Contacts of the helix formed by residues 78 - 86 (chain C) in PDB entry 4E45
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 ASN 78 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C ARG* 3.5 33.1 + - - +
76C THR* 4.3 2.7 - - + +
77C ILE* 1.3 75.2 - - - +
79C THR* 1.3 59.0 + - - +
80C GLU* 3.0 25.3 + - - +
81C ASP* 2.8 36.5 + - - +
82C VAL* 3.4 12.0 + - - +
31D SER* 4.1 8.7 - - - +
34D ALA* 3.8 9.6 - - - -
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Residues in contact with THR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ASN* 1.3 76.4 - - - +
80C GLU* 1.3 67.0 + - - +
82C VAL* 3.3 9.8 + - - +
83C LYS* 3.0 33.0 + - - +
100C SER* 3.5 25.4 + - - +
103C ILE* 6.1 0.4 - - + -
31D SER* 4.6 1.1 + - - +
33D ASP* 3.7 32.8 - - + +
34D ALA* 3.7 11.0 - - - +
37D LEU* 3.8 10.4 - - + +
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Residues in contact with GLU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A HIS* 3.8 18.1 + - + +
74C ARG* 5.1 0.9 - - - +
78C ASN* 3.0 16.2 + - - +
79C THR* 1.3 82.5 + - - +
81C ASP* 1.3 64.2 + - - +
83C LYS* 3.3 37.5 + - - +
84C LEU* 3.1 23.0 + - - +
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Residues in contact with ASP 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A HIS* 2.8 22.2 + - - -
65C LEU* 3.5 22.9 - - + +
68C PHE* 3.6 12.4 - - + -
69C ALA* 3.4 16.6 + - - +
74C ARG* 2.7 45.1 + - - -
77C ILE* 3.3 8.9 - - + -
78C ASN* 2.8 23.4 + - - +
80C GLU* 1.3 75.9 - - - +
82C VAL* 1.3 61.9 - - - +
84C LEU* 3.3 5.8 + - - +
85C LEU 3.1 16.1 + - - -
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Residues in contact with VAL 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LEU* 3.8 18.4 - - + -
77C ILE* 4.8 0.2 - - + -
78C ASN 3.7 13.0 - - - +
79C THR* 3.3 8.4 + - - +
80C GLU 3.2 0.4 - - - -
81C ASP* 1.3 74.1 - - - +
83C LYS* 1.3 59.5 + - - +
85C LEU* 2.8 28.4 + - + +
86C ALA* 3.1 6.5 + - + +
96C ILE* 4.1 11.0 - - + -
34D ALA* 4.1 25.1 - - + +
37D LEU* 4.0 26.0 - - + -
38D MET* 3.9 26.5 - - + -
41D LEU* 4.8 7.0 - - + -
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Residues in contact with LYS 83 (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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79C THR* 3.0 22.3 + - - +
80C GLU* 3.3 36.8 + - - +
82C VAL* 1.3 74.1 - - - +
84C LEU* 1.3 58.3 + - - +
86C ALA* 2.9 19.3 + - - +
87C ARG* 3.2 9.4 + - - +
93C LEU* 3.4 22.3 - - + +
96C ILE* 4.3 13.2 - - + -
97C THR* 3.9 43.5 - - - +
100C SER* 4.2 17.4 + - - -
37D LEU* 5.4 0.7 - - + -
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Residues in contact with LEU 84 (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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67A MET* 4.2 31.6 - - + +
68A PHE* 4.2 12.1 - - + -
71A HIS* 3.7 33.9 - - + +
68C PHE* 3.6 36.8 - - + -
80C GLU 3.1 14.1 + - - +
81C ASP 3.5 8.7 - - - +
82C VAL 3.2 0.2 - - - -
83C LYS* 1.3 76.7 - - - +
85C LEU* 1.3 60.4 + - - +
87C ARG* 3.0 56.4 + - - -
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Residues in contact with LEU 85 (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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61C PHE* 3.9 27.1 - - + +
64C ASP* 3.6 35.7 - - + +
65C LEU* 3.7 21.8 - - + -
68C PHE* 4.0 8.3 - - + -
81C ASP 3.1 6.0 + - - +
82C VAL 2.8 14.9 + - - +
84C LEU* 1.3 75.0 - - - +
86C ALA* 1.3 54.8 + - - +
87C ARG* 3.4 12.0 + - - +
88C ARG* 4.9 4.9 + - - +
92C LEU* 5.5 1.0 - - - +
38D MET* 3.7 35.4 - - + -
41D LEU* 3.9 16.6 - - + -
81D PHE* 4.0 16.1 - - - +
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Residues in contact with ALA 86 (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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82C VAL 3.1 7.6 + - - +
83C LYS 2.9 11.6 + - - +
85C LEU* 1.3 75.5 - - + +
87C ARG* 1.3 64.5 + - - +
88C ARG 3.1 3.7 + - - -
89C SER 3.5 9.9 + - - +
92C LEU* 3.9 30.2 - - + +
93C LEU* 3.5 26.5 + - + +
96C ILE* 4.3 18.2 - - + -
41D LEU* 5.3 4.5 - - + -
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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