Contacts of the strand formed by residues 132 - 138 (chain C) in PDB entry 4A8X
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 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A HIS* 5.5 0.5 - - - -
31C ARG* 3.8 44.3 + - + +
33C PHE* 4.0 21.5 - + + -
46C PHE* 3.5 33.2 - + + -
49C GLY* 4.6 8.8 + - - -
50C ASN 4.6 1.4 + - - -
51C VAL* 3.9 16.3 - - + +
91C ILE* 3.5 8.0 - - - +
92C VAL* 2.8 53.9 + - + +
101C TYR* 3.6 33.7 + + - -
127C PHE* 4.7 2.1 - - - -
130C GLY 3.9 14.4 - - - -
131C ASP* 1.3 74.5 - - - +
133C LEU* 1.3 60.8 + - - +
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Residues in contact with LEU 133 (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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30C LEU* 3.8 32.5 - - + +
31C ARG 3.2 6.7 + - - +
32C VAL* 3.4 12.0 - - + +
33C PHE* 2.9 29.2 + - - +
66C LEU* 5.9 0.2 - - + -
69C LEU* 3.9 22.9 - - + -
89C PHE* 4.1 26.9 - - + -
90C ALA 3.5 20.2 - - - +
91C ILE* 4.2 14.6 - - + -
106C ILE* 4.7 7.9 - - + -
122C LEU* 4.7 10.5 - - + -
127C PHE* 5.4 2.2 - - + -
131C ASP 4.0 0.4 + - - -
132C TYR* 1.3 75.6 - - - +
134C ASP* 1.3 60.7 + - - +
135C ILE* 4.2 9.4 - - + -
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Residues in contact with ASP 134 (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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33C PHE* 3.4 11.2 - - + +
35C THR* 4.9 2.0 - - - +
40C HIS* 2.9 32.0 + - + +
41C HIS* 2.5 57.2 + - - +
46C PHE* 4.2 2.9 - - + -
90C ALA* 2.8 38.0 + - + +
92C VAL* 3.8 23.6 - - + -
103C VAL* 5.4 0.7 - - + -
132C TYR 4.2 0.4 - - - -
133C LEU* 1.3 74.0 - - - +
135C ILE* 1.3 64.2 + - - +
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Residues in contact with ILE 135 (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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32C VAL* 3.6 28.9 - - + -
33C PHE 2.8 11.8 + - - +
34C THR* 3.2 10.2 - - + -
35C THR 3.0 23.6 + - - +
40C HIS* 4.5 0.7 - - - -
69C LEU* 5.7 1.1 - - + -
73C VAL* 3.9 20.2 - - + -
87C PHE* 4.2 23.6 - - + -
88C ASN 3.3 10.5 - - - +
89C PHE* 3.5 32.1 - - + -
133C LEU* 4.4 8.7 - - + -
134C ASP* 1.3 78.9 - - - +
136C ALA* 1.3 62.1 + - - +
137C ILE* 3.5 19.5 + - + +
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Residues in contact with ALA 136 (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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35C THR* 3.2 17.7 - - - +
38C GLY* 3.6 29.0 - - - +
39C ARG 3.8 9.4 - - - -
40C HIS* 3.7 21.0 + - + +
86C HIS* 3.6 4.0 + - - +
88C ASN* 2.9 40.4 + - + +
135C ILE* 1.3 70.0 - - - +
137C ILE* 1.3 60.9 + - - +
138C THR* 4.0 0.7 + - - -
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Residues in contact with ILE 137 (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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34C THR* 4.2 19.3 - - + -
35C THR* 2.8 19.9 + - - +
36C ASN* 2.9 44.1 - - + +
37C ASN 3.3 1.7 + - - -
38C GLY 3.4 1.3 + - - -
73C VAL* 4.3 13.2 - - + -
77C TYR* 5.1 6.3 - - + -
80C ALA* 4.7 9.0 - - + -
85C THR* 3.5 28.7 - - + -
86C HIS 3.2 5.2 - - - +
87C PHE* 3.8 28.7 - - + -
135C ILE* 3.7 10.1 - - + +
136C ALA* 1.3 76.3 - - - +
138C THR* 1.3 63.0 + - - +
139C PRO* 3.8 0.4 - - - +
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Residues in contact with THR 138 (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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36C ASN 4.7 0.2 - - - -
37C ASN 5.3 1.1 - - - -
38C GLY* 3.4 23.7 + - - +
84C GLY 4.3 0.9 - - - +
85C THR* 3.5 4.4 - - - -
86C HIS* 2.8 51.3 + - + +
136C ALA 4.8 0.7 + - - -
137C ILE* 1.3 70.1 - - - +
139C PRO* 1.3 81.6 - - + +
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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