Contacts of the strand formed by residues 18 - 24 (chain J) in PDB entry 4BNR
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 18 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B PHE* 4.4 21.3 - - + -
57B HIS 4.5 9.6 - - - +
58B CYS 5.1 3.8 - - - +
16J ALA* 3.8 24.7 - - + -
17J ARG* 1.3 75.6 - - - +
19J ILE* 1.3 67.9 + - - +
20J ARG* 3.4 35.2 + - + +
33J PHE 3.6 0.3 - - - +
34J VAL* 3.7 0.7 - - - -
35J TYR* 2.8 45.7 + - + +
37J GLY* 4.0 19.1 - - - -
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Residues in contact with ILE 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PHE* 3.6 33.3 - - + -
29I LEU* 3.4 40.6 - - + -
30I CYS 5.7 0.2 - - - +
52I MET* 5.4 3.6 - - + -
17J ARG* 4.3 2.7 - - + +
18J ILE* 1.3 78.6 - - - +
20J ARG* 1.3 69.4 + - - +
21J TYR* 5.2 7.1 - - + -
32J THR* 4.0 32.1 - - + -
33J PHE 3.6 3.1 - - - +
34J VAL* 4.3 10.5 - - + -
46J LYS 5.0 4.9 - - - +
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Residues in contact with ARG 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B TYR 5.7 2.2 + - - -
18J ILE* 3.6 21.7 - - - +
19J ILE* 1.3 79.8 + - - +
21J TYR* 1.3 65.0 + - - +
32J THR* 3.3 6.2 - - - -
33J PHE* 2.8 46.3 + - + -
35J TYR* 3.5 46.2 - - + -
40J ALA* 5.1 2.2 - - - +
44J ASN* 2.9 35.9 + - - +
45J PHE 3.3 19.1 - - - -
46J LYS* 3.8 36.9 - - - +
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Residues in contact with TYR 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I TYR* 3.3 23.8 + + - -
32I THR* 5.0 0.2 - - + -
48I ALA* 3.5 22.2 - - - +
19J ILE* 5.2 7.2 - - + -
20J ARG* 1.3 79.3 - - - +
22J PHE* 1.3 60.6 + - - +
30J CYS* 4.5 7.6 - - + -
31J GLN 3.2 21.3 - - - -
32J THR* 3.6 23.7 - - + +
33J PHE* 3.8 1.6 - - - -
44J ASN* 3.4 7.3 - - - -
45J PHE* 2.8 40.1 + - - +
46J LYS 4.5 3.8 - - - -
47J SER* 3.6 20.4 - - - +
48J ALA* 3.6 40.5 - - + +
51J CYS* 4.0 11.0 - - + -
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Residues in contact with PHE 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J GLU 4.8 1.3 - - - -
9J PRO* 3.6 39.0 - - + -
21J TYR* 1.3 74.5 - - - +
23J TYR* 1.3 70.4 + - - +
24J ASN* 3.5 31.1 + - + -
30J CYS* 3.4 0.5 - - - -
31J GLN* 2.8 63.9 + - + -
32J THR 3.7 11.4 - - - -
33J PHE* 3.6 22.0 - + + -
43J ASN* 3.4 30.3 - - - +
51J CYS* 3.7 6.7 - - - -
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Residues in contact with TYR 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ASN* 4.9 1.0 + - - -
1J ARG* 3.3 47.1 + - - -
5J CYS* 3.2 23.7 - - + +
6J LEU 5.5 0.3 - - - -
7J GLU 4.5 1.6 - - - +
22J PHE* 1.3 75.6 - - - +
24J ASN* 1.3 58.8 + - - +
25J ALA* 3.5 24.7 + - + -
28J GLY* 3.5 23.4 + - - -
29J LEU* 3.8 26.0 - - - -
30J CYS* 4.0 11.9 - - - -
43J ASN* 2.8 29.4 + - - +
51J CYS* 3.6 6.0 - - - -
52J MET* 5.4 3.1 - - - -
55J CYS* 3.5 34.5 - - + -
56J GLY* 4.2 7.9 + - - -
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Residues in contact with ASN 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J PHE* 3.5 24.8 + - + -
23J TYR* 1.3 70.9 - - - +
25J ALA* 1.3 52.2 + - - +
26J LYS* 3.1 25.8 + - - +
27J ALA* 3.2 17.6 + - + +
28J GLY* 2.7 31.4 + - - -
29J LEU 2.7 22.4 + - - +
31J GLN* 2.9 30.0 + - + +
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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