Contacts of the strand formed by residues 77 - 83 (chain C) in PDB entry 2Q41
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 ASP 77 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A GLN* 5.5 1.6 + - - -
77A ASP* 5.2 8.0 - - - +
71C GLY 4.1 10.7 - - - +
72C LYS* 4.2 19.8 - - - +
76C GLN* 1.3 73.5 - - - +
78C VAL* 1.3 72.2 + - - +
79C ILE* 4.3 14.1 - - - +
91C VAL* 4.3 1.2 - - - +
92C LEU* 3.2 9.7 - - - +
93C ASP* 2.8 41.9 + - - +
94C GLY* 3.4 20.9 + - - -
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Residues in contact with VAL 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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69C PHE* 4.1 24.0 - - + -
70C GLN* 3.7 0.3 - - - -
71C GLY 3.2 30.6 + - - +
73C SER* 4.5 2.9 - - - +
76C GLN* 3.7 16.2 - - + +
77C ASP* 1.3 82.0 - - - +
79C ILE* 1.3 81.7 + - - +
80C VAL* 4.8 1.8 - - + -
90C LEU* 4.6 9.9 - - + -
91C VAL 3.4 7.2 - - - +
92C LEU* 4.0 15.9 - - + -
155C MSE 3.8 21.3 - - + -
156C VAL* 4.8 13.0 - - + -
159C VAL* 5.2 6.5 - - + -
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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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70A GLN* 3.2 38.4 - - - +
79A ILE* 5.9 0.7 - - + -
48C PHE* 4.3 9.4 - - + -
69C PHE 3.2 5.8 - - - -
70C GLN* 3.5 28.7 - - + +
77C ASP* 4.3 15.5 - - - +
78C VAL* 1.3 88.0 - - - +
80C VAL* 1.3 71.5 + - - +
81C PHE* 3.5 29.8 - - + -
90C LEU* 3.3 6.6 - - - +
91C VAL* 2.9 42.5 + - + -
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Residues in contact with VAL 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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67C VAL* 4.7 0.2 - - - +
68C LEU* 3.0 20.7 + - + +
69C PHE* 2.6 39.4 + - + +
78C VAL* 4.8 1.6 - - + -
79C ILE* 1.3 81.1 - - - +
81C PHE* 1.3 60.3 + - - +
88C LYS* 5.0 0.4 - - + -
89C VAL 3.4 3.8 - - - +
90C LEU* 3.4 19.5 - - + -
159C VAL* 3.5 28.3 - - + -
163C PHE* 3.9 19.5 - - + -
164C PHE* 3.9 28.9 - - + -
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Residues in contact with PHE 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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48C PHE* 3.9 37.5 - + + -
62C LEU* 4.5 8.5 - - + -
64C VAL* 3.6 28.3 - - + -
66C LYS 3.5 11.0 - - - +
67C VAL* 4.2 7.9 - - - -
68C LEU* 4.1 6.1 - - - -
70C GLN* 4.7 5.6 - - - +
79C ILE* 3.5 21.1 - - + -
80C VAL* 1.3 75.1 - - - +
82C GLN* 1.3 70.5 + - - +
83C SER* 3.7 22.0 - - - -
88C LYS* 3.4 3.5 - - - +
89C VAL* 2.9 64.6 + - + +
91C VAL* 4.3 6.1 - - + -
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Residues in contact with GLN 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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64C VAL 3.6 0.9 - - - -
65C GLU* 2.5 50.2 + - + +
66C LYS* 2.8 40.7 + - + +
68C LEU* 4.0 7.1 - - + +
81C PHE* 1.3 72.7 - - - +
83C SER* 1.3 56.0 + - - +
87C GLY* 3.0 17.3 + - - +
88C LYS* 3.0 48.1 + - - +
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Residues in contact with SER 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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62C LEU* 4.0 15.9 - - - -
63C LYS 4.1 1.6 - - - -
65C GLU* 3.8 5.6 - - - +
81C PHE* 3.4 26.3 + - - -
82C GLN* 1.3 84.3 - - - +
84C ALA* 1.3 63.0 + - - +
85C THR 3.7 0.6 + - - -
86C TYR* 3.2 13.1 + - - +
87C GLY 3.0 37.4 + - - +
88C LYS 4.0 0.5 + - - -
89C VAL* 3.9 11.0 - - - +
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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