Contacts of the strand formed by residues 87 - 98 (chain O) in PDB entry 5IYB
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 LEU 87 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80O GLU* 3.5 29.4 - - + +
81O PHE 3.5 15.5 - - - +
82O ARG* 3.9 33.9 - - + +
83O GLU 5.5 0.2 - - - +
86O GLU* 1.3 84.2 - - - +
88O ILE* 1.3 67.3 + - - +
89O LYS* 4.3 6.3 - - + +
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Residues in contact with ILE 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358N MET* 5.4 3.1 - - + -
360N LEU* 3.4 41.1 - - + +
365N TYR* 3.6 20.2 - - + +
56O VAL* 6.3 1.3 - - + -
79O VAL 4.0 0.3 - - - +
80O GLU* 3.4 2.1 - - - -
81O PHE* 2.7 54.5 + - + +
86O GLU* 3.6 29.2 - - + +
87O LEU* 1.3 81.5 - - - +
89O LYS* 1.3 65.1 + - - +
90O VAL* 4.2 16.8 - - + +
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Residues in contact with LYS 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O ASP* 3.4 26.3 + - - -
79O VAL 3.4 3.6 + - - -
80O GLU* 3.7 37.8 + - + +
87O LEU* 4.3 6.9 - - + +
88O ILE* 1.3 75.3 - - - +
90O VAL* 1.3 66.6 + - - +
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Residues in contact with VAL 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333N ASN* 4.0 24.9 - - + +
360N LEU* 4.8 9.9 - - + -
361N ASN* 6.2 1.1 - - + -
78O ASP* 3.4 4.2 - - - +
79O VAL* 2.7 64.4 + - + +
81O PHE* 5.1 9.6 - - + -
88O ILE* 4.2 17.9 - - + +
89O LYS* 1.3 80.1 - - - +
91O ASP* 1.3 57.7 + - - +
92O LYS 4.4 15.0 - - - +
93O VAL* 4.7 7.0 - - + -
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Residues in contact with ASP 91 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332N GLU* 5.7 1.9 - - + +
77O ASN* 3.2 7.1 - - - +
78O ASP* 2.6 30.1 + - - +
90O VAL* 1.3 73.6 - - - +
92O LYS* 1.3 65.7 + - + +
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Residues in contact with LYS 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326N GLN* 3.1 53.5 + - - +
332N GLU* 3.2 56.8 + - + +
333N ASN* 3.9 6.1 + - - +
63O ASN* 4.6 9.9 - - - +
75O VAL* 3.6 25.4 - - + -
76O LEU 3.3 13.7 - - - +
77O ASN* 4.0 6.3 - - + +
79O VAL* 5.3 0.4 - - - -
90O VAL* 3.4 12.2 - - - +
91O ASP* 1.3 89.3 - - - +
93O VAL* 1.3 67.1 + - - +
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Residues in contact with VAL 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332N GLU* 4.7 1.1 - - - -
333N ASN* 3.2 20.0 - - + +
335N VAL* 3.6 29.8 - - + -
360N LEU* 5.5 0.4 - - + -
75O VAL* 3.2 8.2 - - - +
76O LEU* 2.7 48.8 + - + +
79O VAL* 3.5 32.8 - - + -
81O PHE* 4.7 6.5 - - + -
90O VAL* 4.7 7.6 - - + -
92O LYS* 1.3 76.9 - - - +
94O LYS* 1.3 66.6 + - - +
95O ILE* 4.1 13.9 + - + +
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Residues in contact with LYS 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327N GLU* 4.9 6.7 + - - +
330N ASP* 2.8 44.9 + - + +
332N GLU* 5.5 3.2 + - - +
333N ASN 3.4 5.7 + - - +
334N VAL* 3.4 18.3 - - + +
335N VAL 3.0 26.5 + - - +
66O ARG* 6.1 1.3 - - - +
73O THR* 4.7 11.0 - - + -
74O PHE 3.7 10.1 - - - +
75O VAL* 4.3 13.5 - - + +
93O VAL* 1.3 74.9 - - - +
95O ILE* 1.3 67.6 + - - +
96O VAL* 4.3 17.0 - - + -
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Residues in contact with ILE 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335N VAL* 3.4 20.4 - - + +
337N CYS* 4.2 22.7 - - - -
351N PHE* 6.5 0.2 - - + -
353N LEU* 5.4 9.2 - - + -
58O PHE* 5.5 9.6 - - + -
72O TRP 3.8 0.5 - - - +
73O THR* 3.4 3.6 - - - +
74O PHE* 2.9 56.1 + - + +
76O LEU* 3.8 29.2 - - + -
81O PHE* 5.6 6.1 - - + -
93O VAL* 4.2 21.5 - - + -
94O LYS* 1.3 76.8 - - - +
96O VAL* 1.3 67.5 + - - +
97O ALA* 4.9 4.3 - - + -
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Residues in contact with VAL 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334N VAL* 5.9 2.9 - - + -
335N VAL 3.3 7.0 + - - +
336N VAL* 3.8 8.8 - - + -
337N CYS* 3.2 26.9 + - - +
5O LEU* 3.9 28.2 - - + +
8O ASN* 6.1 1.1 - - - +
71O VAL* 3.7 24.2 - - + -
72O TRP 3.5 3.6 - - - +
73O THR* 4.3 16.4 - - + +
94O LYS* 4.6 16.8 - - + -
95O ILE* 1.3 78.0 - - - +
97O ALA* 1.3 64.3 + - - +
98O CYS* 6.1 0.7 - - + -
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Residues in contact with ALA 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337N CYS* 3.3 23.3 - - - +
338N GLN 4.0 6.7 - - - +
339N TYR* 3.2 23.4 - - + +
353N LEU* 4.8 4.3 - - + -
71O VAL* 3.6 2.4 - - - -
72O TRP* 2.7 47.1 + - + +
74O PHE* 6.1 2.5 - - + -
95O ILE* 4.2 4.9 - - + +
96O VAL* 1.3 77.9 - - - +
98O CYS* 1.3 61.7 + - - +
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Residues in contact with CYS 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337N CYS 3.4 5.1 + - - -
338N GLN* 3.1 29.6 - - - +
339N TYR* 3.3 7.6 + - - -
3O TYR* 2.9 53.8 - - + -
5O LEU* 4.2 20.1 - - + +
70O ASN 4.0 4.0 - - - +
71O VAL* 4.4 18.6 - - + -
96O VAL* 6.1 0.4 - - + -
97O ALA* 1.3 73.3 - - - +
99O ASP* 1.3 64.4 + - - +
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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