Contacts of the strand formed by residues 29 - 35 (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 ALA 29 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C TYR* 3.7 3.5 - - - -
24C ASN* 2.7 36.9 + - - +
27C ALA* 3.2 16.7 - - + +
28C GLY* 1.3 79.8 - - - +
30C ALA* 1.3 60.6 + - - +
31C GLN* 4.8 5.8 - - + -
52C LEU* 4.0 9.6 - - - -
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Residues in contact with ALA 30 (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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21C TYR* 4.5 5.9 - - + -
22C PHE 3.2 11.0 - - - +
23C TYR* 4.4 0.9 - - - +
29C ALA* 1.3 75.2 - - - +
31C GLN* 1.3 64.6 + - - +
48C ALA* 3.5 39.7 - - + +
51C ALA* 3.9 13.7 - - + -
52C LEU* 3.7 15.6 - - + +
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Residues in contact with GLN 31 (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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21C TYR* 3.2 9.3 - - - -
22C PHE* 2.9 56.6 + - + -
24C ASN* 2.8 41.3 + - - +
27C ALA* 5.5 2.6 - - - +
29C ALA* 4.1 9.2 + - + +
30C ALA* 1.3 81.0 - - - +
32C ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 32 (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* 4.3 10.8 - - + -
20C ARG 3.3 8.1 - - - +
21C TYR* 3.7 23.8 - - + +
22C PHE* 4.1 6.3 - - - -
31C GLN* 1.3 77.5 - - - +
33C PHE* 1.3 64.7 - - - +
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Residues in contact with PHE 33 (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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9C PRO* 3.8 20.6 - - + -
10C TYR 3.5 28.3 - - - -
11C ALA* 4.1 6.1 - - + -
19C ILE* 3.5 5.1 - - - +
20C ARG* 2.9 54.3 + - + -
21C TYR 3.8 15.7 - - - -
22C PHE* 3.9 24.2 - + + -
32C ALA* 1.3 75.7 - - - +
34C VAL* 1.3 72.9 + - - +
35C TYR* 4.0 13.5 - - + -
43C ASN 4.1 4.3 - - - -
44C ASN* 3.7 28.0 - - + -
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Residues in contact with VAL 34 (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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11C ALA* 3.3 24.4 - - - +
16C ALA 4.5 2.2 - - - +
17C ARG* 3.5 40.4 - - + +
18C ILE 3.5 3.1 - - - +
19C ILE* 5.0 10.3 - - + -
33C PHE* 1.3 78.8 - - - +
35C TYR* 1.3 62.6 + - - +
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Residues in contact with TYR 35 (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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10C TYR 3.9 7.4 - - - -
11C ALA 3.4 9.9 - - - -
12C GLY* 5.5 0.2 - - - -
16C ALA 3.5 4.3 - - - +
18C ILE* 2.7 47.4 + - + +
20C ARG* 3.6 32.5 - - + -
33C PHE* 3.8 10.9 + - + -
34C VAL* 1.3 72.5 - - - +
36C GLY* 1.3 66.4 - - - +
37C GLY* 3.2 28.5 + - - -
38C VAL 3.2 29.0 + - - -
39C ARG 3.6 0.2 + - - -
40C ALA* 3.1 33.3 + - + +
44C ASN* 3.7 9.9 - - - -
64C SO4 2.6 40.7 + - - -
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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