Contacts of the helix formed by residues 70 - 78 (chain C) in PDB entry 1JI5
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 THR 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C VAL 4.0 0.6 - - - -
69C ALA* 1.3 84.0 - - - +
71C MET* 1.3 66.6 + - - +
72C LYS* 3.9 5.1 - - + +
73C GLU* 2.8 45.5 + - - +
74C TYR* 3.1 26.9 + - - -
21D THR* 4.1 1.8 - - - -
82D GLU* 3.1 27.8 - - + +
83D ALA* 4.1 16.8 - - + +
85D TYR* 3.9 14.4 - - + +
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Residues in contact with MET 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C THR* 5.2 0.7 - - - +
70C THR* 1.3 72.3 - - - +
72C LYS* 1.3 61.5 + - - +
74C TYR* 3.2 11.2 + - - +
75C LEU* 2.9 26.7 + - - +
17D SER* 4.2 13.2 - - - +
18D VAL* 4.2 16.8 - - - -
21D THR* 3.5 23.7 - - + +
71D MET* 3.1 65.9 - - + +
74D TYR* 3.7 17.9 - - + -
75D LEU* 3.9 23.8 - - + -
82D GLU* 2.5 16.1 + - - +
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Residues in contact with LYS 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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70C THR* 3.0 5.8 - - - +
71C MET* 1.3 80.0 - - - +
73C GLU* 1.3 67.0 + - + +
75C LEU* 3.3 5.1 + - - +
76C GLU* 3.2 45.5 + - - +
75D LEU* 3.9 14.7 - - + +
82D GLU* 3.4 19.1 + - - +
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Residues in contact with GLU 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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68C VAL* 3.9 28.6 - - + +
69C ALA 3.9 0.5 + - - -
70C THR* 2.8 27.2 + - - +
72C LYS* 1.3 77.9 - - + +
74C TYR* 1.3 60.9 + - - +
76C GLU* 2.9 27.8 + - + +
77C ILE* 2.5 32.8 + - + +
85D TYR* 2.3 39.2 + - - -
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Residues in contact with TYR 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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13C VAL* 3.6 17.8 - - + +
14C ALA* 3.4 31.2 - - + +
17C SER* 3.5 22.0 + - - -
18C VAL* 4.9 0.7 - - + -
53C ILE* 5.2 0.5 - - - +
68C VAL* 2.9 46.0 + - + -
69C ALA* 3.5 6.4 - - - -
70C THR 3.1 16.6 + - - -
71C MET* 3.3 15.5 - - - +
73C GLU* 1.3 75.3 - - - +
75C LEU* 1.3 56.6 + - - +
78C SER* 2.7 38.8 + - - -
21D THR* 3.5 27.8 - - + +
28D TRP* 3.8 11.1 - - - -
71D MET* 3.7 20.2 - - + -
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Residues in contact with LEU 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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18C VAL* 4.9 7.4 - - + -
71C MET 2.9 10.5 + - - +
72C LYS* 3.6 7.4 - - - +
74C TYR* 1.3 79.0 - - - +
76C GLU* 1.3 61.3 + - - +
77C ILE 3.3 0.7 + - - -
78C SER* 4.1 10.5 + - - +
82C GLU* 4.1 15.7 - - + +
71D MET* 3.9 34.8 - - + -
72D LYS* 3.9 15.3 - - + +
75D LEU* 3.4 33.7 - - + -
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Residues in contact with GLU 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 LYS* 3.2 41.6 + - - +
73C GLU* 3.1 27.8 - - - +
75C LEU* 1.3 78.1 - - - +
77C ILE* 1.3 58.7 + - + +
78C SER 5.1 0.4 - - - -
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Residues in contact with ILE 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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7C GLU* 4.3 15.9 - - - +
10C ASN* 3.6 13.0 - - + +
11C LYS* 2.9 47.2 + - + +
14C ALA* 3.9 7.6 - - + -
68C VAL* 5.0 9.2 - - + -
73C GLU* 2.5 43.5 + - + +
74C TYR* 3.7 6.1 - - + +
76C GLU* 1.3 80.0 - - + +
78C SER* 1.3 68.0 + - - +
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Residues in contact with SER 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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11C LYS* 3.7 0.9 - - - +
14C ALA* 3.9 10.5 - - - +
15C ASP* 3.0 15.3 + - - -
18C VAL* 3.2 31.1 - - - +
74C TYR 2.7 22.8 + - - -
75C LEU* 4.1 9.7 + - - +
76C GLU 5.1 0.2 - - - -
77C ILE* 1.3 76.6 - - - +
79C SER* 1.3 61.5 + - - +
80C ILE* 2.9 19.9 + - - +
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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