Contacts of the strand formed by residues 50 - 54 (chain F) 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 GLY 50 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F ARG* 6.1 0.2 - - - +
28F PRO* 3.6 18.6 - - - +
29F PRO 3.2 15.3 - - - -
30F ASN* 3.8 4.0 - - - -
46F GLU* 4.4 6.6 + - - -
47F GLY* 2.9 28.7 + - - -
49F CYS* 1.3 75.8 - - - +
51F MET* 1.3 65.5 + - - -
52F ALA* 4.7 1.6 - - - +
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Residues in contact with MET 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F PRO* 3.6 42.6 - - - -
29F PRO 4.6 0.2 - - - +
30F ASN* 2.9 31.2 + - - +
31F ARG* 3.0 26.3 + - - +
32F CYS* 3.5 13.2 - - - +
33F LEU* 3.5 29.4 - - + +
44F CYS* 3.7 11.9 - - - -
45F CYS 3.2 15.0 - - - +
46F GLU* 3.8 21.3 + - - +
50F GLY* 1.3 75.4 - - - -
52F ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ARG* 3.8 23.3 - - - -
32F CYS* 3.5 9.9 - - - -
43F LYS 3.4 0.5 - - - +
44F CYS* 3.4 1.9 - - - -
45F CYS 2.8 33.0 + - - +
47F GLY* 5.5 1.1 - - - -
50F GLY 3.8 3.3 + - - +
51F MET* 1.3 76.6 - - - +
53F CYS* 1.3 61.8 + - - +
54F PHE* 3.5 21.5 - - + -
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Residues in contact with CYS 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ARG* 5.1 6.0 - - - +
32F CYS* 3.9 11.7 - - - -
37F ASP 4.6 2.5 - - - -
38F CYS* 2.1 52.3 - - + -
39F PRO* 4.2 6.5 - - + -
42F LYS* 4.3 16.9 + - + +
43F LYS 3.3 5.2 - - - -
52F ALA* 1.3 77.1 - - - +
54F PHE* 1.3 68.1 + - - +
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Residues in contact with PHE 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F PRO* 4.0 25.6 - - + -
19F ILE* 4.2 24.2 - - + -
42F LYS* 3.2 8.6 - - - +
43F LYS* 2.9 31.7 + - - +
45F CYS* 3.6 29.4 - - + -
46F GLU 4.3 4.3 - - - -
47F GLY* 4.3 15.0 - - - -
48F SER 5.6 0.2 - - - -
52F ALA* 3.5 34.1 - - + -
53F CYS* 1.3 79.0 - - - +
55F VAL* 1.3 70.7 + - - +
56F PRO* 3.4 0.9 - - - +
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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