Contacts of the strand formed by residues 43 - 48 (chain C) in PDB entry 2UZ3
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 TYR 43 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 3.4 51.0 + - + +
34C HIS 5.0 0.2 + - - -
36C LEU* 3.7 19.1 - - + -
37C GLU* 2.7 35.1 + - + -
41C VAL 3.9 8.3 - - - -
42C LYS* 1.3 77.6 - - - +
44C LEU* 1.3 67.7 + - - +
45C VAL* 4.0 14.1 - - + -
67C PRO* 6.0 2.9 - - + +
90C THR* 4.0 5.6 + - - -
92C VAL* 3.2 28.9 - - + +
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Residues in contact with LEU 44 (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 TYR* 1.3 77.7 - - - +
45C VAL* 1.3 68.6 + - - +
46C PHE* 3.8 24.9 - - + -
68C SER* 6.3 0.2 - - - -
69C VAL* 3.9 24.0 - - + +
80C TYR* 3.7 30.1 - - + +
81C ILE* 4.9 1.3 - - + -
86C PHE* 4.1 20.9 - - + -
87C ASN 6.1 0.2 - - - +
90C THR* 4.0 13.2 - - + +
92C VAL 3.0 6.6 + - - +
93C ILE* 3.3 11.2 - - + +
94C GLY 2.8 23.8 + - - +
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Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 5.0 2.7 - - + -
33C LEU* 3.5 31.0 - - + -
43C TYR* 4.0 13.4 - - + -
44C LEU* 1.3 81.6 - - - +
46C PHE* 1.3 73.5 + - - +
47C LYS* 5.2 0.4 - - + -
66C LEU* 4.0 21.5 - - + -
67C PRO 3.7 16.8 - - - +
68C SER* 3.3 9.8 - - - +
69C VAL* 2.8 29.6 + - - +
94C GLY* 3.2 16.2 - - - +
95C ILE 4.7 0.4 - - - +
96C ASP* 4.7 6.7 - - + +
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Residues in contact with PHE 46 (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 LEU* 3.8 31.0 - - + -
45C VAL* 1.3 77.4 - - - +
47C LYS* 1.3 65.9 + - - +
69C VAL* 3.4 35.7 - - + -
71C VAL* 4.0 9.0 - - + -
77C ILE* 3.6 66.0 - - + -
80C TYR* 4.0 15.0 - + + -
81C ILE* 4.6 5.4 - - + -
93C ILE* 3.7 27.4 - - + -
94C GLY 2.7 11.4 + - - +
95C ILE* 3.5 8.9 - - + +
96C ASP 3.0 26.5 + - - +
101C PHE* 5.4 0.9 - - + -
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Residues in contact with LYS 47 (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 VAL* 5.2 0.4 - - + -
46C PHE* 1.3 78.1 - - - +
48C PRO* 1.3 72.7 - - + +
65C SER* 5.4 5.1 - - - +
66C LEU* 3.8 32.5 + - + +
68C SER* 3.3 28.5 - - - +
69C VAL 3.0 5.6 + - - +
70C GLU* 3.4 15.0 - - - +
71C VAL* 2.9 27.1 + - - +
96C ASP* 4.1 16.7 + - + -
97C GLU* 3.6 25.3 + - - +
101C PHE* 4.3 4.7 - - - -
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Residues in contact with PRO 48 (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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47C LYS* 1.3 92.3 - - + +
49C LYS* 1.3 64.8 + - - +
70C GLU* 4.4 5.7 - - - +
71C VAL 3.4 7.6 - - - +
72C GLU 6.1 0.4 - - - +
96C ASP 3.2 19.7 - - - +
97C GLU* 3.4 29.5 - - + +
100C PHE* 3.9 26.2 - - + +
101C PHE* 3.8 29.3 - - + -
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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