Contacts of the strand formed by residues 51 - 56 (chain I) in PDB entry 1ACB
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 ARG 51 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I ASP* 3.3 12.1 - - + +
35I TYR* 3.9 23.1 - - + -
44I THR* 4.1 0.6 + - - -
46I ASP* 2.8 61.2 + - - -
48I ARG* 3.3 25.5 + - + +
49I TYR 3.4 0.2 - - - -
50I ASN* 1.3 78.4 - - - +
52I VAL* 1.3 77.7 + - - +
53I ARG* 3.0 38.7 - - + +
69I VAL* 3.1 2.6 - - - +
70I GLY* 2.7 52.5 + - - +
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Residues in contact with VAL 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I PHE* 4.0 11.9 - - + -
25I PHE* 4.1 18.2 - - + -
32I TYR* 4.0 16.4 - - + -
33I ASP 2.8 9.5 + - - +
34I VAL* 3.3 16.0 - - + +
35I TYR* 3.0 24.9 + - - +
51I ARG* 1.3 84.0 - - - +
53I ARG* 1.3 62.2 + - - +
54I VAL* 4.1 4.5 - - + -
67I PRO* 4.0 25.6 - - + -
68I HIS 4.0 7.2 - - - +
69I VAL* 3.5 24.9 - - + -
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Residues in contact with ARG 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E MET* 3.8 13.6 - - - +
35I TYR* 3.4 8.9 - - + -
37I LEU* 4.2 12.0 - - + +
43I VAL* 3.5 27.8 - - - +
44I THR* 2.9 47.7 + - - +
51I ARG* 3.0 41.7 - - - +
52I VAL* 1.3 74.3 - - - +
54I VAL* 1.3 61.5 + - - +
55I PHE* 3.8 36.4 - - + -
67I PRO* 3.9 16.3 - - - +
68I HIS 4.1 8.9 + - - +
70I GLY 4.1 16.7 + - - +
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Residues in contact with VAL 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I VAL* 4.7 2.2 - - + -
25I PHE* 4.0 25.6 - - + -
34I VAL* 4.0 15.7 - - + -
35I TYR 2.6 10.1 + - - +
36I PHE* 3.3 31.8 - - + -
37I LEU 2.7 32.4 + - - +
52I VAL* 4.1 3.1 - - + -
53I ARG* 1.3 73.5 - - - +
55I PHE* 1.3 59.7 + - - +
56I TYR* 3.9 1.8 + - - +
63I VAL* 3.8 31.0 - - + -
67I PRO* 4.0 17.3 - - + -
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Residues in contact with PHE 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E TYR* 5.1 15.3 - + - -
218E SER* 2.8 40.2 - - - -
37I LEU* 2.9 34.3 - - + -
38I PRO 3.8 11.0 - - - -
39I GLU* 4.4 9.0 - - - -
40I GLY 5.1 0.2 - - - -
41I SER 4.6 1.6 - - - -
43I VAL* 4.1 11.4 - - + -
53I ARG* 3.8 39.0 + - + -
54I VAL* 1.3 71.5 - - - +
56I TYR* 1.3 60.9 + - - +
63I VAL* 4.0 5.4 - - - +
64I ASN 3.9 7.6 + - - -
65I HIS* 3.3 41.7 + - + +
67I PRO* 5.7 1.5 - - + +
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Residues in contact with TYR 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I VAL* 3.5 29.4 - - + -
36I PHE* 3.6 16.0 + + + -
37I LEU* 2.9 37.9 + - - -
38I PRO* 3.7 21.6 - - + +
39I GLU* 2.9 29.4 + - - +
54I VAL 4.1 2.7 - - - -
55I PHE* 1.3 75.9 - - - +
57I ASN* 1.3 70.6 + - - +
58I PRO* 3.4 21.0 - - + +
61I ASN* 4.1 11.7 - - - -
62I VAL 3.3 20.4 - - - +
63I VAL* 4.0 7.6 - - + +
64I ASN* 4.3 2.5 - - - +
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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
------------------------------------------------------------
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