Contacts of the strand formed by residues 22 - 33 (chain F) in PDB entry 3BXB
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 HIS 22 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18F THR* 3.2 6.8 - - - +
19F VAL 3.0 42.7 + - - +
20F ASN* 2.9 17.9 + - - +
21F ASN* 1.3 75.6 + - - +
23F HIS* 1.3 66.4 + - - +
24F PHE* 3.7 6.1 - - - -
52F PRO* 3.5 34.6 - - + +
53F PHE* 4.5 6.9 - + + -
133F MET* 3.4 31.6 - - + +
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Residues in contact with HIS 23 (chain F).
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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16F GLU* 2.7 34.8 + - - +
17F GLY* 3.3 25.4 - - - -
18F THR* 4.1 10.2 - - + +
21F ASN 4.0 2.8 + - - -
22F HIS* 1.3 76.9 - - - +
24F PHE* 1.3 72.2 + - - +
25F LYS* 3.7 5.2 - - - -
47F GLU* 3.2 29.8 + - - +
48F GLY* 3.2 22.1 + - - +
51F LEU* 5.2 0.2 - - - +
53F PHE* 6.0 0.2 - - - -
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Residues in contact with PHE 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F MET* 4.1 20.4 - - + -
16F GLU* 3.4 8.3 - - - +
17F GLY 3.0 53.7 + - - +
18F THR* 3.5 4.5 - - - -
19F VAL* 3.9 10.1 - - + -
22F HIS 3.7 10.8 - - - -
23F HIS* 1.3 82.3 - - - +
25F LYS* 1.3 64.2 + - - +
26F CYS* 4.0 14.8 - - - -
45F VAL* 5.0 0.2 - - + -
47F GLU 3.2 15.0 - - - +
51F LEU* 3.6 20.2 - - + -
53F PHE* 3.8 17.7 - + - -
58F LEU* 3.7 37.2 - - + -
121F ILE* 3.9 18.4 - - + -
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Residues in contact with LYS 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F MET 3.2 17.7 - - - +
16F GLU* 3.2 32.1 + - + +
23F HIS* 3.7 0.6 - - - -
24F PHE* 1.3 72.6 - - - +
26F CYS* 1.3 64.4 + - - +
27F THR* 5.5 4.3 - - + -
45F VAL* 3.5 6.1 - - - +
46F VAL* 2.7 45.3 + - + -
47F GLU* 3.0 50.3 + - + +
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Residues in contact with CYS 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LEU* 4.6 0.4 - - - -
14F TYR* 3.8 0.5 - - - -
15F MET* 2.8 46.3 + - + +
24F PHE* 4.0 19.5 - - - -
25F LYS* 1.3 82.4 - - - +
27F THR* 1.3 66.3 + - - +
43F ILE* 4.3 4.3 - - + -
44F LYS 3.2 9.4 - - - +
45F VAL* 4.1 22.2 - - - -
46F VAL* 4.3 0.9 - - - +
51F LEU* 5.6 0.7 - - - -
55F PHE* 4.8 1.1 - - - -
58F LEU* 4.7 5.8 - - - -
62F PHE* 4.2 26.5 - - + -
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Residues in contact with THR 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LEU* 3.4 9.0 - - - -
14F TYR* 4.4 21.3 - - + -
25F LYS* 5.5 4.3 - - + -
26F CYS* 1.3 78.6 - - - +
28F SER* 1.3 64.2 + - - +
42F ARG 4.2 0.2 - - - +
43F ILE* 3.7 1.7 - - - +
44F LYS* 3.0 41.9 + - - +
46F VAL* 4.0 25.2 - - + +
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Residues in contact with SER 28 (chain F).
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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11F MET 4.6 0.2 - - - -
12F LYS* 3.4 4.2 - - - +
13F LEU* 2.8 54.1 + - - +
27F THR* 1.3 77.9 - - - +
29F GLU* 1.3 66.2 + - - +
41F MET* 2.8 34.5 - - - +
42F ARG 3.3 12.9 + - - -
43F ILE* 3.5 15.1 - - - +
62F PHE* 4.5 0.7 - - - -
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Residues in contact with GLU 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F MET 3.4 5.3 - - - +
12F LYS* 3.5 27.2 + - - +
28F SER* 1.3 79.7 - - - +
30F GLY* 1.3 57.5 + - - +
41F MET* 3.4 2.6 - - - -
42F ARG* 2.7 56.8 + - + +
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Residues in contact with GLY 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F HIS* 3.3 8.8 + - - +
11F MET* 2.9 39.1 + - - +
29F GLU* 1.3 78.0 - - - +
31F GLU* 1.3 70.3 + - - +
40F THR 3.1 14.8 - - - -
41F MET* 4.1 2.7 - - - +
42F ARG* 4.1 4.2 - - - +
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Residues in contact with GLU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F MET 3.0 15.5 - - - +
10F HIS* 3.7 22.3 + - + +
11F MET* 3.6 8.2 - - - +
30F GLY* 1.3 73.9 - - - +
32F GLY* 1.3 61.8 + - - +
40F THR* 3.0 36.8 + - - +
42F ARG* 2.6 42.3 + - - -
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Residues in contact with GLY 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ASN* 3.4 8.8 - - - +
9F MET 2.9 27.7 + - - -
31F GLU* 1.3 78.8 - - - +
33F LYS* 1.3 67.6 + - - +
38F THR 3.5 11.9 - - - -
39F GLN* 4.0 2.2 - - - -
69F PHE* 3.5 15.7 - - - -
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Residues in contact with LYS 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F GLU* 3.4 15.0 - - + +
8F ASN* 3.1 20.7 + - - +
32F GLY* 1.3 76.4 - - - +
34F PRO* 1.3 63.4 - - - +
35F TYR 3.1 2.8 + - - +
36F GLU* 3.1 40.8 + - + +
37F GLY 2.9 26.5 + - - -
38F THR* 3.0 28.6 + - - +
69F PHE* 4.1 0.2 - - - -
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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