Contacts of the strand formed by residues 65 - 70 (chain C) in PDB entry 1WZN
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 GLU 65 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C ARG* 2.9 14.4 + - + +
44C ARG* 2.8 45.7 + - - +
45C VAL 2.8 26.9 + - - +
63C GLY 3.7 2.5 + - - +
64C TYR* 1.3 69.6 - - - +
66C VAL* 1.3 61.1 + - - +
67C VAL* 5.9 0.4 - - + -
89C LYS* 5.5 13.9 - - + +
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Residues in contact with VAL 66 (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* 3.3 18.4 - - + +
47C ASP* 4.1 11.0 - - + -
56C THR* 3.6 31.9 - - + +
59C LEU* 3.9 19.5 - - + -
60C ALA* 4.0 9.2 - - + +
64C TYR* 3.5 27.8 + - + +
65C GLU* 1.3 81.0 - - - +
67C VAL* 1.3 73.4 + - - +
68C GLY 4.1 0.2 - - - -
89C LYS* 5.1 6.1 + - - -
90C ILE* 3.4 10.5 - - + +
91C GLU* 3.2 21.1 + - - +
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Residues in contact with VAL 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ARG* 3.9 19.1 - - - +
45C VAL 2.9 6.6 + - - +
46C LEU* 3.5 17.3 - - + +
47C ASP 2.9 24.1 + - - -
65C GLU* 5.6 1.1 - - + -
66C VAL* 1.3 79.7 - - - +
68C GLY* 1.3 59.9 + - - +
69C LEU* 5.7 0.4 - - + -
91C GLU* 3.2 35.2 - - + +
93C LEU* 3.8 26.0 - - + -
102C PHE* 5.0 2.5 - - + -
106C PHE* 3.8 30.3 - - + -
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Residues in contact with GLY 68 (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 ASP* 3.5 10.1 - - - -
50C CYS* 3.6 18.8 - - - -
56C THR* 4.6 2.0 - - - -
66C VAL 4.1 1.0 - - - -
67C VAL* 1.3 75.0 - - - +
69C LEU* 1.3 55.0 + - - -
90C ILE* 4.4 3.8 - - - +
91C GLU 2.8 9.9 + - - +
92C PHE* 3.3 11.7 - - - -
93C LEU* 2.7 34.8 + - - +
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Residues in contact with LEU 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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46C LEU* 4.6 7.4 - - + -
47C ASP 3.1 10.3 + - - +
48C LEU* 3.9 17.3 - - + -
49C ALA 2.6 31.5 + - - -
50C CYS* 3.0 6.5 + - - -
67C VAL* 4.0 1.5 + - + -
68C GLY* 1.3 74.1 - - - -
70C ASP* 1.3 59.0 + - - +
93C LEU* 3.3 26.9 - - + +
94C GLN 3.8 3.8 - - - +
95C GLY* 3.5 28.9 - - - +
96C ASP 4.2 4.0 - - - +
97C VAL* 4.0 13.9 - - + -
100C ILE* 3.3 34.1 - - + -
102C PHE* 4.9 6.3 - - + -
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Residues in contact with ASP 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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49C ALA 3.4 4.5 - - - -
50C CYS* 3.8 4.7 - - - -
51C GLY* 2.9 17.6 + - - -
69C LEU* 1.3 75.9 - - - +
71C LEU* 1.3 64.4 + - - +
72C HIS* 2.9 24.9 + - - +
75C MET* 3.9 2.5 - - - +
76C LEU* 3.6 24.5 - - + +
93C LEU 3.0 7.1 + - - -
94C GLN* 3.2 9.2 - - - +
95C GLY 2.9 22.2 + - - -
1003C SAH 2.7 55.1 + - - -
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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