Contacts of the strand formed by residues 19 - 26 (chain A) in PDB entry 4BC4
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 GLN 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASP 3.7 0.5 - - - +
16A SER* 2.9 46.8 + - - +
18A GLN* 1.3 85.9 - - + +
20A VAL* 1.3 56.7 + - - +
21A LYS* 3.5 32.2 - - + +
36A SER* 3.4 14.9 - - - -
37A VAL 3.1 16.2 - - - +
38A HIS* 3.3 30.6 + - + -
39A PHE* 3.3 13.8 - - - -
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Residues in contact with VAL 20 (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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13A TRP* 4.1 20.2 - - + -
14A ASP 3.4 7.6 - - - +
15A PHE* 3.9 47.3 - - + -
19A GLN* 1.3 72.5 - - - +
21A LYS* 1.3 62.3 + - - +
36A SER* 3.3 3.8 - - - -
37A VAL* 2.9 34.8 + - + +
39A PHE* 3.8 13.2 - - + -
68A TRP* 4.6 2.2 - - - +
71A ALA* 3.8 30.1 - - + +
72A LEU* 5.2 1.3 - - - -
75A ILE* 3.6 12.7 - - + +
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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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13A TRP* 3.4 6.6 - - - -
14A ASP* 2.8 45.7 + - + +
19A GLN* 3.5 33.1 - - + +
20A VAL* 1.3 76.1 - - - +
22A VAL* 1.3 67.7 + - - +
23A VAL* 5.1 1.1 - - + -
34A GLU* 5.7 3.1 - - + -
35A GLU 3.4 14.1 - - - +
36A SER* 4.2 7.0 - - - -
75A ILE* 4.3 2.0 - - - -
466A ALA* 3.0 19.4 + - - +
467A ASN* 2.9 33.9 + - - +
470A CYS* 3.8 19.9 - - - -
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Residues in contact with VAL 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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11A LEU* 4.1 15.3 - - + -
12A GLY 3.3 11.2 - - - +
13A TRP* 3.6 35.9 - - + -
21A LYS* 1.3 77.5 - - - +
23A VAL* 1.3 78.5 + - - +
33A TYR* 4.6 3.6 - - + -
34A GLU* 3.3 4.2 - - - +
35A GLU* 3.0 48.2 + - + +
75A ILE* 3.8 13.7 - - + -
79A MSE 4.0 21.5 - - + -
470A CYS* 4.3 1.1 - - - -
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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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10A CYS 3.9 0.3 - - - +
11A LEU* 3.4 4.4 - - - -
12A GLY 2.9 33.2 + - - +
21A LYS* 5.1 1.1 - - + -
22A VAL* 1.3 82.2 - - - +
24A ALA* 1.3 59.7 + - - +
25A VAL* 3.9 20.0 - - + -
31A VAL* 4.2 12.1 - - + -
33A TYR* 3.2 13.7 - - - +
34A GLU* 4.2 10.8 - - + -
467A ASN* 4.3 20.2 - - + +
470A CYS* 3.7 44.2 - - + +
471A VAL* 4.0 5.8 - - + +
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Residues in contact with ALA 24 (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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9A CYS* 4.4 1.8 - - - -
10A CYS 3.5 4.9 - - - +
11A LEU* 3.8 6.3 - - + -
23A VAL* 1.3 73.2 - - - +
25A VAL* 1.3 60.1 + - - +
31A VAL* 3.6 4.7 - - - +
32A PHE* 3.1 50.1 + - + -
33A TYR* 2.9 18.0 + - + +
84A PHE* 3.6 28.7 - - + -
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Residues in contact with VAL 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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9A CYS* 3.1 2.1 - - - +
10A CYS 2.9 31.2 + - - +
23A VAL* 3.9 9.4 - - + -
24A ALA* 1.3 77.0 - - - +
26A ASP* 1.4 72.7 + - - +
29A LEU* 3.6 31.0 - - + +
30A ASN 3.4 4.3 - - - +
31A VAL* 3.8 22.7 - - + -
32A PHE* 3.8 2.7 - - - -
471A VAL* 5.0 5.8 - - + -
474A ALA* 3.4 30.3 - - + -
475A TYR* 4.6 6.7 - - + -
478A PHE* 3.3 11.1 - - + -
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Residues in contact with ASP 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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7A ARG* 4.1 27.1 + - + +
8A ARG 3.5 12.8 - - - +
25A VAL* 1.4 76.4 - - - +
27A ALA* 1.3 59.3 + - - +
28A GLU* 3.1 19.7 + - - +
29A LEU* 2.8 20.8 + - - -
30A ASN* 2.9 51.5 + - - +
32A PHE* 3.6 16.8 - - + +
478A PHE* 3.4 9.9 - - - -
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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