Contacts of the strand formed by residues 18 - 24 (chain G) in PDB entry 3AUH
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 ILE 18 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ALA* 5.3 13.2 - - + -
16G ALA* 3.8 14.6 - - + -
17G ARG* 1.3 76.1 - - - +
19G ILE* 1.3 68.9 + - - +
20G ARG* 3.4 33.8 + - + +
34G VAL* 3.5 4.0 - - - +
35G TYR* 2.7 47.6 + - + +
37G GLY* 3.8 28.7 - - - -
64G SO4 5.8 0.4 - - - +
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Residues in contact with ILE 19 (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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46A ALA* 6.0 1.2 - - - +
47A SER* 6.0 6.5 - - - -
19E ILE* 3.9 35.2 - - + -
32E ALA* 4.2 16.2 - - + +
33E PHE* 4.4 11.4 - - - +
34E VAL* 3.8 27.8 - - + -
17G ARG 4.0 1.2 + - - -
18G ILE* 1.3 74.7 - - - +
20G ARG* 1.3 73.9 + - - +
21G TYR* 3.8 31.6 - - + +
32G ALA* 4.2 6.1 - - + -
33G PHE 3.5 6.5 - - - +
34G VAL* 4.3 2.0 - - + -
46G ALA 4.8 5.7 - - - +
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Residues in contact with ARG 20 (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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18G ILE* 3.4 22.1 + - + +
19G ILE* 1.3 79.6 - - - +
21G TYR* 1.3 68.5 - - - +
32G ALA* 3.3 6.4 - - - +
33G PHE* 2.8 46.2 + - + -
35G TYR* 3.5 33.4 - - + -
44G ASN* 3.0 29.6 + - - +
45G PHE 3.5 17.5 - - - +
46G ALA* 4.3 8.7 - - - +
64G SO4 2.9 42.8 + - - -
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Residues in contact with TYR 21 (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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21E TYR* 5.3 4.0 - + - -
32E ALA* 4.1 19.9 + - - +
19G ILE* 3.8 20.8 - - + +
20G ARG* 1.3 77.4 - - - +
22G PHE* 1.3 61.7 + - - +
30G ALA 4.7 1.3 - - - -
31G GLN* 3.3 10.8 - - - +
32G ALA* 3.7 26.2 - - + +
33G PHE* 3.7 2.9 - - - -
44G ASN* 3.5 5.0 - - - -
45G PHE* 2.8 36.2 + - - +
46G ALA 3.8 13.2 - - - -
47G SER* 3.6 31.4 - - - +
48G ALA* 3.5 31.6 - - + +
51G ALA* 4.4 5.2 - - + -
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Residues in contact with PHE 22 (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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7G GLU 4.2 4.0 - - - -
8G PRO* 5.0 1.1 - - + -
9G PRO* 3.7 45.8 - - + -
21G TYR* 1.3 73.4 - - - +
23G TYR* 1.3 70.8 + - - +
24G ASN* 3.6 24.4 + - + -
30G ALA* 3.4 1.9 - - - -
31G GLN* 2.8 80.3 + - + -
32G ALA 4.5 5.8 - - - -
33G PHE* 3.8 11.2 - + + -
43G ASN* 3.3 34.3 - - + +
45G PHE* 4.7 0.4 - - - -
51G ALA* 4.2 5.4 - - - -
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Residues in contact with TYR 23 (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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1G ARG* 3.6 33.0 + - - -
5G CYS 3.2 13.6 - - - +
7G GLU 4.4 1.2 - - - +
22G PHE* 1.3 75.0 - - - +
24G ASN* 1.3 57.3 + - - +
25G ALA* 3.4 27.2 + - + -
28G GLY* 3.5 22.9 + - - -
29G ALA 3.8 23.1 - - - -
30G ALA* 4.2 2.2 - - - +
43G ASN* 2.9 29.8 + - - +
51G ALA* 4.2 11.0 - - + +
52G LEU* 3.9 23.8 - - + -
55G CYS* 3.4 43.5 - - + -
56G ALA* 4.0 13.1 + - + +
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Residues in contact with ASN 24 (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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22G PHE* 3.6 15.8 + - + -
23G TYR* 1.3 71.8 - - - +
25G ALA* 1.3 58.3 + - - +
26G ALA* 3.1 13.1 + - - +
27G ALA* 3.0 26.5 + - + +
28G GLY* 2.8 23.9 + - - -
29G ALA 2.8 23.5 + - - +
31G GLN* 2.9 36.6 + - - +
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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