Contacts of the strand formed by residues 95 - 100 (chain C) in PDB entry 3DBI
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 GLN 95 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A GLN* 5.7 0.2 - - - +
97A LEU* 3.7 19.9 - - + +
114A TYR* 3.3 21.8 - - - +
118A LEU* 3.6 31.9 - - + +
61C THR 5.7 1.8 + - - -
62C GLN 3.0 15.0 + - - +
63C THR* 3.4 12.4 + - - +
64C LEU* 2.6 35.2 + - - +
94C ARG* 1.3 73.4 - - - +
96C LEU* 1.3 57.2 + - - +
97C LEU* 4.0 12.1 - - + +
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Residues in contact with LEU 96 (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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97A LEU* 3.5 5.8 - - - +
98A LEU* 2.9 71.8 + - + +
64C LEU* 3.4 38.1 - - + +
66C LEU* 4.2 15.7 - - + -
82C LEU 4.7 1.8 - - - +
85C ALA* 4.1 9.4 - - + +
86C ALA* 3.8 33.7 - - + +
89C ALA* 4.1 12.1 - - + +
94C ARG 3.8 1.8 + - - -
95C GLN* 1.3 70.7 - - - +
97C LEU* 1.3 68.7 + - - +
98C LEU* 4.6 3.4 - - + -
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Residues in contact with LEU 97 (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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95A GLN* 3.8 38.6 - - + +
96A LEU 3.5 14.8 - - - +
97A LEU* 3.7 24.5 - - + -
63C THR* 3.7 24.0 - - + -
64C LEU 2.8 13.8 + - - +
65C GLY* 3.6 0.7 - - - -
66C LEU* 2.9 26.9 + - - +
95C GLN* 4.2 7.9 - - + +
96C LEU* 1.3 75.1 - - - +
98C LEU* 1.3 67.5 + - - +
114C TYR* 4.7 1.3 - - - +
115C LEU* 4.0 17.8 - - + +
118C LEU* 4.4 12.8 - - + -
120C CYS* 4.4 3.8 - - - -
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Residues in contact with LEU 98 (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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82A LEU* 4.1 18.2 - - + -
86A ALA* 5.2 1.3 - - + -
96A LEU* 2.9 53.0 + - + +
98A LEU* 3.7 39.5 - - + -
66C LEU* 3.3 36.1 - - + +
68C VAL* 3.8 21.3 - - + -
82C LEU* 4.6 0.7 - - + -
96C LEU* 4.6 2.9 - - + -
97C LEU* 1.3 82.8 - - - +
99C ALA* 1.3 61.0 + - - +
114C TYR* 4.4 10.0 - - - -
115C LEU* 4.5 2.4 - - - +
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Residues in contact with ALA 99 (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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86A ALA* 5.3 1.3 - - - -
66C LEU 3.0 7.2 + - - +
67C VAL* 3.5 2.6 - - - -
68C VAL* 2.7 37.2 + - - +
98C LEU* 1.3 75.8 - - - +
100C ASP* 1.3 58.0 + - - +
101C GLY 3.8 0.2 - - - -
111C ALA* 3.7 31.6 - - + +
114C TYR* 3.9 15.0 - - + -
115C LEU* 3.8 18.6 - - + -
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Residues in contact with ASP 100 (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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83A PHE* 5.3 3.8 - - - +
86A ALA* 3.8 26.7 + - + +
87A ARG* 3.4 37.0 + - - -
90A GLU* 4.2 19.3 - - + +
68C VAL* 4.0 13.5 - - - +
99C ALA* 1.3 71.7 - - - +
101C GLY* 1.3 60.3 + - - +
102C LYS* 3.2 46.4 + - + +
107C GLU 4.3 2.4 - - - +
111C ALA* 3.5 12.3 - - - +
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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