Contacts of the strand formed by residues 31 - 34 (chain A) in PDB entry 3ADB
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 VAL 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA* 3.7 28.7 - - + +
24A LEU* 3.9 19.7 - - + -
25A SER 4.5 0.2 - - - +
29A ILE* 3.4 7.4 + - + +
30A ASP* 1.3 74.6 - - - +
32A ILE* 1.3 73.3 + - - +
69A TYR* 4.4 1.1 - - - -
70A TRP* 3.4 24.2 - - + +
72A ILE* 3.8 28.5 - - + -
43B PHE* 3.7 8.5 - - - -
44B PRO* 2.9 36.2 - - + +
50B TYR* 4.7 2.2 + - - -
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Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 1.3 77.2 - - - +
33A VAL* 1.3 68.2 + - - +
34A LEU* 4.0 18.8 + - + -
65A ALA* 4.1 11.9 - - + -
69A TYR* 4.4 6.7 - - + -
70A TRP 3.0 16.2 + - - +
71A VAL* 3.5 15.2 - - + -
72A ILE* 2.9 24.1 + - - -
39B ILE* 4.1 4.9 - - + +
42B SER* 3.5 31.2 - - - +
43B PHE* 3.6 35.4 - - + +
53B PHE* 4.1 15.7 - - + -
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 3.7 30.7 - - - +
18A LYS* 4.9 11.0 - - + +
21A ALA* 4.0 26.0 - - + -
32A ILE* 1.3 76.9 - - - +
34A LEU* 1.3 61.1 + - - +
38A LEU* 4.2 3.6 - - - +
72A ILE* 3.4 21.8 - - + +
74A ASP* 3.8 15.9 - - + +
42B SER* 3.0 40.1 + - - +
44B PRO* 6.4 0.2 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 4.0 27.7 + - + -
33A VAL* 1.3 84.1 - - - +
35A GLY* 1.3 58.6 + - - +
38A LEU* 3.7 19.7 - - + -
58A THR* 5.4 1.3 - - + +
61A LEU* 3.6 29.6 - - + +
62A ILE* 3.6 46.0 - - + +
65A ALA* 4.0 13.7 - - + -
71A VAL* 4.4 5.8 - - + -
72A ILE 3.0 6.1 + - - -
73A VAL* 3.2 10.7 - - - +
74A ASP* 2.7 27.6 + - - -
39B ILE* 5.5 3.6 - - + -
42B SER* 4.2 3.1 - - - +
53B PHE* 5.6 0.4 - - + -
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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