Contacts of the strand formed by residues 43 - 47 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11P THR* 4.2 7.5 - - - +
12P LYS* 2.9 25.1 + - + -
13P PRO 3.6 16.2 - - - +
14P GLY 3.3 25.5 + - - +
15P SER 4.1 3.1 - - - +
16P CYS* 4.0 18.4 - - - +
35P ASP* 2.7 39.1 + - - +
38P CYS* 3.9 3.6 - - - -
41P ILE 4.2 5.2 - - - +
42P LYS* 1.3 76.2 - - - +
44P CYS* 1.3 61.2 + - - +
45P CYS* 3.7 13.9 - - - -
52P ALA 3.5 1.2 - - - +
53P CYS* 3.2 4.9 - - - -
54P PHE 2.8 32.9 + - - +
56P PRO* 4.1 12.1 - - + -
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Residues in contact with CYS 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P CYS* 3.6 9.7 - - - -
32P CYS* 2.1 64.4 - - - -
33P LEU 3.6 9.9 - - - +
34P LYS* 3.6 26.0 - - - +
35P ASP* 2.8 13.5 + - - +
38P CYS* 4.2 0.7 - - - -
43P LYS* 1.3 69.5 - - - +
45P CYS* 1.3 59.8 + - - +
51P MET* 3.7 19.7 - - + +
52P ALA 3.6 0.2 - - - -
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Residues in contact with CYS 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P CYS* 2.1 57.2 - - + -
17P PRO* 4.1 13.2 - - - +
43P LYS* 3.7 17.7 - - - -
44P CYS* 1.3 75.0 - - - +
46P GLU* 1.3 66.9 + - - +
51P MET* 3.2 8.7 - - - -
52P ALA 3.0 30.1 + - - +
54P PHE* 3.7 19.1 - - + -
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Residues in contact with GLU 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P PRO 4.5 1.6 - - - +
19P ILE* 3.5 26.7 + - + +
22P ARG* 3.6 43.3 + - - +
28P PRO* 4.8 6.8 - - - +
30P ASN* 4.8 1.0 - - - +
45P CYS* 1.3 73.1 - - - +
47P GLY* 1.3 60.2 + - - +
50P GLY* 3.8 10.6 + - - -
51P MET* 3.8 29.8 + - - +
54P PHE* 4.1 0.6 - - - -
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Residues in contact with GLY 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19P ILE* 4.2 7.4 - - - -
22P ARG* 3.8 17.5 - - - +
45P CYS 3.3 1.2 + - - -
46P GLU* 1.3 79.2 - - - +
48P SER* 1.3 64.5 + - - -
49P CYS 3.2 3.2 + - - -
50P GLY 3.0 23.6 + - - +
52P ALA* 5.0 2.0 - - - -
54P PHE* 4.1 20.6 - - - -
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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