Contacts of the helix formed by residues 74 - 81 (chain C) in PDB entry 3PRJ
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 74 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C VAL* 3.8 9.6 - - - +
72C SER* 2.9 14.8 + - - +
73C THR* 1.3 75.5 + - - +
75C ILE* 1.3 62.7 + - - +
76C ASP* 3.5 6.8 + - - +
77C ASP* 3.3 43.9 + - - +
78C ALA* 3.6 10.9 + - - +
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Residues in contact with ILE 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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10C ILE* 4.8 9.6 - - + -
35C VAL* 3.8 31.9 - - + -
36C ASP 3.5 28.7 - - - +
37C VAL* 3.8 14.1 - - + -
73C THR 3.2 7.5 + - - +
74C ASN* 1.3 72.5 - - - +
76C ASP* 1.3 65.4 + - - +
78C ALA* 3.2 5.2 + - - +
79C ILE* 3.1 44.9 + - + +
115C ARG* 3.5 41.5 - - - +
500C NAI 4.1 7.0 - - + +
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Residues in contact with ASP 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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74C ASN* 3.3 5.7 - - - +
75C ILE* 1.3 78.6 - - - +
77C ASP* 1.3 60.6 + - - +
79C ILE* 3.5 4.2 + - - +
80C LYS* 3.1 25.7 + - - +
115C ARG* 3.1 32.8 + - - +
119C ASN* 2.6 43.4 + - - +
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Residues in contact with ASP 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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74C ASN* 3.3 31.8 + - - +
76C ASP* 1.3 78.3 - - - +
78C ALA* 1.3 65.7 + - - +
80C LYS* 3.2 31.3 + - - +
81C GLU* 3.2 30.8 + - - +
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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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8C CYS* 3.5 24.6 - - + +
33C THR* 4.4 17.5 - - + -
35C VAL* 3.8 20.6 - - + -
74C ASN 3.6 5.9 + - - +
75C ILE 3.2 8.8 + - - +
77C ASP* 1.3 78.1 - - - +
79C ILE* 1.3 61.2 + - - +
81C GLU* 3.6 7.3 + - - +
82C ALA* 3.1 25.8 + - - +
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Residues in contact with ILE 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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8C CYS* 4.4 11.2 - - - -
10C ILE* 4.0 22.7 - - + -
75C ILE* 3.1 37.3 + - + +
76C ASP* 3.7 6.5 - - - +
78C ALA* 1.3 75.9 - - - +
80C LYS* 1.3 63.5 + - - +
81C GLU 3.4 0.2 + - - -
82C ALA* 3.5 6.5 + - - +
85C VAL* 4.4 8.9 - - + +
115C ARG* 4.0 24.2 - - + +
116C ILE* 4.0 26.7 - - + +
119C ASN* 4.2 7.0 - - + -
120C SER* 3.5 19.3 - - - +
124C LYS* 3.1 19.2 + - - +
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Residues in contact with LYS 80 (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 ASP* 3.1 16.9 + - - +
77C ASP* 3.2 29.3 + - - +
79C ILE* 1.3 78.2 - - - +
81C GLU* 1.3 55.4 + - + +
119C ASN* 3.3 30.1 - - - +
120C SER* 5.5 0.3 - - - -
121C ASN 5.5 1.5 + - - +
124C LYS* 2.7 20.8 + - - -
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Residues in contact with GLU 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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6C LYS* 3.3 45.4 + - + +
31C ARG* 4.1 22.7 + - - -
33C THR* 5.6 1.2 + - - -
77C ASP* 3.2 22.2 + - - +
78C ALA* 4.2 6.7 - - - +
80C LYS* 1.3 76.6 - - + +
82C ALA* 1.3 60.1 + - - +
83C ASP* 5.1 1.4 - - - +
124C LYS* 4.0 0.9 - - - -
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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