Contacts of the strand formed by residues 28 - 33 (chain G) in PDB entry 3BSU
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 PHE 28 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G HIS 4.4 10.1 - - - -
27G MET* 1.3 75.1 - - - +
29G TYR* 1.3 63.0 + - - +
30G ALA 3.5 1.6 + - - -
39G VAL* 3.7 21.8 - - + -
40G PHE 3.6 2.2 - - - -
41G LEU* 3.4 30.3 - - + -
60G LYS* 3.1 4.7 - - - -
61G PHE* 2.8 34.2 + - - +
62G ALA 3.3 27.1 - - - -
63G THR* 3.6 9.4 - - - -
64G GLU* 3.7 33.7 - - + -
67G ALA* 3.8 10.1 - - + -
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Residues in contact with TYR 29 (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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27G MET* 3.8 19.4 + - + +
28G PHE* 1.3 73.4 - - - +
30G ALA* 1.3 62.8 + - - +
31G VAL 3.9 0.2 - - - -
39G VAL* 3.4 2.5 - - - -
40G PHE* 2.6 54.4 + - + +
41G LEU 4.0 2.2 - - - -
42G THR* 3.7 14.8 - - - -
43G TRP* 3.6 48.9 + + - +
46G CYS* 3.6 26.5 - - + -
58G PHE* 5.9 0.4 - + - -
59G LYS 4.1 2.9 - - - -
60G LYS* 4.2 23.9 - - + +
5J C 3.5 28.0 + - - -
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Residues in contact with ALA 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G PHE 3.5 1.6 + - - -
29G TYR* 1.3 71.6 - - - +
31G VAL* 1.3 61.0 + - - +
32G ARG 3.9 0.7 - - - -
38G GLY 3.6 4.9 - - - -
39G VAL* 4.5 2.0 - - - +
58G PHE* 3.1 5.9 - - - +
59G LYS 3.0 40.6 + - - +
61G PHE* 4.0 0.9 - - + -
67G ALA* 3.2 42.4 - - + +
70G PHE* 3.8 15.7 - - + -
71G VAL* 3.9 2.9 - - + -
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Residues in contact with VAL 31 (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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30G ALA* 1.3 71.2 - - - +
32G ARG* 1.3 60.2 + - - +
33G ARG 3.7 27.4 - - - +
34G GLY* 3.8 2.7 - - - +
36G LYS 3.6 17.0 - - - +
37G THR* 3.1 20.4 - - - -
38G GLY 2.9 14.8 + - - +
40G PHE* 3.7 27.6 - - + -
46G CYS* 3.5 32.1 - - - -
49G GLN* 4.3 5.2 - - + -
50G VAL* 3.9 17.3 - - + -
57G ARG 3.6 2.7 - - - +
58G PHE* 3.9 0.9 - - + -
71G VAL* 3.9 5.4 - - - +
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Residues in contact with ARG 32 (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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30G ALA 3.9 2.6 + - - -
31G VAL* 1.3 73.0 - - - +
33G ARG* 1.3 73.3 + - + +
37G THR* 3.4 13.6 - - - +
57G ARG* 2.6 67.8 + - + +
70G PHE* 2.9 49.9 + - + +
71G VAL* 3.6 22.7 - - - +
73G LYS* 3.3 39.4 - - - +
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Residues in contact with ARG 33 (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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31G VAL* 3.7 8.3 - - - +
32G ARG* 1.3 95.8 - - + +
34G GLY* 1.3 57.8 + - - +
37G THR* 4.2 0.9 - - - -
50G VAL* 4.1 0.9 - - - +
53G PHE* 4.0 7.9 - - + -
54G PRO 5.6 0.4 - - - -
55G ALA* 2.7 41.2 + - - +
56G ALA* 3.3 10.6 + - - +
57G ARG* 3.0 54.3 + - + +
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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