Contacts of the strand formed by residues 80 - 87 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C GLN* 2.9 44.4 + - - +
21C GLY* 3.1 29.7 + - - +
22C PHE* 2.9 22.7 + - - +
73C ASP* 5.6 12.0 + - + +
74C ILE 3.5 7.4 - - - +
75C GLU* 4.3 16.2 - - + +
79C VAL* 1.3 80.6 - - - +
81C MET* 1.3 62.0 + - - +
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Residues in contact with MET 81 (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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21C GLY* 5.6 0.2 - - - -
22C PHE* 3.3 15.3 - - + +
24C PHE* 4.1 19.1 - - + -
73C ASP* 3.4 3.8 - - - -
74C ILE* 2.7 53.1 + - + +
76C GLU* 5.9 3.1 - - + +
79C VAL 3.8 2.4 + - - +
80C ARG* 1.3 75.6 - - - +
82C LYS* 1.3 62.5 + - - +
83C LEU* 3.3 21.8 + - + +
266C ILE* 3.6 45.3 - - + +
270C MET* 3.7 31.0 - - + -
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Residues in contact with LYS 82 (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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21C GLY* 5.4 2.0 - - - -
22C PHE 2.8 16.2 + - - +
23C GLU* 3.6 37.3 + - + +
24C PHE 3.5 14.6 + - - +
25C ASN* 4.8 1.6 + - - +
71C THR* 3.7 19.2 + - + +
72C HIS 3.9 0.2 - - - -
73C ASP* 3.2 24.0 - - - +
81C MET* 1.3 71.0 - - - +
83C LEU* 1.3 63.8 + - - +
84C THR* 3.4 22.2 + - - -
130C ASP 5.3 1.6 + - - -
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Residues in contact with LEU 83 (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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24C PHE* 3.6 23.3 - - + +
26C ILE* 3.9 27.4 - - + -
43C LEU* 3.6 28.7 - - + +
44C PHE* 3.7 17.4 - - + -
70C ILE 3.7 1.4 - - - +
71C THR* 3.3 2.8 - - - -
72C HIS 3.0 38.8 + - - +
74C ILE* 3.8 27.8 - - + -
81C MET* 3.3 9.8 + - + -
82C LYS* 1.3 71.9 - - - +
84C THR* 1.3 66.1 + - - +
85C VAL* 4.2 5.2 - - + -
266C ILE* 4.5 11.7 - - + -
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Residues in contact with THR 84 (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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24C PHE 2.9 7.7 + - - +
25C ASN* 3.2 22.6 + - - +
26C ILE* 2.8 27.0 + - - +
69C SER* 4.1 23.1 - - - +
70C ILE 3.2 5.8 - - - +
71C THR* 2.9 29.0 + - - +
82C LYS* 3.4 12.3 + - - -
83C LEU* 1.3 74.5 - - - +
85C VAL* 1.3 66.2 + - - +
86C ILE* 4.1 11.3 + - + +
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Residues in contact with VAL 85 (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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26C ILE* 3.1 16.8 - - + +
28C VAL* 4.6 10.3 - - + -
40C ILE* 3.7 35.4 - - + -
43C LEU* 3.7 22.7 - - + -
44C PHE* 3.5 32.3 - - + -
70C ILE* 2.7 43.2 + - - +
83C LEU* 4.2 7.4 - - + -
84C THR* 1.3 75.9 - - - +
86C ILE* 1.3 64.0 + - - +
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Residues in contact with ILE 86 (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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25C ASN* 4.5 17.5 - - + -
26C ILE 2.8 18.1 + - - +
27C MET* 3.6 23.2 - - + +
28C VAL* 3.2 25.0 + - - +
67C ILE* 3.6 31.4 - - + -
68C LYS 3.4 5.8 - - - +
69C SER* 3.5 18.8 - - - +
84C THR* 4.3 7.4 - - + -
85C VAL* 1.3 73.0 - - - +
87C ASP* 1.3 62.6 + - - +
88C THR* 3.8 0.6 + - + -
107C PHE* 3.7 13.7 - - + -
131C THR 5.2 3.1 - - - +
133C VAL* 3.7 29.6 - - + -
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Residues in contact with ASP 87 (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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28C VAL* 3.4 17.1 - - - +
36C LYS* 4.3 1.4 - - - +
37C SER* 2.8 27.1 + - - -
40C ILE* 3.5 19.6 - - + +
64C THR* 3.3 17.9 + - + +
66C GLU 4.0 0.5 - - - +
67C ILE* 3.3 6.4 - - - +
68C LYS* 2.8 41.2 + - + +
70C ILE* 4.3 8.1 - - + -
85C VAL 3.7 2.0 + - - -
86C ILE* 1.3 73.9 - - - +
88C THR* 1.3 69.6 + - - +
302C MG 3.5 11.8 - - - -
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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