Contacts of the strand formed by residues 103 - 108 (chain C) in PDB entry 5ZR1
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 ASN 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C LEU 5.0 0.2 + - - -
91C LEU* 3.5 20.6 + - - +
94C GLU* 3.4 28.1 + - - +
101C CYS 4.4 0.6 + - - -
102C PHE* 1.3 70.5 - - - +
104C THR* 1.3 62.5 + - - +
105C ILE* 4.5 4.6 - - + +
234C ILE 3.5 4.2 - - - +
235C SER* 3.1 35.5 + - - -
236C LEU 3.4 8.9 + - - +
262C ASN* 3.5 28.1 + - + +
264C HIS* 5.2 3.6 - - - +
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Residues in contact with THR 104 (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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102C PHE* 3.2 31.2 + - - -
103C ASN* 1.3 71.8 - - - +
105C ILE* 1.3 65.2 + - - +
106C PHE* 3.6 21.8 - - + -
236C LEU* 3.5 5.8 - - + +
238C PHE* 3.6 35.9 - - + -
259C LEU* 3.8 10.3 + - + +
262C ASN 3.0 10.4 + - - -
263C TYR* 3.3 9.5 - - - -
264C HIS* 2.9 27.5 + - - +
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Residues in contact with ILE 105 (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 ILE* 4.6 9.9 - - + +
90C LEU* 3.7 36.1 - - + +
91C LEU* 3.7 42.4 - - + +
103C ASN* 4.5 7.2 - - + +
104C THR* 1.3 78.9 - - - +
106C PHE* 1.3 63.2 + - - +
107C LEU* 3.7 26.4 + - + -
235C SER* 4.6 1.3 - - - +
236C LEU 2.9 13.9 + - - +
237C ILE* 3.4 17.7 - - + +
238C PHE 2.8 27.1 + - - +
264C HIS* 3.6 6.3 - - + +
266C LEU* 4.9 1.3 - - + -
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Residues in contact with PHE 106 (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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104C THR* 3.6 22.0 - - + -
105C ILE* 1.3 71.1 - - - +
107C LEU* 1.3 61.4 + - - +
108C LEU* 3.6 3.2 + - + +
238C PHE* 3.6 33.2 - + + -
240C ILE* 3.8 17.9 - - + -
244C LEU* 3.7 25.8 - - + -
247C ILE* 5.3 9.0 - - + -
259C LEU* 4.3 14.6 - - + -
263C TYR* 3.7 23.3 - + + -
264C HIS 3.0 10.8 + - - +
265C LYS* 3.7 11.8 - - + -
266C LEU* 2.9 28.2 + - - +
299E LEU* 3.6 34.8 - - + -
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Residues in contact with LEU 107 (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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83C LEU* 5.4 2.0 - - + -
87C ILE* 3.7 24.9 - - + -
105C ILE* 3.7 21.1 - - + -
106C PHE* 1.3 69.6 - - - +
108C LEU* 1.3 62.6 + - - +
109C GLY 3.2 0.2 + - - -
110C SER* 3.4 23.6 + - - +
114C THR* 5.2 7.2 - - + -
116C ILE* 5.5 1.1 - - + -
237C ILE* 3.8 15.7 - - + -
238C PHE 2.8 16.0 + - - +
239C ASN* 3.3 22.7 - - - +
240C ILE* 3.0 25.9 + - - +
266C LEU* 3.4 20.4 - - + -
268C VAL* 3.7 20.6 - - + -
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Residues in contact with LEU 108 (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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106C PHE* 4.6 4.3 - - + +
107C LEU* 1.3 68.3 - - - +
109C GLY* 1.3 59.3 + - - +
240C ILE* 3.7 27.1 - - + -
242C THR 6.5 0.2 - - - -
243C ASN* 4.9 4.0 - - - +
244C LEU* 4.3 13.9 - - + +
265C LYS* 3.7 42.4 - - + +
266C LEU 2.9 12.1 + - - +
267C ASP* 3.7 36.3 - - + +
268C VAL 2.9 30.0 + - - +
269C SER* 4.9 0.7 - - - -
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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