25.4 - - - -
11C VAL* 3.6 31.0 - - + -
33C LYS* 3.7 32.8 - - + -
34C THR 4.3 5.2 - - - -
62C GLU 3.0 13.5 + - - +
63C LEU* 3.5 16.4 - - + +
64C GLY 3.3 0.2 - - - -
65C GLN* 1.3 75.7 - - - +
67C ILE* 1.3 65.2 + - + +
69C LYS* 3.3 5.4 + - + +
70C LYS* 3.1 56.1 + - + +
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Residues in contact with ILE 67 (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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9C PRO* 4.0 9.6 - - + -
10C SER 3.8 26.2 - - - +
11C VAL* 3.8 10.3 - - + +
35C ALA* 4.1 20.4 - - + +
40C LEU* 3.6 24.7 - - + -
59C ILE* 3.9 15.0 - - + -
63C LEU 3.1 10.0 + - - +
64C GLY 3.6 7.0 - - - +
66C PHE* 1.3 76.8 - - + +
68C ALA* 1.3 64.3 + - - +
70C LYS* 3.1 5.0 + - - +
71C LEU* 3.0 32.4 + - + +
80C PHE* 4.3 2.2 - - + -
87C THR* 3.8 27.6 - - + -
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Residues in contact with ALA 68 (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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59C ILE* 6.0 0.9 - - + -
64C GLY 3.1 13.7 + - - +
65C GLN* 3.8 7.4 - - - +
66C PHE 3.4 0.2 - - - -
67C ILE* 1.3 80.6 - - - +
69C LYS* 1.3 57.6 + - - +
71C LEU* 3.3 6.3 + - - +
72C ASP* 2.8 40.8 + - - +
78C HIS* 4.3 21.8 - - + -
80C PHE* 5.0 6.3 - - + -
20D LEU 6.2 0.2 - - - +
96D GLU* 5.5 1.6 - - - +
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Residues in contact with LYS 69 (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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98A GLN* 2.6 34.1 + - - +
61B GLY* 6.2 1.0 - - - -
62B GLU* 3.1 26.7 + - - +
65C GLN* 3.0 19.4 + - - +
66C PHE* 3.5 7.0 - - + +
68C ALA* 1.3 74.1 - - - +
70C LYS* 1.3 60.8 + - + +
72C ASP* 3.2 6.8 + - - +
73C HIS* 2.9 64.0 + - + +
22D LEU* 3.7 28.3 - - - +
23D ASP* 4.1 8.7 + - + +
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Residues in contact with LYS 70 (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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86B GLU* 5.5 2.6 + - - -
33C LYS 4.0 11.6 + - - +
34C THR* 5.7 0.4 - - - -
35C ALA* 3.9 22.2 - - + +
44C ARG* 5.7 4.3 - - - -
66C PHE* 3.1 54.8 + - + +
67C ILE 3.1 6.7 + - - +
69C LYS* 1.3 76.5 - - + +
71C LEU* 1.3 63.8 + - + +
73C HIS* 3.5 14.4 + - + +
74C ALA* 3.3 21.8 + - - +
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Residues in contact with LEU 71 (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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35C ALA* 4.3 11.9 - - + -
40C LEU* 4.2 17.5 - - + -
43C THR* 5.1 0.9 - - + -
44C ARG* 4.1 17.7 - - + -
55C ALA* 4.7 1.1 - - + -
67C ILE* 3.0 21.7 + - + +
68C ALA 3.8 6.1 - - - +
70C LYS* 1.3 75.5 - - - +
72C ASP* 1.3 57.3 + - - +
74C ALA* 3.2 3.5 + - - -
75C ASP 3.0 7.6 + - - -
76C ILE* 2.8 63.1 + - + +
78C HIS* 4.0 19.3 - - + -
80C PHE* 3.6 37.2 - - + -
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Residues in contact with ASP 72 (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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68C ALA* 2.8 29.0 + - - +
69C LYS* 3.2 7.6 + - - +
71C LEU* 1.3 74.1 - - - +
73C HIS* 1.3 69.3 + - + +
75C ASP* 3.1 19.8 + - - +
76C ILE 4.5 2.6 - - - +
78C HIS* 2.7 30.6 + - - -
19D ALA* 4.0 8.8 - - - +
20D LEU 3.9 5.9 - - - +
21D LYS* 3.7 50.7 + - + +
22D LEU 4.7 1.2 + - - -
24D ASP* 5.3 1.3 - - - +
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Residues in contact with HIS 73 (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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69C LYS* 2.9 48.7 + - + +
70C LYS* 3.8 15.7 - - + +
71C LEU 3.3 0.2 - - - -
72C ASP* 1.3 79.5 - - + +
74C ALA* 1.3 60.5 + - + +
75C ASP* 3.5 7.3 + - - +
22D LEU 4.8 9.4 - - - -
23D ASP* 5.4 3.8 - - + -
24D ASP* 4.9 15.7 + - + -
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Residues in contact with ALA 74 (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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44C ARG* 6.2 1.6 - - + -
47C ALA* 5.9 0.3 - - - +
70C LYS 3.3 13.6 + - - +
71C LEU 3.2 4.8 + - - +
72C ASP 3.2 0.6 - - - -
73C HIS* 1.3 76.5 - - + +
75C ASP* 1.3 71.0 + - - +
76C ILE* 3.2 22.6 + - + +
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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