Contacts of the strand formed by residues 63 - 68 (chain C) in PDB entry 3IXK
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 63 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C ASN 3.9 0.2 - - - +
54C LEU* 3.4 9.2 - - - +
55C ARG* 2.9 65.5 + - + +
56C GLY* 3.6 16.7 + - - -
61C GLY 4.2 1.6 - - - -
62C TYR* 1.3 75.8 - - - +
64C VAL* 1.3 59.5 - - - +
65C GLU 4.9 0.2 - - - -
76C ASN* 3.4 38.4 - - + -
77C ILE 2.9 27.1 - - - +
78C LEU* 3.8 3.1 - - - +
79C VAL* 4.2 1.3 - - - +
161C SER 3.7 15.7 - - - -
162C ASN* 3.0 27.1 + - + +
163C TRP* 4.0 23.3 - + + -
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Residues in contact with VAL 64 (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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53C ASN* 3.7 27.1 - - + +
54C LEU* 3.7 14.4 - - + -
63C TYR* 1.3 73.7 - - - +
65C GLU* 1.3 74.5 + - - +
66C MET* 3.5 18.1 + - + -
76C ASN* 4.3 3.4 - - - -
77C ILE* 2.8 39.5 + - + +
79C VAL* 4.0 12.6 - - + -
135C ILE* 4.1 16.8 - - + -
137C HIS* 5.4 1.3 - - + +
167C LEU* 4.8 7.9 - - + -
222C MET* 5.1 7.2 - - - -
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Residues in contact with GLU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ASN 4.5 3.2 + - - -
63C TYR* 4.9 0.4 - - - -
64C VAL* 1.3 75.4 - - - +
66C MET* 1.3 69.8 + - - +
67C THR* 5.3 0.2 - - - +
74C THR* 3.7 31.8 + - + +
75C LEU 3.7 4.3 - - - +
76C ASN* 3.7 15.9 + - - +
135C ILE* 3.5 12.0 - - - +
136C PRO* 3.4 39.2 - - + +
137C HIS* 4.9 19.1 + - + -
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Residues in contact with MET 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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64C VAL* 3.5 9.2 + - + +
65C GLU* 1.3 80.5 - - - +
67C THR* 1.3 67.9 + - - +
68C VAL* 5.5 2.0 - - + +
73C GLN 3.4 0.3 - - - +
74C THR* 3.4 5.4 - - - +
75C LEU* 2.8 38.2 + - + +
77C ILE* 3.5 40.6 - - + -
86C PHE* 4.0 16.2 - - + -
133C VAL* 3.5 26.7 - - + -
134C SER 3.5 5.4 - - - +
135C ILE* 3.7 26.9 - - + -
136C PRO* 3.9 1.8 - - - -
167C LEU* 4.0 19.5 - - + -
184C PHE* 4.1 9.9 - - + -
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Residues in contact with THR 67 (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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65C GLU* 5.3 0.2 - - - +
66C MET* 1.3 78.1 - - - +
68C VAL* 1.3 67.2 + - - +
72C PRO* 3.7 26.5 - - + +
73C GLN 3.1 4.9 - - - -
74C THR* 4.0 16.8 - - + +
132C LEU 4.3 0.2 - - - -
133C VAL* 3.1 8.5 - - - +
134C SER* 2.8 54.5 + - - +
136C PRO* 3.9 20.8 - - + +
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Residues in contact with VAL 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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66C MET* 5.5 2.7 - - + -
67C THR* 1.3 80.0 - - - +
69C GLY* 1.3 64.0 + - - +
73C GLN* 2.7 58.2 + - + +
75C LEU* 3.9 20.9 - - + -
86C PHE* 4.1 15.7 - - + -
88C VAL* 5.2 4.9 - - + -
100C TYR* 3.8 28.9 - - + -
131C ASP* 4.4 0.2 - - - -
132C LEU 3.3 4.0 - - - +
133C VAL* 3.9 20.6 - - + -
147C ILE* 4.1 14.4 - - + -
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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