Contacts of the strand formed by residues 20 - 26 (chain A) in PDB entry 1BF4
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 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A VAL* 4.2 12.6 - - + -
15A VAL* 3.9 23.6 - - + -
17A ILE* 3.0 36.0 + - + +
18A SER 4.3 4.2 - - - +
19A LYS* 1.3 76.1 - - - +
21A LYS* 1.3 63.7 + - - +
22A LYS 3.9 14.4 - - - +
23A VAL* 4.4 0.9 - - + -
32A PHE* 3.7 29.4 - - + -
33A THR 3.6 9.0 - - - +
34A TYR* 4.0 2.5 - - + -
55A LEU* 3.9 21.5 - - + -
58A MET* 3.6 27.1 - - + +
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LYS 3.1 2.3 + - - +
20A ILE* 1.3 75.4 - - - +
22A LYS* 1.3 61.3 + - + +
33A THR* 2.8 27.0 + - - +
34A TYR* 4.2 4.7 - - - -
35A ASP* 3.6 22.7 + - - +
41A THR* 3.6 25.2 + - + +
62A GLN* 3.8 18.4 + - - +
106B C 4.9 3.6 + - - -
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE* 3.9 1.4 - - - +
21A LYS* 1.3 80.9 - - + +
23A VAL* 1.3 66.0 + - - +
24A TRP* 3.7 23.8 - - + -
32A PHE* 3.0 7.6 - - - +
33A THR* 2.9 40.3 + - - +
62A GLN* 4.3 2.5 - - - +
64A LYS* 2.9 42.1 + - - +
104B T 3.5 21.3 - - - -
105B 5IU 3.1 30.4 + - - +
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE* 4.4 0.4 - - + -
22A LYS* 1.3 81.4 - - - +
24A TRP* 1.3 67.9 + - - +
30A ILE* 3.5 30.5 - - + -
31A SER 3.3 9.2 - - - +
32A PHE* 3.9 6.1 - - + -
55A LEU* 4.1 17.3 - - + +
58A MET* 3.6 36.8 - - + -
59A LEU* 3.9 27.7 - - + +
62A GLN* 3.7 13.8 + - - +
63A LYS* 4.8 9.4 + - - -
64A LYS 4.7 4.7 - - - +
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Residues in contact with TRP 24 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LYS* 3.7 33.4 - - + -
23A VAL* 1.3 81.6 - - - +
25A ARG* 1.3 59.3 + - - +
26A VAL* 3.5 15.9 - - + -
30A ILE* 3.7 2.9 - - - -
31A SER* 2.8 61.2 + - - -
32A PHE* 4.0 13.9 - - - -
33A THR* 3.9 27.1 - - + -
43A ARG* 5.8 2.0 - - + -
59A LEU* 3.8 11.2 - - - -
63A LYS* 6.1 1.1 - - + -
103B G 2.9 36.9 + - - +
104B T 3.3 50.2 + - - +
105B 5IU 4.0 13.2 - - - -
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Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TRP* 1.3 72.4 - - - +
26A VAL* 1.3 64.6 + - - +
27A GLY 2.7 47.9 + - - +
28A LYS* 3.9 3.8 - - - +
29A MET 3.5 5.2 - - - +
30A ILE* 3.8 23.7 - - + +
48A GLU* 3.0 31.2 + - - +
56A LEU* 4.5 8.9 - - - +
59A LEU* 3.9 21.9 - - + +
63A LYS* 4.5 16.7 + - - +
103B G 3.7 19.2 - - - +
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TRP* 3.5 10.8 - - + +
25A ARG* 1.3 76.8 - - - +
27A GLY* 1.3 59.4 + - - +
29A MET* 2.8 51.1 + - + +
31A SER* 4.2 4.7 - - - -
102B C 3.3 47.3 - - + +
103B G 3.4 42.4 - - + +
115C G 3.1 13.7 + - - -
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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