Contacts of the helix formed by residues 64 - 79 (chain C) in PDB entry 2JBG
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 SER 64 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515B ARG* 6.0 2.0 - - - -
61C ARG* 4.2 1.2 - - - +
62C ASP* 2.9 19.9 + - - +
63C ASP* 1.3 77.3 + - - +
65C PRO* 1.3 77.5 - - - +
66C GLU* 3.4 15.3 + - - +
67C GLY 3.0 16.1 + - - -
68C ILE* 2.9 30.8 + - - +
515D ARG* 4.0 11.2 - - - +
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Residues in contact with PRO 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B ASP* 3.9 13.7 - - - +
16C VAL* 4.1 16.4 - - + -
19C LEU* 3.7 24.8 - - + +
20C LYS* 3.9 15.0 - - + +
23C GLU* 3.6 24.7 - - - +
64C SER* 1.3 90.0 - - - +
66C GLU* 1.3 74.1 + - - +
68C ILE* 3.5 3.9 + - + -
69C VAL* 3.1 30.8 + - - +
515D ARG* 5.8 0.4 - - - +
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B SER* 5.0 12.6 - - - +
518B ASN* 4.5 18.3 - - + +
519B ASP* 2.6 38.4 - - - +
522B LYS* 3.7 39.1 + - + +
16C VAL* 4.7 1.4 - - - +
62C ASP* 6.2 0.2 - - + -
64C SER* 3.4 19.5 + - - +
65C PRO* 1.3 81.3 - - - +
67C GLY* 1.3 57.5 + - - +
69C VAL* 3.3 7.9 + - - +
70C LYS* 2.9 30.4 + - - +
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Residues in contact with GLY 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ARG* 3.9 15.2 - - - +
62C ASP* 3.5 25.7 - - - +
64C SER* 3.0 10.0 + - - -
66C GLU* 1.3 79.4 - - - +
68C ILE* 1.3 61.4 + - - +
70C LYS* 3.2 8.8 + - - +
71C GLU* 2.9 25.6 + - - +
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Residues in contact with ILE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 4.1 24.9 - - + -
41C PHE* 4.3 15.5 - - + -
53C LEU* 3.8 20.4 - - + +
54C ILE* 4.1 23.8 - - + +
61C ARG* 3.6 21.5 - - - +
63C ASP* 5.7 2.0 - - - +
64C SER 2.9 25.0 + - - +
65C PRO* 3.7 5.8 - - + +
67C GLY* 1.3 76.1 - - - +
69C VAL* 1.3 63.4 + - - +
71C GLU* 3.4 1.6 + - - +
72C ILE* 2.9 42.6 + - + +
516D ASN* 5.3 4.9 - - - +
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Residues in contact with VAL 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B LYS* 4.6 4.0 - - - +
12C GLU* 3.4 42.4 - - + +
15C PHE* 3.8 25.4 - - + -
16C VAL* 4.1 19.3 - - + -
19C LEU* 4.2 1.8 - - + -
65C PRO 3.1 18.1 + - - +
66C GLU* 3.5 7.0 - - - +
68C ILE* 1.3 79.0 - - - +
70C LYS* 1.3 58.0 + - - +
72C ILE* 3.3 7.9 + - - +
73C LYS* 2.8 30.8 + - + +
84C PHE* 4.1 12.0 - - + -
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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
----------------------------------------------------------
61C ARG* 5.6 10.1 - - + -
66C GLU 2.9 17.4 + - - +
67C GLY* 3.2 8.9 + - - +
69C VAL* 1.3 75.1 - - - +
71C GLU* 1.3 67.0 + - - +
73C LYS* 3.2 14.1 + - - +
74C GLU* 2.9 53.6 + - + +
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Residues in contact with GLU 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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47C HIS* 4.2 11.6 + - - +
49C ASP* 5.3 1.4 - - - +
53C LEU* 3.5 26.0 - - + +
58C SER* 3.7 19.7 + - - -
60C ASN* 5.3 3.6 - - - +
61C ARG* 2.7 48.9 + - + +
67C GLY 2.9 19.1 + - - +
68C ILE* 3.8 3.6 - - - +
70C LYS* 1.3 73.4 - - - +
72C ILE* 1.3 64.1 + - - +
74C GLU* 3.2 12.9 + - - +
75C TRP* 3.0 24.0 + - + +
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Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 4.7 4.7 - - + -
