Contacts of the strand formed by residues 73 - 79 (chain C) in PDB entry 3RIE
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 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67C THR 3.8 3.8 - - - +
68C LYS* 3.3 37.5 - - - +
72C GLN* 1.3 72.7 - - - +
74C VAL* 1.3 58.0 + - - +
75C LEU* 4.2 0.4 + - - -
87C VAL 3.6 1.0 - - - +
88C LEU* 3.3 7.8 - - - +
89C ASP* 2.9 51.9 + - - +
90C GLY 4.9 1.5 + - - +
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Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C TYR* 4.5 5.6 - - + -
66C GLU* 3.2 6.8 - - - +
67C THR* 2.8 46.9 + - + +
69C SER* 4.5 6.5 - - - +
72C GLN 4.0 9.4 - - - +
73C ASN* 1.3 73.3 - - - +
75C LEU* 1.4 65.1 + - - +
86C LEU* 4.2 22.2 - - + -
87C VAL 3.6 2.9 - - - -
88C LEU* 3.7 18.4 - - + -
149C ASP* 4.8 2.9 - - - +
151C THR* 4.1 20.9 - - + -
152C VAL* 4.9 4.5 - - + -
155C VAL* 4.3 24.9 - - + -
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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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44C PHE* 3.9 34.1 - - + -
63C ILE* 4.1 20.4 - - + -
65C TYR 3.4 4.0 - - - +
66C GLU* 3.5 29.4 - - + +
73C ASN 5.6 0.4 - - - +
74C VAL* 1.4 74.9 - - - +
76C VAL* 1.3 80.9 + - - +
77C PHE* 4.0 16.6 - - + -
85C VAL 3.8 0.3 - - - +
86C LEU* 3.7 0.7 - - - +
87C VAL* 2.8 50.4 + - + +
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Residues in contact with VAL 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 2.9 35.2 + - + -
65C TYR* 2.7 29.1 + - + +
74C VAL* 4.6 2.0 - - + -
75C LEU* 1.3 83.5 - - - +
77C PHE* 1.3 66.0 + - - +
84C LYS* 4.8 1.1 - - + -
85C VAL 3.3 9.4 - - - +
86C LEU* 3.8 13.5 - - + -
155C VAL* 3.3 34.1 - - + -
159C TYR* 4.0 18.2 - - + -
160C PHE* 3.8 20.4 - - + -
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Residues in contact with PHE 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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44C PHE* 3.6 39.3 - + + -
58C LEU* 4.2 10.8 - - + -
60C ILE* 3.9 22.4 - - + -
62C LYS 3.5 12.6 - - - +
63C ILE* 3.9 16.6 - - + -
64C LEU* 4.0 5.4 - - - +
75C LEU* 4.0 18.6 - - + -
76C VAL* 1.3 76.5 - - - +
78C GLU* 1.3 71.3 + - - +
79C SER* 3.6 24.7 - - - -
84C LYS* 3.2 3.8 - - - +
85C VAL* 2.7 69.5 + - + +
87C VAL* 4.0 7.4 - - + -
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Residues in contact with GLU 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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61C LYS* 2.6 69.3 + - + +
62C LYS* 2.7 38.3 + - + +
64C LEU* 4.1 7.5 - - + +
77C PHE* 1.3 78.9 - - - +
79C SER* 1.3 61.9 + - - +
83C GLY* 3.9 13.6 - - - -
84C LYS* 4.1 15.9 - - + +
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Residues in contact with SER 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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53B GLY 5.8 0.2 - - - -
58C LEU* 4.4 13.5 - - - -
59C LYS 3.1 13.7 - - - -
61C LYS* 4.1 4.5 - - - +
77C PHE* 3.6 19.9 + - - -
78C GLU* 1.3 86.6 - - - +
80C THR* 1.3 63.7 + - - +
81C THR 3.5 1.1 + - - -
82C TYR* 2.9 26.1 + - - +
83C GLY* 2.8 30.0 + - - +
85C VAL* 3.9 5.8 - - - -
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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