Contacts of the strand formed by residues 84 - 90 (chain C) in PDB entry 3Q2P
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 ARG 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C PHE* 3.3 30.5 + - - -
14C ASN* 4.6 8.9 - - - +
15C LEU* 3.2 43.5 - - + +
18C PHE* 3.6 42.9 - - + +
75C ILE* 4.6 2.2 - - + -
76C SER 3.3 11.2 - - - +
77C GLU* 3.0 32.3 + - + +
82C ARG 3.9 5.5 + - - +
83C GLY* 1.3 79.2 - - - +
85C LYS* 1.3 66.3 + - - +
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Residues in contact with LYS 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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18C PHE* 4.1 6.5 - - - -
22C GLU* 5.7 4.0 - - - +
75C ILE* 3.3 4.9 - - - +
76C SER* 3.2 41.9 + - - +
84C ARG* 1.3 78.7 - - - +
86C LEU* 1.3 77.3 + - - +
87C LEU* 3.3 9.4 + - + -
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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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18C PHE* 4.1 7.0 - - + -
19C ALA* 3.6 40.8 - - + +
22C GLU* 3.7 20.5 + - + +
23C GLU* 3.6 34.3 - - + +
26C ILE* 4.2 15.3 - - + +
73C ALA* 4.6 0.7 - - + -
74C ASP 4.0 4.7 - - - +
75C ILE* 4.3 6.5 - - + -
85C LYS* 1.3 84.9 - - + +
87C LEU* 1.3 63.4 + - - +
88C ARG* 3.3 30.3 - - - +
89C PHE* 4.3 7.2 - - + -
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Residues in contact with LEU 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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68B ASP* 4.7 14.3 - - - +
59C GLU* 3.8 25.8 - - + -
74C ASP* 2.7 42.4 + - + +
75C ILE 4.1 0.2 - - - -
76C SER* 3.6 35.0 - - - +
85C LYS* 3.3 8.9 + - + +
86C LEU* 1.3 75.9 - - - +
88C ARG* 1.3 78.8 + - + +
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Residues in contact with ARG 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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35B ASN* 5.6 4.0 - - - +
68B ASP* 3.6 33.9 + - - -
72C ARG* 4.4 6.2 - - - +
73C ALA* 3.4 1.2 - - - -
74C ASP* 2.8 44.5 + - + +
86C LEU* 3.3 12.4 - - - +
87C LEU* 1.3 98.0 + - - +
89C PHE* 1.3 63.4 + - - +
90C ASN* 4.2 12.3 - - - +
94D PRO* 3.3 44.1 - - - +
95D PRO* 4.4 18.2 + - - +
96D PRO 6.2 0.6 - - - -
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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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19C ALA* 4.4 4.5 - - + -
20C VAL* 4.4 19.1 - - + -
23C GLU* 3.3 39.0 - - + +
28C GLN* 4.6 5.5 + - - +
29C TYR* 3.2 27.0 + + - -
32C LEU* 3.7 25.6 - - + -
64C VAL* 4.2 9.9 - - + -
66C ALA* 5.1 0.4 - - + -
71C PHE* 3.3 44.9 - + + -
72C ARG 3.7 2.2 - - - -
73C ALA* 3.8 24.2 - - + -
86C LEU* 4.3 11.7 - - + -
88C ARG* 1.3 77.2 - - - +
90C ASN* 1.3 66.3 + - - +
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Residues in contact with ASN 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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28C GLN* 6.1 1.0 - - - +
29C TYR* 3.5 6.8 + - - -
71C PHE* 3.2 9.9 - - - +
72C ARG* 2.9 51.0 + - + +
88C ARG* 4.2 14.6 - - - +
89C PHE* 1.3 83.3 + - - +
91C GLY* 1.3 58.9 + - - +
93C VAL* 4.5 4.8 - - + +
94D PRO* 4.0 27.8 - - - +
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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