Contacts of the helix formed by residues 80 - 90 (chain C) in PDB entry 4WMJ
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 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C LYS* 4.3 9.0 - - - +
77C LYS 3.0 17.9 + - - +
78C SER 3.8 11.7 + - - -
79C ARG* 1.3 78.7 - - - +
81C VAL* 1.3 65.8 + - - +
82C GLU 3.2 2.7 - - - +
83C LYS* 3.3 34.7 + - + +
84C ALA* 3.0 22.7 + - - +
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Residues in contact with VAL 81 (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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76C ALA* 3.2 37.7 + - + +
77C LYS* 5.3 0.2 - - - +
79C ARG* 4.3 10.3 - - + +
80C ASN* 1.3 76.2 - - - +
82C GLU* 1.3 65.0 + - + +
84C ALA* 3.4 6.9 + - - +
85C ARG* 2.9 30.6 + - + +
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Residues in contact with GLU 82 (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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76C ALA 5.0 0.4 + - - -
77C LYS* 4.8 16.5 - - - +
80C ASN 3.2 1.0 - - - -
81C VAL* 1.3 83.3 - - + +
83C LYS* 1.3 65.0 + - + +
85C ARG* 3.2 33.9 + - - +
86C ASP* 3.0 30.8 + - - +
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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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80C ASN* 3.3 34.9 + - + +
81C VAL 3.4 0.2 - - - -
82C GLU* 1.3 80.2 - - + +
84C ALA* 1.3 63.8 + - - +
86C ASP* 3.3 12.1 + - - +
87C ALA* 3.0 23.7 + - - +
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Residues in contact with ALA 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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4C LYS* 5.3 8.1 - - - +
79C ARG 5.3 0.7 - - - +
80C ASN* 3.0 18.7 + - - +
81C VAL* 3.5 8.7 - - - +
83C LYS* 1.3 77.3 - - - +
85C ARG* 1.3 62.4 + - - +
87C ALA* 3.3 7.6 + - - +
88C MET* 3.1 20.8 + - - +
94C ILE* 5.0 4.9 - - - +
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Residues in contact with ARG 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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81C VAL* 2.9 18.3 + - + +
82C GLU* 3.4 41.7 + - - +
84C ALA* 1.3 74.3 - - - +
86C ASP* 1.3 87.2 + - - +
88C MET* 3.1 13.1 + - + +
89C PHE* 2.9 53.2 + - + -
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Residues in contact with ASP 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 GLU* 3.0 18.6 + - - +
83C LYS* 3.6 13.3 - - - +
84C ALA 3.2 0.2 - - - -
85C ARG* 1.3 109.2 + - - +
87C ALA* 1.3 57.0 + - - +
89C PHE* 3.3 6.1 + - - +
90C ALA* 2.9 32.0 + - - +
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Residues in contact with ALA 87 (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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83C LYS 3.0 13.2 + - - +
84C ALA* 3.5 10.5 - - - +
86C ASP* 1.3 73.6 - - - +
88C MET* 1.4 64.9 + - - +
90C ALA 3.3 4.2 + - - -
92C GLU* 3.1 59.0 + - - +
94C ILE* 3.9 13.9 - - + -
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Residues in contact with MET 88 (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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84C ALA 3.1 10.8 + - - +
85C ARG* 3.1 13.0 + - + +
87C ALA* 1.4 74.8 - - - +
89C PHE* 1.3 89.1 + - + +
91C GLY* 3.1 12.1 + - - -
92C GLU 5.0 1.2 - - - +
94C ILE* 3.7 28.8 - - + +
102C VAL* 3.3 35.4 - - - +
103C LEU* 3.5 12.6 - - - +
104C HIS* 4.3 14.8 - - - +
105C VAL* 4.6 13.0 - - + -
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Residues in contact with PHE 89 (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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85C ARG* 2.9 49.8 + - + +
86C ASP* 3.9 5.8 - - - +
88C MET* 1.3 97.1 - - + +
90C ALA* 1.3 59.4 + - - +
91C GLY 3.5 0.5 + - - -
103C LEU* 4.4 1.4 - - - +
105C VAL* 3.8 33.9 - - + -
113C ARG* 3.0 48.1 + - - +
115C ILE* 4.0 7.6 - - - +
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Residues in contact with ALA 90 (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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86C ASP 2.9 17.7 + - - +
87C ALA 3.9 4.5 - - - +
88C MET 3.2 0.4 - - - -
89C PHE* 1.3 75.5 - - - +
91C GLY* 1.3 60.3 + - - +
92C GLU* 3.5 17.0 + - + +
113C ARG* 5.0 3.8 - - - +
115C ILE* 4.4 6.9 - - - +
116C MET* 4.2 11.6 + - - +
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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