15C PHE* 3.6 36.1 - - + -
41C PHE* 3.9 4.9 - - + -
45C THR* 3.7 19.5 - - + -
47C HIS* 5.3 4.0 - - + -
53C LEU* 3.8 19.5 - - + -
68C ILE* 2.9 31.5 + - + +
69C VAL* 3.6 4.0 - - - +
71C GLU* 1.3 76.9 - - - +
73C LYS* 1.3 57.8 + - - +
75C TRP* 3.3 5.5 + - + +
76C ARG* 2.9 50.8 + - + +
84C PHE* 4.0 16.8 - - + -
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Residues in contact with LYS 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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505B LYS* 5.0 11.1 - - - +
12C GLU* 2.5 40.2 + - - +
69C VAL 2.8 21.3 + - - +
70C LYS* 3.2 13.4 + - - +
72C ILE* 1.3 76.2 - - - +
74C GLU* 1.3 64.6 + - + +
76C ARG* 3.6 4.5 + - - +
77C ALA* 3.1 25.2 + - + +
84C PHE* 4.4 18.8 - - + +
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Residues in contact with GLU 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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60C ASN* 5.9 0.9 + - - -
70C LYS* 2.9 52.4 + - + +
71C GLU* 3.7 12.0 - - - +
73C LYS* 1.3 79.8 - - + +
75C TRP* 1.3 58.8 - - - +
77C ALA* 3.8 4.5 - - - +
78C ALA* 3.0 30.0 + - - +
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Residues in contact with TRP 75 (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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45C THR 4.0 10.1 - - - -
46C GLU 3.3 26.2 - - - -
47C HIS* 3.6 36.1 - + + +
48C PRO* 3.5 25.9 - - + +
71C GLU* 3.0 17.6 + - + +
72C ILE* 3.8 2.9 - - - +
74C GLU* 1.3 74.9 - - - +
76C ARG* 1.3 77.6 + - + +
78C ALA* 3.2 5.1 + - + -
79C ASN* 3.0 54.8 + - - +
81C LYS* 3.8 36.1 - - + -
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Residues in contact with ARG 76 (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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6C SER* 6.1 1.2 - - - -
7C ILE* 3.7 32.8 - - - +
8C SER 5.4 0.2 - - - +
44C ILE 3.6 6.0 + - - -
45C THR 3.0 20.7 + - - +
46C GLU* 2.7 29.7 + - - -
72C ILE* 2.9 33.6 + - + +
73C LYS* 4.1 4.5 - - - +
75C TRP* 1.3 93.5 - - + +
77C ALA* 1.3 57.7 + - - +
79C ASN* 3.4 1.5 + - - -
80C GLY 3.2 3.5 + - - -
81C LYS* 2.7 51.8 + - + +
82C PRO* 2.8 55.5 + - - +
83C GLY* 5.2 4.0 - - - -
84C PHE* 5.7 0.7 - - - -
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Residues in contact with ALA 77 (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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73C LYS* 3.1 20.9 + - + +
74C GLU* 3.8 5.6 - - - +
76C ARG* 1.3 73.6 - - - +
78C ALA* 1.3 63.6 + - - +
79C ASN 2.9 5.8 + - - -
80C GLY* 3.0 13.1 + - - -
81C LYS 4.7 4.0 - - - +
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Residues in contact with ALA 78 (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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74C GLU 3.0 18.5 + - - +
75C TRP* 3.7 8.5 - - + +
77C ALA* 1.3 75.7 - - - +
79C ASN* 1.3 66.5 + - - +
80C GLY 3.5 0.2 - - - -
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Residues in contact with ASN 79 (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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75C TRP* 3.0 65.0 + - + +
76C ARG 4.1 2.9 - - - +
77C ALA 2.9 1.2 - - - -
78C ALA* 1.3 85.4 - - - +
80C GLY* 1.3 62.7 + - - +
81C LYS* 3.2 21.5 + - + +
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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