Contacts of the strand formed by residues 81 - 89 (chain C) in PDB entry 4N3E
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 TYR 81 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C PHE* 3.3 7.8 - - - -
74C GLU* 3.2 48.1 + - + -
75C ILE* 3.9 1.4 - - - -
76C ASP* 3.1 47.1 + - + +
79C ASN* 4.4 6.1 - - + +
80C PHE* 1.3 77.6 - - - +
82C CYS* 1.3 71.4 + - - +
83C LYS* 4.0 0.2 - - - +
102C GLU* 2.4 39.6 + - + +
103C VAL 3.4 11.0 - - - -
104C LYS* 4.0 22.4 - - + -
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Residues in contact with CYS 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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20C PHE* 4.0 4.5 - - + -
24C VAL* 3.2 36.1 - - + -
72C PHE* 4.3 10.1 - - - -
74C GLU 3.7 17.3 - - - -
75C ILE* 4.3 11.9 - - - -
81C TYR* 1.3 82.8 - - - +
83C LYS* 1.3 68.8 + - - +
84C TYR* 4.2 12.6 - - + -
101C TYR 4.4 0.4 - - - -
102C GLU* 3.2 9.9 - - - +
103C VAL* 2.9 42.3 + - + +
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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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72C PHE* 3.8 0.3 - - - -
73C ASP* 2.9 37.2 + - + +
74C GLU* 3.3 47.4 + - + +
81C TYR* 4.0 2.0 - - - +
82C CYS* 1.3 74.8 - - - +
84C TYR* 1.3 60.2 + - - +
100C VAL* 3.2 36.3 - - + +
101C TYR 3.3 7.4 - - - +
102C GLU* 3.7 29.8 - - + +
115D LYS* 5.7 5.3 - - - +
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Residues in contact with TYR 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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23C LEU 4.5 1.1 + - - -
24C VAL* 4.9 12.3 - - + -
27C ARG* 3.6 31.9 + - - -
70C HIS* 3.8 37.9 - + + -
71C LYS 3.2 17.0 - - - +
72C PHE* 4.3 18.4 - + + -
73C ASP* 4.4 1.6 - - - +
82C CYS* 4.2 15.5 - - + -
83C LYS* 1.3 75.8 - - - +
85C THR* 1.3 60.0 + - - +
100C VAL* 3.5 4.0 - - - +
101C TYR* 2.8 78.1 + + + +
103C VAL* 4.2 16.4 - - + -
202C 2AN 3.8 9.9 - - - -
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Residues in contact with THR 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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70C HIS* 3.0 8.0 - - - -
71C LYS* 2.6 42.8 + - + -
73C ASP* 3.4 23.2 + - - -
84C TYR* 1.3 72.2 - - - +
86C LEU* 1.3 71.5 + - - +
87C PHE* 3.8 13.1 + - + -
98C LYS* 3.8 28.5 + - + +
99C VAL 3.3 4.9 - - - +
100C VAL* 3.3 21.5 - - - +
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Residues in contact with LEU 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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68C MET* 3.7 19.1 - - + -
69C LEU 3.5 15.3 - - - +
70C HIS* 3.3 38.4 - - + +
85C THR* 1.3 69.2 - - - +
87C PHE* 1.3 58.4 + - - +
88C GLU 4.2 3.4 - - - +
91C VAL* 3.6 20.0 - - + -
92C LEU* 3.1 31.4 - - + +
98C LYS* 3.1 8.8 - - - +
99C VAL* 2.7 43.2 + - + +
101C TYR* 4.3 4.0 - - + +
201C 2AN 4.0 19.5 - - + -
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Residues in contact with PHE 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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54C VAL* 3.8 13.2 - - + -
69C LEU* 3.1 42.6 + - + -
70C HIS 3.8 6.3 - - - -
71C LYS* 3.3 59.2 - - + -
85C THR* 3.9 14.8 - - + -
86C LEU* 1.3 73.1 - - - +
88C GLU* 1.3 72.3 + - + +
92C LEU* 3.6 13.3 - - - +
97C GLU 3.8 8.4 - - - +
98C LYS* 4.3 7.9 - - + -
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Residues in contact with GLU 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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67C TYR* 3.0 25.8 + - - +
68C MET* 3.4 2.6 - - - -
69C LEU* 2.8 63.0 + - + +
86C LEU* 4.2 2.8 - - - +
87C PHE* 1.3 90.7 - - + +
89C GLY* 1.3 59.6 + - - +
92C LEU* 4.1 5.4 - - - +
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Residues in contact with GLY 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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67C TYR* 2.8 31.3 - - - -
68C MET* 4.4 0.9 - - - -
88C GLU* 1.3 78.0 - - - +
90C ASP* 1.3 64.6 + - - +
91C VAL* 3.5 4.5 - - - -
92C LEU* 3.9 15.3 + - - +
93C ARG 5.2 1.0 - - - +
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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