Contacts of the strand formed by residues 55 - 59 (chain C) in PDB entry 6P59
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 ILE 55 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C TYR* 4.9 6.1 - - + -
44C PHE* 4.7 7.4 - - + +
47C ALA* 3.5 35.2 - - + +
48C CYS* 3.9 24.0 - - + +
53C SER 4.3 1.0 + - - +
54C GLU* 1.3 79.9 - - - +
56C ALA* 1.3 61.1 + - - +
57C PHE* 3.7 30.5 - - + -
67C GLN* 3.2 2.5 + - - -
68C PHE* 3.0 37.6 + - + +
86C VAL* 4.2 26.7 - - + -
6F TRP* 4.6 8.1 - - - +
77F THR* 4.6 1.3 - - - -
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Residues in contact with ALA 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C TYR* 3.8 20.7 - - - -
30C THR* 4.5 7.0 + - - +
55C ILE* 1.3 74.7 - - - +
57C PHE* 1.3 72.2 + - - +
58C VAL* 5.5 1.3 - - + -
65C SER* 4.6 5.8 - - - +
66C LEU 3.6 8.3 - - - +
67C GLN* 3.4 28.9 - - - +
13F ARG* 4.4 24.2 - - - +
77F THR* 4.6 6.1 + - - +
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Residues in contact with PHE 57 (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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27C ILE* 4.4 18.5 - - + +
28C LYS 3.4 13.5 - - - +
29C TYR* 4.4 6.3 - + + -
44C PHE* 3.4 36.1 - + - -
55C ILE* 3.7 26.7 - - + -
56C ALA* 1.3 81.3 - - - +
58C VAL* 1.3 63.2 + - - +
59C ALA 3.9 0.5 + - - -
65C SER* 3.2 4.1 - - - -
66C LEU* 3.0 32.3 + - + +
68C PHE* 3.9 19.3 - + - -
95C VAL* 5.8 0.2 - - + -
97C LEU* 3.6 39.3 - - + -
110C TRP* 6.1 0.7 - - + -
114C ILE* 3.7 26.9 - - + -
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Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ILE* 3.6 3.6 - - - -
28C LYS* 3.1 28.9 + - - +
30C THR* 3.2 41.5 + - + +
56C ALA 5.5 0.2 - - - -
57C PHE* 1.3 74.9 - - - +
59C ALA* 1.3 69.3 + - - +
60C THR* 3.3 5.1 + - - -
62C THR 3.4 25.1 - - - +
63C ASN* 4.8 3.6 - - - -
64C LEU 3.6 7.0 - - - +
65C SER* 4.1 4.5 - - - -
13F ARG* 3.7 26.9 - - - +
79F GLU* 5.2 0.9 - - - +
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Residues in contact with ALA 59 (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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20C LYS 4.8 5.8 - - - +
21C LEU* 5.1 7.6 - - + -
25C CYS* 4.8 18.8 - - + -
26C GLU 3.8 7.9 - - - +
27C ILE* 4.4 6.6 - - + +
57C PHE 3.9 1.6 + - - -
58C VAL* 1.3 69.9 - - - +
60C THR* 1.3 68.2 + - - +
62C THR* 2.9 41.8 + - + +
64C LEU* 3.1 16.5 + - + +
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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