Contacts of the strand formed by residues 28 - 33 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H HIS* 4.2 15.5 - - + -
27H MET* 1.3 74.5 - - - +
29H TYR* 1.3 63.2 + - - +
30H ALA 3.5 2.3 + - - -
39H VAL* 3.5 14.4 - - + -
40H PHE 3.8 2.7 - - - -
41H LEU* 3.7 24.0 - - + -
60H LYS* 3.4 1.7 - - - -
61H PHE* 2.9 42.1 + - - +
62H ALA 3.6 15.3 - - - -
63H THR* 3.3 9.0 - - - -
64H GLU* 3.3 53.8 - - + -
67H ALA* 3.8 10.4 - - + +
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Residues in contact with TYR 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H MET* 3.6 22.6 - - + +
28H PHE* 1.3 71.6 - - - +
30H ALA* 1.3 62.6 + - - +
31H VAL* 3.7 0.5 + - - +
38H GLY 3.6 2.1 - - - +
39H VAL* 3.4 3.7 - - - +
40H PHE* 2.8 48.0 + - - +
41H LEU 4.1 1.6 - - - -
42H THR* 3.9 19.7 - - - -
43H TRP* 3.8 37.2 + + - +
46H CYS* 3.6 26.9 - - + -
59H LYS 3.9 5.2 - - - +
60H LYS* 3.9 24.4 + - + +
11J T 3.7 23.1 - - - -
12J C 2.8 19.3 + - - -
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Residues in contact with ALA 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H PHE 3.5 2.0 + - - -
29H TYR* 1.3 72.9 - - - +
31H VAL* 1.3 59.9 + - - +
32H ARG 4.1 0.4 - - - -
38H GLY 3.8 2.0 - - - -
39H VAL* 4.2 2.7 - - - -
58H PHE* 3.5 2.9 - - - +
59H LYS 2.9 37.9 + - - +
61H PHE* 4.0 6.7 - - + -
67H ALA* 3.1 41.3 - - + +
70H PHE* 4.0 7.6 - - + -
71H VAL* 3.4 12.8 - - + -
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Residues in contact with VAL 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H TYR 3.9 1.3 - - - +
30H ALA* 1.3 75.5 - - - +
32H ARG* 1.3 57.2 + - - +
33H ARG 4.0 15.7 - - - +
34H GLY 4.1 0.9 - - - +
36H LYS 3.4 19.3 - - - +
37H THR* 3.0 30.0 - - + -
38H GLY 3.1 9.5 + - - +
40H PHE* 3.1 39.7 - - + -
46H CYS* 4.4 9.9 - - - -
49H GLN* 4.2 9.0 - - + -
50H VAL* 4.6 4.9 - - + -
57H ARG 3.8 4.0 - - - -
58H PHE* 4.3 10.3 - - + +
71H VAL* 3.5 6.4 - - - +
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Residues in contact with ARG 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H ALA 4.1 1.6 + - - -
31H VAL* 1.3 73.9 - - - +
33H ARG* 1.3 87.0 + - - +
37H THR* 3.2 12.8 - - - +
57H ARG* 2.8 41.3 + - + +
70H PHE* 2.9 59.0 + - + +
71H VAL* 3.8 18.2 - - - +
72H ARG* 6.0 0.2 + - - -
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Residues in contact with ARG 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F ARG* 5.3 8.7 - - - +
31H VAL* 3.4 7.4 - - - +
32H ARG* 1.3 106.9 - - - +
34H GLY* 1.3 58.0 + - - +
37H THR* 3.9 2.2 - - - -
50H VAL* 4.2 2.1 - - - +
53H PHE* 4.0 7.2 - - + -
55H ALA* 2.9 41.8 + - + +
56H ALA* 3.1 24.2 + - - +
57H ARG* 3.2 40.3 + - - +
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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
------------------------------------------------------------
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