Contacts of the strand formed by residues 87 - 92 (chain C) in PDB entry 5ODS
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 THR 87 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LEU 3.8 1.2 - - - +
83C LYS* 3.7 1.4 - - - -
84C ALA* 2.9 42.5 + - - +
85C GLY 3.0 7.6 + - - -
86C LYS* 1.3 78.7 - - - +
88C LEU* 1.3 68.9 + - - +
89C GLN* 5.2 2.5 - - + +
101C ALA* 6.2 1.6 - - + -
102C HIS 3.6 4.0 - - - +
103C THR* 3.7 24.7 + - - +
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Residues in contact with LEU 88 (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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82C LEU 3.7 3.4 - - - -
83C LYS* 4.7 9.6 - - + -
86C LYS* 3.5 26.2 - - - +
87C THR* 1.3 78.9 - - - +
89C GLN* 1.3 65.0 + - - +
101C ALA* 3.4 4.2 - - - +
102C HIS* 2.6 38.3 + - + +
104C MET* 3.9 17.3 - - + -
108C VAL* 4.3 11.7 - - + -
111C TRP* 3.6 22.2 - - + -
121C LEU* 3.6 43.1 - - + -
130C TRP* 3.6 18.4 - - + -
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Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ALA* 3.5 1.8 - - - -
82C LEU* 2.9 56.9 + - + +
87C THR* 5.2 2.6 - - + +
88C LEU* 1.3 79.6 - - - +
90C ILE* 1.3 69.9 + - - +
91C PHE* 3.4 30.8 + - - +
98C LYS* 3.5 18.1 - - + +
100C LYS 3.6 12.6 - - - +
101C ALA* 4.2 4.9 - - + +
111C TRP* 5.3 0.6 - - - -
130C TRP* 4.2 2.1 - - - -
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Residues in contact with ILE 90 (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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79C VAL* 3.7 25.4 - - + -
80C ILE 3.6 4.3 - - - +
81C ALA* 4.4 12.1 - - + +
89C GLN* 1.3 71.8 - - - +
91C PHE* 1.3 55.0 + - - +
98C LYS* 3.8 1.0 - - - -
99C MET* 2.8 43.4 + - + +
100C LYS* 3.0 36.9 + - + +
113C TRP* 4.7 5.6 - - + -
119C VAL* 4.6 9.2 - - + -
130C TRP* 3.9 31.8 - - + -
131C SER 4.3 0.7 - - - +
132C MET* 3.8 33.4 - - + +
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Residues in contact with PHE 91 (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 ARG* 5.5 3.6 - - - -
66C ILE* 5.0 12.8 - - + -
79C VAL* 3.7 2.3 - - - +
80C ILE* 2.7 59.1 + - + +
82C LEU* 4.0 10.1 - - + -
89C GLN* 3.4 25.8 + - - +
90C ILE* 1.3 75.0 - - - +
92C ASN* 1.3 72.0 + - - +
93C ILE* 3.5 15.6 + - + -
96C LYS* 3.5 40.4 - - + -
97C SER 3.4 15.3 - - - -
98C LYS* 3.6 16.4 - - + -
99C MET* 4.1 3.4 - - - +
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Residues in contact with ASN 92 (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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78C LYS 4.1 3.8 - - - +
79C VAL* 4.1 11.7 - - - +
91C PHE* 1.3 73.5 - - - +
93C ILE* 1.3 61.5 + - - +
94C GLU* 3.4 9.7 + - - +
95C MET* 3.2 32.2 + - + +
96C LYS* 3.0 27.9 + - - -
97C SER* 2.8 28.0 + - - +
99C MET* 3.9 28.7 - - + +
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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