Contacts of the strand formed by residues 68 - 74 (chain C) in PDB entry 8ATC
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 ALA 68 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C LEU* 3.5 26.7 + - + +
42C LYS* 3.8 4.5 - - + +
44C ILE* 4.3 15.7 - - + -
63C MET* 2.7 39.2 + - + +
64C HIS* 3.7 18.4 - - - -
66C LEU 3.5 1.6 + - - -
67C GLY* 1.3 76.7 - - - +
69C SER* 1.3 63.9 + - - +
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Residues in contact with SER 69 (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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42C LYS 3.1 16.3 + - - -
43C VAL* 3.9 17.3 - - - -
44C ILE* 2.8 28.8 + - - +
64C HIS* 4.8 2.9 - - - -
67C GLY 5.1 1.0 + - - -
68C ALA* 1.3 73.5 + - - +
70C VAL* 1.3 69.6 + - - +
71C VAL* 6.2 0.2 - - - -
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Residues in contact with VAL 70 (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 ILE 3.3 5.4 - - - +
46C SER* 4.2 9.2 - - - -
60C GLN* 3.9 29.2 - - - +
63C MET* 3.4 35.0 - - + -
64C HIS* 3.5 33.0 + - + +
69C SER* 1.3 83.5 - - - +
71C VAL* 1.3 73.7 + - - +
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Residues in contact with VAL 71 (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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43C VAL* 3.8 15.5 - - + -
44C ILE 2.9 7.0 + - - +
45C ALA* 3.1 11.9 - - + -
46C SER* 2.7 23.0 + - - -
69C SER* 6.2 0.7 - - - -
70C VAL* 1.3 82.0 - - - +
72C GLY* 1.3 60.5 + - - +
98C TYR* 6.1 3.4 - - + -
99C VAL* 4.0 26.0 - - + -
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Residues in contact with GLY 72 (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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45C ALA* 4.9 0.7 - - - -
46C SER* 3.1 15.3 - - - -
47C CYS* 4.9 3.8 - - - -
60C GLN* 6.0 0.4 - - - -
71C VAL* 1.3 81.5 - - - +
73C PHE* 1.3 72.8 + - - +
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Residues in contact with PHE 73 (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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46C SER 2.9 9.5 + - - +
47C CYS* 3.7 27.8 - - + -
48C PHE* 2.9 36.6 + - - +
49C PHE* 3.4 48.0 - + - -
56C ARG* 4.6 2.0 - - - -
72C GLY* 1.3 79.2 - - - +
74C SER* 1.3 61.6 + - - +
75C ASP 3.7 14.4 - - - +
76C SER* 4.9 0.2 - - - -
79C THR* 3.6 29.4 - - + -
91C THR* 4.8 4.0 - - + -
95C ILE* 4.1 16.6 - - + -
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Residues in contact with SER 74 (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* 3.4 21.5 - - - +
50C GLU 4.6 8.7 + - - +
51C ALA* 5.5 2.1 - - - -
56C ARG* 3.5 37.6 + - - -
73C PHE* 1.3 73.5 - - - +
75C ASP* 1.3 61.1 + - - +
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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