Contacts of the strand formed by residues 97 - 103 (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 SER 97 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C PHE* 3.4 5.8 - - - -
92C ASN* 2.8 32.6 + - - +
95C MET* 3.0 23.4 - - - +
96C LYS* 1.3 78.5 - - - +
98C LYS* 1.3 70.7 + - - +
99C MET* 5.6 0.9 - - - +
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Residues in contact with LYS 98 (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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89C GLN* 3.5 32.1 - - + +
90C ILE 4.0 3.4 - - - +
91C PHE* 3.6 22.4 - - + -
96C LYS 3.9 11.3 + - - -
97C SER* 1.3 78.1 - - - +
99C MET* 1.3 63.6 + - - +
100C LYS 4.9 3.8 - - - +
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Residues in contact with MET 99 (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 36.1 - - + -
90C ILE* 2.8 21.5 + - + +
92C ASN* 3.9 32.8 - - + +
97C SER* 3.6 1.1 + - - +
98C LYS* 1.3 74.9 - - - +
100C LYS* 1.3 68.1 + - + +
132C MET* 3.8 42.4 - - + +
135C GLU* 5.7 0.3 - - - +
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Residues in contact with LYS 100 (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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89C GLN* 3.6 6.2 - - - +
90C ILE* 3.0 37.8 + - + +
98C LYS* 4.9 2.6 - - - +
99C MET* 1.3 85.0 + - + +
101C ALA* 1.3 68.1 + - - +
130C TRP* 3.3 21.1 - - + +
131C SER 3.2 28.0 - - - +
132C MET 3.4 18.6 - - - +
133C GLU 4.0 1.8 - - - -
134C GLY 3.1 27.4 - - - +
135C GLU* 4.0 17.2 + - - +
136C SER 2.8 36.6 + - - +
137C GLN* 4.5 3.2 + - - -
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Residues in contact with ALA 101 (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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87C THR* 6.2 1.8 - - + -
88C LEU 3.4 12.3 - - - +
89C GLN* 4.6 5.8 - - + -
98C LYS* 6.2 1.8 - - + -
100C LYS* 1.3 82.5 + - - +
102C HIS* 1.3 66.4 + - - +
130C TRP* 3.7 6.7 - - - -
135C GLU* 5.7 1.7 + - - +
137C GLN* 4.4 9.2 - - - +
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Residues in contact with HIS 102 (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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86C LYS 3.7 1.2 - - - +
87C THR* 3.5 1.7 - - - +
88C LEU* 2.6 46.4 + - + +
101C ALA* 1.3 76.5 - - - +
103C THR* 1.3 80.2 + - - +
104C MET* 3.6 31.9 - - + +
130C TRP* 3.7 21.0 - - + -
137C GLN* 3.3 43.6 + - + +
138C PRO* 3.5 19.0 - - + +
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Residues in contact with THR 103 (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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85C GLY 5.6 0.2 - - - +
86C LYS* 3.3 15.0 - - + +
87C THR* 3.7 25.6 + - - +
102C HIS* 1.3 89.3 + - - +
104C MET* 1.3 69.8 + - - +
105C THR* 4.0 1.4 + - - +
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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