Contacts of the helix formed by residues 65 - 76 (chain C) in PDB entry 2JC6
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 65 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C ILE* 1.3 57.5 + - - +
67C GLU* 3.1 10.3 - - - +
68C ASN* 3.1 16.3 + - - +
69C GLU* 2.8 41.8 + - - +
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Residues in contact with ILE 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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54C ILE* 5.1 20.2 - - + -
65C SER* 1.3 79.1 - - - +
67C GLU* 1.3 61.8 + - + +
69C GLU* 4.2 8.5 - - + -
70C ILE* 3.0 51.0 + - + +
94C LEU* 4.8 15.5 - - + -
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Residues in contact with GLU 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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15A GLN* 4.4 5.9 + - - +
65C SER 3.1 6.9 - - - +
66C ILE* 1.3 85.7 - - + +
68C ASN* 1.3 60.8 + - - +
70C ILE* 3.9 4.9 - - - +
71C ALA* 3.3 21.5 + - - +
94C LEU* 6.5 0.2 - - - -
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Residues in contact with ASN 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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65C SER* 3.1 17.0 + - - +
67C GLU* 1.3 76.6 - - - +
69C GLU* 1.3 65.4 + - + +
71C ALA* 3.2 20.8 + - - +
72C VAL* 3.4 7.4 + - - +
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Residues in contact with GLU 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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65C SER* 2.8 25.1 + - - +
66C ILE* 4.0 9.4 - - + +
68C ASN* 1.3 74.2 - - + +
70C ILE* 1.3 63.9 + - + +
71C ALA 3.3 0.3 + - - -
72C VAL* 3.5 8.0 + - - +
73C LEU* 3.3 27.7 + - + +
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Residues in contact with ILE 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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15A GLN* 4.1 6.5 - - - +
54C ILE* 5.5 1.3 - - + -
66C ILE* 3.0 35.2 + - + +
67C GLU* 3.9 5.6 - - - +
69C GLU* 1.3 75.4 - - + +
71C ALA* 1.3 62.8 + - - +
73C LEU* 3.4 15.0 + - + +
74C ARG* 3.2 18.2 + - - +
84C LEU* 3.7 5.9 - - + +
87C ILE* 3.2 37.7 - - + -
94C LEU* 3.6 31.0 - - + -
96C LEU* 3.7 26.5 - - + -
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Residues in contact with ALA 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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15A GLN* 4.2 25.5 + - - +
11C SER 6.0 1.3 - - - +
67C GLU 3.3 10.6 + - - +
68C ASN* 3.2 13.3 + - - +
70C ILE* 1.3 74.7 - - - +
72C VAL* 1.3 66.9 + - - +
74C ARG* 3.1 16.2 + - - +
75C LYS* 3.5 8.7 + - - +
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Residues in contact with VAL 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 ASN 3.4 6.8 + - - +
69C GLU* 3.6 11.2 - - - +
71C ALA* 1.3 76.4 - - - +
73C LEU* 1.3 67.1 + - + +
75C LYS* 3.0 22.5 + - - +
76C ILE* 3.5 12.2 + - + +
140C ILE* 4.9 17.3 - - + +
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Residues in contact with LEU 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 GLU* 3.3 16.7 + - + +
70C ILE* 3.5 19.1 - - + +
71C ALA 3.3 0.8 - - - -
72C VAL* 1.3 79.2 - - + +
74C ARG* 1.3 63.0 + - - +
76C ILE* 3.0 42.2 + - + +
84C LEU* 3.6 26.2 + - + +
96C LEU* 5.5 7.9 - - + -
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Residues in contact with ARG 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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15A GLN* 5.4 4.7 - - + -
70C ILE 3.2 8.7 + - - +
71C ALA* 3.1 13.3 + - - +
73C LEU* 1.3 77.7 - - - +
75C LYS* 1.3 59.0 + - - +
76C ILE 3.3 3.0 + - - +
84C LEU* 3.7 23.7 - - + +
85C GLU 6.1 1.1 - - - -
86C ASP* 6.2 0.7 - - - -
87C ILE* 4.1 19.1 - - + -
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Residues in contact with LYS 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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71C ALA 3.5 6.3 + - - +
72C VAL* 3.0 14.6 + - - +
74C ARG* 1.3 77.9 - - - +
76C ILE* 1.3 61.2 + - + +
77C LYS* 3.3 8.6 + - - +
134C TYR* 3.4 7.4 + - - -
138C MET* 5.3 8.8 - - + +
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Residues in contact with ILE 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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72C VAL* 3.5 11.0 - - + +
73C LEU* 3.0 44.9 + - + +
74C ARG 3.3 2.7 - - - +
75C LYS* 1.3 75.2 - - + +
77C LYS* 1.3 59.7 + - - +
78C HIS 4.3 0.5 + - - -
81C ILE* 3.8 43.1 - - + +
82C VAL 5.4 1.0 - - - +
83C ALA* 4.7 15.9 - - - +
84C LEU 4.9 1.9 + - - +
134C TYR* 3.6 8.1 - - + -
135C LEU* 3.8 20.2 - - + -
138C MET* 5.8 1.3 - - + -
140C ILE* 3.8 28.5 - - + -
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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