Contacts of the strand formed by residues 43 - 46 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10G SER* 2.9 21.9 + - - -
12G LYS* 2.8 28.5 + - + -
13G PRO 3.7 15.5 - - - +
14G GLY 3.4 20.6 + - - +
15G SER* 4.3 3.1 - - - +
16G CYS* 4.1 19.3 - - - +
35G ASP* 2.8 34.2 + - - +
38G CYS* 3.8 5.2 - - - -
41G ILE 4.3 0.2 - - - +
42G LYS* 1.3 76.6 - - - +
44G CYS* 1.3 60.8 + - - +
45G CYS* 3.5 13.8 + - - -
52G ALA 3.4 3.1 - - - +
53G CYS* 3.4 1.2 - - - -
54G PHE 2.9 32.1 + - - +
56G PRO* 3.7 19.3 - - + -
20R LEU 4.2 2.9 + - - -
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Residues in contact with CYS 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL 5.4 1.8 + - - +
16G CYS* 3.9 4.2 - - - -
32G CYS* 2.1 64.8 - - + -
33G LEU* 3.4 13.5 - - - +
34G LYS 3.5 21.8 - - - +
35G ASP* 2.7 17.5 + - - +
38G CYS* 3.8 2.5 - - - -
43G LYS* 1.3 69.8 - - - +
45G CYS* 1.3 62.8 + - - +
51G MET* 3.8 13.1 - - - +
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Residues in contact with CYS 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G CYS* 2.1 57.0 - - + -
17G PRO* 4.1 8.7 - - + -
43G LYS* 3.7 19.7 - - - -
44G CYS* 1.3 76.1 - - - +
46G GLU* 1.3 69.6 + - - +
47G GLY* 3.2 0.7 + - - -
51G MET* 3.3 7.2 - - - -
52G ALA* 2.9 31.0 + - - +
54G PHE* 4.0 18.0 - - + -
56G PRO* 6.5 0.4 - - - -
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Residues in contact with GLU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G CYS* 5.2 0.6 - - - +
17G PRO* 4.7 4.3 - - - +
19G ILE* 3.7 15.4 - - - +
22G ARG* 5.5 9.4 - - - -
28G PRO* 5.0 4.2 - - - +
30G ASN* 5.0 0.3 - - - +
45G CYS* 1.3 78.3 - - - +
47G GLY* 1.3 65.1 + - - +
50G GLY* 3.5 31.2 + - - -
51G MET* 3.1 32.5 - - + +
54G PHE* 4.5 1.0 - - - -
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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