Contacts of the strand formed by residues 42 - 48 (chain C) in PDB entry 5F28
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 GLU 42 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ASP* 4.0 4.3 - - - +
41C CYS* 1.3 74.8 - - - +
43C ILE* 1.3 59.8 + - - +
59C SER* 3.5 10.1 - - - +
60C THR* 6.0 1.1 - - - +
64C LYS* 5.5 12.6 - - - +
65C VAL* 4.5 17.4 - - + +
68C LYS* 2.8 32.9 + - + +
46D ILE 3.7 0.5 - - - +
47D ILE* 3.4 3.1 - - - -
48D PHE* 2.8 58.2 + - + +
49D ASN 3.3 17.3 - - - +
50D SER* 4.7 2.4 - - - -
52D ASN* 4.0 3.3 - - - +
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Residues in contact with ILE 43 (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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32C ALA* 3.3 29.8 - - + +
35C LEU* 3.7 28.5 - - + -
36C SER* 4.0 12.1 - - - +
41C CYS* 4.1 13.0 - - + +
42C GLU* 1.3 79.5 - - - +
44C ALA* 1.3 64.3 + - - +
57C TYR* 4.0 19.7 - - + -
58C ALA* 3.3 4.3 - - - +
59C SER* 2.9 35.4 + - - -
65C VAL* 4.4 6.2 - - - +
28D LEU* 4.4 2.2 - - + -
45D LEU* 3.8 23.1 - - + -
46D ILE 3.1 9.2 - - - +
47D ILE* 4.1 8.3 - - + -
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Residues in contact with ALA 44 (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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43C ILE* 1.3 76.1 - - - +
45C LEU* 1.3 61.6 + - - +
46C ILE* 5.4 2.2 - - + -
57C TYR 3.5 4.9 - - - -
58C ALA* 4.4 1.1 - - + +
62C MET* 3.8 23.1 - - - -
65C VAL* 3.7 23.8 - - + +
66C LEU* 4.6 4.3 - - + -
44D ALA 4.5 0.4 - - - -
45D LEU* 3.4 7.8 - - - +
46D ILE* 2.8 44.3 + - + +
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Residues in contact with LEU 45 (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 LEU* 4.0 36.6 - - + +
29C MET* 4.2 20.4 - - + -
32C ALA* 4.8 4.0 - - + -
43C ILE* 5.2 0.2 - - + -
44C ALA* 1.3 75.8 - - - +
46C ILE* 1.3 61.0 + - - +
47C ILE* 4.0 15.9 - - + -
55C PHE 4.9 0.2 - - - -
56C GLN* 3.2 7.8 - - - +
57C TYR* 2.7 54.5 + - + +
62C MET* 3.9 0.9 - - - +
32D ALA* 5.1 2.9 - - + -
43D ILE* 4.1 18.6 - - + -
44D ALA 3.3 16.4 - - - +
45D LEU* 3.7 20.6 - - + -
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Residues in contact with ILE 46 (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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44C ALA* 5.4 1.8 - - + -
45C LEU* 1.3 77.7 - - - +
47C ILE* 1.3 66.5 + - - +
48C PHE* 3.7 20.2 - - + -
54C LEU* 3.7 20.0 - - + -
55C PHE 3.9 2.5 - - - -
56C GLN* 4.6 1.3 - - + +
62C MET* 4.3 12.6 - - + -
66C LEU* 4.6 12.1 - - + -
42D GLU 3.7 0.5 - - - +
43D ILE* 3.3 6.8 - - - +
44D ALA* 2.9 42.6 + - + +
46D ILE* 6.4 0.9 - - + -
65D VAL* 4.3 7.1 - - + +
66D LEU* 4.0 25.4 - - + -
69D TYR* 3.8 33.7 - - + -
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Residues in contact with ILE 47 (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 PHE* 4.7 7.9 - - + -
25C LYS* 4.3 18.2 - - + -
28C LEU* 4.2 5.2 - - + -
29C MET* 4.7 6.5 - - + -
45C LEU* 4.0 29.6 - - + +
46C ILE* 1.3 82.3 - - - +
48C PHE* 1.3 63.8 + - - +
53C LYS 3.5 2.3 - - - +
54C LEU* 3.5 3.0 - - - +
55C PHE* 2.8 56.0 + - + +
35D LEU* 4.1 20.4 - - + -
41D CYS* 4.2 22.7 - - - -
42D GLU 3.4 3.1 - - - -
43D ILE* 4.0 15.7 - - + -
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Residues in contact with PHE 48 (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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46C ILE* 3.7 18.4 - - + -
47C ILE* 1.3 75.2 - - - +
49C ASN* 1.3 67.1 + - - +
52C ASN* 4.4 16.2 - - + +
53C LYS 3.4 7.4 - - - +
54C LEU* 3.6 38.6 - - + -
41D CYS* 3.2 5.9 - - - +
42D GLU* 2.9 50.7 + - + +
65D VAL* 3.9 24.0 - - + -
68D LYS* 3.7 47.6 - - + -
69D TYR* 3.9 7.0 - - - -
72D TYR* 4.0 14.8 - + - -
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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