Contacts of the strand formed by residues 20 - 26 (chain C) in PDB entry 3BYB
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 PHE 20 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C ARG* 1.3 111.2 - - + +
21C PRO* 1.3 75.6 - - + +
22C SER* 3.4 5.3 + - - +
36C ILE* 3.3 7.3 - - - -
37C TYR* 2.8 48.6 + + + +
38C GLY 3.5 23.6 - - - -
39C GLY* 3.7 11.0 - - - -
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Residues in contact with PRO 21 (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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19C ARG 4.3 4.0 - - - +
20C PHE* 1.3 88.5 - - + +
22C SER* 1.3 63.6 + - - +
23C PHE* 5.4 4.7 - - + -
34C GLU* 3.5 22.4 - - - +
35C PHE 3.7 6.1 - - - +
36C ILE* 4.5 6.9 - - + -
48C ILE* 4.6 9.2 - - - +
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Residues in contact with SER 22 (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 PHE* 3.4 2.6 + - - +
21C PRO* 1.3 79.2 + - - +
23C PHE* 1.3 65.3 + - - +
34C GLU* 3.3 8.5 - - - +
35C PHE* 2.8 51.7 + - - -
37C TYR* 3.3 31.3 - - - +
46C ASN* 4.1 9.1 + - - -
47C PHE 3.5 12.6 - - - -
48C ILE* 4.9 5.3 - - - +
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Residues in contact with PHE 23 (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 PRO* 5.4 3.8 - - + -
22C SER* 1.3 80.1 - - - +
24C TYR* 1.3 60.6 + - - +
33C LEU* 3.2 9.6 - - - +
34C GLU* 3.6 46.2 - - + -
35C PHE* 3.7 3.7 - - - -
46C ASN* 3.4 6.8 - - - -
47C PHE* 2.8 36.4 + - - +
48C ILE 3.6 16.8 - - - -
49C THR* 3.5 15.3 - - - +
50C LYS* 3.5 50.3 - - + -
53C CYS* 4.2 12.1 - - + -
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Residues in contact with TYR 24 (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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24A TYR* 2.7 35.1 + - - -
33A LEU* 3.9 5.5 - - - +
34A GLU 4.3 4.6 + - - -
9C LEU 4.7 1.1 - - - -
10C PRO* 5.0 1.3 - - + -
11C ALA* 3.8 32.8 - - + -
23C PHE* 1.3 74.0 - - - +
25C TYR* 1.3 71.5 + - - +
26C ASN* 3.5 33.6 + - + -
27C PRO* 5.8 0.4 - - + -
32C CYS* 3.3 0.5 - - - -
33C LEU* 2.8 56.8 + - + -
34C GLU 4.5 0.7 - - - -
35C PHE* 3.6 29.6 - + + -
45C ASN* 3.3 31.2 - - - +
53C CYS* 3.7 7.2 - - - -
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Residues in contact with TYR 25 (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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3C ARG* 3.3 42.2 + - - -
7C CYS* 3.2 35.1 - - + +
9C LEU 4.4 0.2 - - - +
24C TYR* 1.3 77.6 - - - +
26C ASN* 1.3 58.0 + - - +
27C PRO* 3.5 26.4 + - + +
30C LYS* 3.4 30.6 - - - +
31C LYS* 3.6 28.3 - - - -
32C CYS* 3.9 7.9 - - - -
45C ASN* 2.8 33.2 + - - +
53C CYS* 3.6 6.5 - - - -
57C CYS* 3.5 33.2 - - + -
58C ALA 4.7 7.3 + - - -
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Residues in contact with ASN 26 (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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33A LEU* 3.6 26.5 - - - +
34A GLU* 4.6 4.9 + - - +
24C TYR* 3.5 26.6 + - + -
25C TYR* 1.3 74.2 - - - +
27C PRO* 1.4 62.9 - - - +
28C ASP* 2.9 16.5 + - - +
29C GLU* 2.8 36.2 + - + +
30C LYS* 2.8 23.7 + - - -
31C LYS 2.8 23.8 + - - +
33C LEU* 3.7 16.2 - - + -
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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