Contacts of the strand formed by residues 43 - 47 (chain I) in PDB entry 6ATU
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 LYS 43 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B SER* 5.9 1.3 - - - -
10I SER* 2.9 24.3 + - - -
12I LYS* 2.9 24.8 + - + -
13I PRO 3.8 3.1 - - - +
14I GLY 3.4 25.2 + - - +
15I SER* 4.1 3.4 - - - +
16I CYS* 4.0 17.0 - - - +
35I ASP* 2.8 35.8 + - - +
38I CYS* 4.0 3.4 - - - -
42I LYS* 1.3 77.0 - - - +
44I CYS* 1.3 63.2 + - - +
45I CYS* 3.5 15.4 - - - -
53I CYS* 3.3 2.4 - - - -
54I PHE 2.9 31.6 + - - +
56I PRO* 3.6 27.1 - - + -
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Residues in contact with CYS 44 (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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9I VAL* 4.6 7.5 - - + +
16I CYS* 3.7 5.9 - - - -
32I CYS* 2.1 64.8 - - + -
33I LEU 3.5 10.1 - - - +
34I LYS* 3.5 26.0 - - - +
35I ASP* 2.8 13.6 + - - +
38I CYS* 3.9 3.5 - - - -
43I LYS* 1.3 70.9 - - - +
45I CYS* 1.3 61.8 + - - +
51I MET* 3.8 18.1 - - - +
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Residues in contact with CYS 45 (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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16I CYS* 2.0 57.2 - - + -
17I PRO* 4.2 3.6 - - + +
43I LYS* 3.5 17.9 - - - -
44I CYS* 1.3 76.9 - - - +
46I GLU* 1.3 67.0 + - - +
47I GLY 3.0 0.9 + - - -
51I MET* 3.4 7.6 - - - -
52I ALA 2.9 30.2 + - - +
54I PHE* 3.7 26.6 - - + -
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Residues in contact with GLU 46 (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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17I PRO 4.8 2.8 - - - +
19I ILE* 3.6 17.5 - - - +
22I ARG* 3.0 33.8 + - - +
45I CYS* 1.3 74.3 - - - +
47I GLY* 1.3 65.8 + - - +
50I GLY* 4.4 7.2 - - - +
51I MET* 3.7 22.3 - - - +
54I PHE* 4.8 0.2 - - - -
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Residues in contact with GLY 47 (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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19I ILE* 4.2 9.6 - - - -
22I ARG* 3.5 16.6 + - - -
45I CYS 3.0 6.5 + - - -
46I GLU* 1.3 78.4 - - - +
48I SER* 1.3 65.8 + - - -
49I CYS 3.2 3.8 + - - -
50I GLY 3.2 16.9 + - - -
52I ALA* 5.6 0.2 - - - -
54I PHE* 3.7 24.9 - - - -
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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