Contacts of the strand formed by residues 18 - 24 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C ALA* 3.8 25.4 - - + -
17C ARG* 1.3 73.7 - - - +
19C ILE* 1.3 68.7 + - - +
20C ARG* 3.3 35.3 + - + +
34C VAL* 3.5 1.6 - - - -
35C TYR* 2.7 47.9 + - + +
37C GLY* 3.8 19.3 - - - -
64C SO4 5.3 1.3 - - - +
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Residues in contact with ILE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ARG 3.8 6.0 + - - +
18C ILE* 1.3 74.6 - - - +
20C ARG* 1.3 79.2 + - - +
21C TYR* 4.1 20.0 - - + +
32C ALA* 4.3 12.1 - - + -
33C PHE 3.5 7.6 - - - +
34C VAL* 4.8 10.5 - - + +
46C ALA 4.7 6.8 - - - +
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Residues in contact with ARG 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 3.3 23.0 + - + +
19C ILE* 1.3 79.9 + - - +
21C TYR* 1.3 68.9 + - - +
32C ALA* 3.3 6.1 - - - +
33C PHE* 2.9 47.6 + - + +
35C TYR* 3.6 31.8 - - + -
44C ASN* 2.8 43.7 + - - +
45C PHE 3.4 17.4 - - - +
46C ALA* 4.3 7.8 - - - +
64C SO4 2.9 44.1 + - - -
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Residues in contact with TYR 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 4.1 19.2 - - + +
20C ARG* 1.3 74.7 - - - +
22C PHE* 1.3 61.2 + - - +
30C ALA* 4.5 2.0 - - + -
31C GLN* 3.2 23.3 - - - -
32C ALA* 3.7 22.2 - - + +
33C PHE* 3.8 2.7 - - - -
44C ASN* 3.4 4.9 - - - -
45C PHE* 2.8 34.6 + - - +
46C ALA 4.0 8.1 - - - -
47C SER* 3.7 26.9 - - - +
48C ALA* 3.5 39.3 - - + +
51C ALA* 4.4 5.4 - - + -
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Residues in contact with PHE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C GLU 4.8 1.1 - - - -
9C PRO* 3.7 48.7 - - + -
21C TYR* 1.3 73.5 - - - +
23C TYR* 1.3 71.5 + - - +
24C ASN* 3.7 22.4 - - + -
30C ALA* 3.2 3.5 - - - -
31C GLN* 2.9 85.6 + - + -
32C ALA 4.1 8.5 - - - -
33C PHE* 3.9 9.0 - + + -
43C ASN* 3.4 29.6 - - - +
51C ALA* 4.2 5.6 - - - -
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Residues in contact with TYR 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ARG* 3.2 38.7 + - - -
5C CYS* 3.4 21.4 - - + +
7C GLU 4.6 0.9 - - - +
22C PHE* 1.3 75.4 - - - +
24C ASN* 1.3 57.6 + - - +
25C ALA* 3.4 22.9 + - + -
28C GLY* 3.3 35.3 - - - -
29C ALA 3.7 8.3 - - - -
30C ALA* 4.4 1.8 - - - +
43C ASN* 2.8 31.7 + - - +
51C ALA* 4.0 14.8 - - + +
52C LEU* 4.1 19.1 - - + -
55C CYS* 3.3 47.1 + - + -
56C ALA* 5.5 0.8 - - - -
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Residues in contact with ASN 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C PHE* 3.7 14.2 + - + -
23C TYR* 1.3 70.5 - - - +
25C ALA* 1.3 59.6 + - - +
26C ALA* 3.2 21.4 + - - +
27C ALA* 3.3 18.9 + - + +
28C GLY* 2.8 23.7 + - - -
29C ALA 2.7 18.8 + - - +
31C GLN* 2.8 36.2 + - + +
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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