Contacts of the strand formed by residues 81 - 87 (chain B) in PDB entry 5CYO
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 MET 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B GLY* 5.3 1.3 - - - -
22B PHE* 3.3 19.5 - - + +
24B PHE* 4.0 17.7 - - + -
73B ASP* 3.3 6.4 - - - -
74B ILE* 2.5 67.1 + - + +
75B GLU 5.9 0.7 - - - +
80B ARG* 1.3 77.4 - - - +
82B LYS* 1.3 70.1 + - - +
83B LEU* 3.5 10.9 + - - +
266B ILE* 3.6 29.8 - - + +
270B MET* 3.8 32.1 - - + -
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLY* 4.6 8.3 - - - +
22B PHE 2.4 26.2 + - - +
23B GLU* 3.5 15.6 - - + +
24B PHE 3.0 24.4 + - - +
25B ASN* 4.9 0.2 - - - +
71B THR* 4.8 9.9 - - + -
72B HIS 4.0 3.8 - - - -
73B ASP* 4.3 15.0 - - - +
81B MET* 1.3 66.5 - - - +
83B LEU* 1.3 61.2 + - - +
84B THR* 3.6 3.2 + - - +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 3.5 24.7 - - + +
26B ILE* 4.0 25.4 - - + -
43B LEU* 4.4 19.1 - - + +
44B PHE* 3.5 28.8 - - + -
47B LYS* 5.9 1.6 - - + -
71B THR* 3.3 2.5 - - - -
72B HIS 3.0 37.9 + - - +
74B ILE* 4.0 30.5 - - + -
81B MET* 3.5 8.1 + - - -
82B LYS* 1.3 70.7 - - - +
84B THR* 1.3 64.8 + - - +
85B VAL* 4.1 9.6 - - + -
266B ILE* 5.1 6.7 - - + -
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE 2.9 7.6 + - - +
25B ASN* 3.3 22.3 + - - +
26B ILE* 2.7 27.0 + - - +
69B SER* 4.0 22.2 - - - -
70B ILE 3.3 4.9 - - - +
71B THR* 2.8 31.5 + - - +
82B LYS* 3.6 3.0 + - - +
83B LEU* 1.3 73.8 - - - +
85B VAL* 1.3 64.7 + - - +
86B ILE* 4.1 15.3 - - + -
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE* 3.1 15.0 - - + +
28B VAL* 4.3 12.6 - - + -
40B ILE* 3.6 34.5 - - + -
43B LEU* 4.1 25.6 - - + -
44B PHE* 3.7 29.6 - - + -
68B LYS 3.9 0.3 - - - +
70B ILE* 2.8 37.3 + - - +
83B LEU* 4.1 9.4 - - + -
84B THR* 1.3 77.9 - - - +
86B ILE* 1.3 65.1 + - - +
87B ASP 3.7 2.3 + - - -
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASN* 4.6 13.2 - - + -
26B ILE 2.6 19.9 + - - +
27B MET* 3.5 21.0 - - + +
28B VAL* 3.0 28.8 + - - +
40B ILE* 4.5 2.0 - - - -
67B ILE* 3.6 29.4 - - + -
68B LYS 3.6 6.7 - - - +
69B SER* 4.0 14.4 - - - +
84B THR* 4.1 9.6 - - + -
85B VAL* 1.3 74.9 - - - +
87B ASP* 1.3 62.1 + - - +
88B THR* 4.5 0.2 - - + -
107B PHE* 3.6 27.1 - - + -
131B THR 5.1 3.4 - - - +
133B VAL* 3.8 20.0 - - + -
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 3.6 12.3 - - - +
36B LYS* 4.6 1.9 - - - +
37B SER* 2.4 36.1 + - - -
40B ILE* 3.5 19.3 - - + +
64B THR* 3.3 12.6 + - + -
66B GLU 4.5 1.1 - - - -
67B ILE* 3.3 7.0 - - - +
68B LYS* 2.9 61.2 + - + +
70B ILE* 4.6 1.8 - - + -
85B VAL 3.7 2.6 + - - -
86B ILE* 1.3 73.7 - - - +
88B THR* 1.3 77.1 + - - +
302B MG 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