Contacts of the strand formed by residues 80 - 87 (chain A) in PDB entry 5CYP
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 ARG 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A MET 5.7 2.2 - - - +
19A LYS* 2.8 47.0 + - + +
20A GLN* 2.9 42.9 + - - +
21A GLY* 3.2 10.5 - - - +
22A PHE* 3.1 14.1 + - - +
73A ASP* 5.9 6.0 + - + -
74A ILE 3.5 6.7 - - - +
75A GLU* 4.2 16.2 - - + +
79A VAL* 1.3 78.6 - - - +
81A MET* 1.3 62.5 + - - +
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Residues in contact with MET 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLY* 5.7 0.2 - - - -
22A PHE* 3.2 13.7 - - + +
24A PHE* 5.7 5.4 - - + -
73A ASP* 3.5 3.7 - - - -
74A ILE* 2.7 51.3 + - + +
76A GLU* 5.8 4.0 - - + +
79A VAL 3.8 2.7 + - - +
80A ARG* 1.3 75.6 - - - +
82A LYS* 1.3 61.5 + - - +
83A LEU* 3.3 7.2 + - + +
266A ILE* 5.7 6.7 - - + -
270A MET* 6.3 2.9 - - + -
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Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLY* 5.5 2.9 - - - -
22A PHE 2.8 16.0 + - - +
23A GLU* 3.9 24.8 - - + +
24A PHE 3.5 16.1 + - - +
25A ASN* 4.8 0.5 - - - +
71A THR* 3.8 21.3 - - + +
72A HIS 4.1 0.2 - - - -
73A ASP* 3.3 31.7 + - - +
81A MET* 1.3 69.6 - - - +
83A LEU* 1.3 62.6 + - - +
84A THR* 3.4 7.7 + - - +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.6 25.1 - - + +
26A ILE* 4.0 26.5 - - + -
43A LEU* 3.5 29.2 - - + +
44A PHE* 3.6 18.3 - - + -
47A LYS* 5.7 2.2 - - + -
70A ILE 3.7 1.4 - - - +
71A THR* 3.2 3.6 - - - +
72A HIS 3.0 39.7 + - - +
74A ILE* 3.7 27.1 - - + -
81A MET* 3.3 4.2 + - + -
82A LYS* 1.3 71.5 - - - +
84A THR* 1.3 65.7 + - - +
85A VAL* 4.2 3.1 - - + -
266A ILE* 4.1 12.6 - - + -
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Residues in contact with THR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE 2.9 8.3 + - - +
25A ASN* 3.2 22.5 + - - +
26A ILE* 2.9 27.0 + - - +
69A SER* 4.0 23.8 - - - +
70A ILE 3.2 5.6 - - - +
71A THR* 2.7 31.6 + - - +
82A LYS* 3.4 5.4 + - - +
83A LEU* 1.3 71.3 - - - +
85A VAL* 1.3 65.2 + - - +
86A ILE* 4.4 10.7 - - + +
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.2 17.9 - - + +
28A VAL* 4.6 9.9 - - + -
40A ILE* 3.6 43.5 - - + +
43A LEU* 3.9 20.2 - - + -
44A PHE* 3.5 26.7 - - + -
68A LYS 3.6 2.8 - - - +
70A ILE* 2.7 42.0 + - - +
83A LEU* 4.2 7.9 - - + -
84A THR* 1.3 74.9 - - - +
86A ILE* 1.3 62.8 + - - +
87A ASP 3.7 0.9 + - - -
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ASN* 4.5 15.5 - - + -
26A ILE 2.8 21.0 + - - +
27A MET* 3.6 22.8 - - + +
28A VAL* 3.1 28.0 + - - +
67A ILE* 3.6 29.6 - - + -
68A LYS 3.4 5.8 - - - +
69A SER* 3.5 18.4 - - - +
84A THR* 4.4 7.4 - - + +
85A VAL* 1.3 73.6 - - - +
87A ASP* 1.3 63.9 + - - +
88A THR* 4.7 0.4 - - + -
107A PHE* 3.8 13.7 - - + -
131A THR 5.2 3.4 - - - +
133A VAL* 3.9 28.3 - - + -
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 3.5 16.2 - - - +
36A LYS* 4.2 1.4 - - - +
37A SER* 2.7 33.4 + - - -
40A ILE* 3.6 18.1 - - + +
64A THR* 3.1 18.8 + - + +
66A GLU 4.1 0.3 - - - +
67A ILE* 3.4 7.8 - - - +
68A LYS* 2.8 44.5 + - + +
70A ILE* 5.2 6.5 - - + +
85A VAL 3.7 1.8 + - - -
86A ILE* 1.3 73.5 - - - +
88A THR* 1.3 69.8 + - - +
302A MG 3.6 6.1 - - - -
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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