Contacts of the helix formed by residues 53 - 61 (chain B) in PDB entry 3PSR
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 TYR 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B MET* 3.9 22.2 - - + -
42B PHE* 3.5 41.5 - + - -
43B LEU* 4.3 12.7 - - + +
46B CYS* 4.1 18.3 - - + +
47B ASP* 4.8 1.0 + - - -
51B THR* 3.5 12.0 + - + +
52B ASN* 1.3 73.7 - - - +
54B LEU* 1.3 63.5 + - + +
55B ALA 3.1 1.2 + - - -
56B ASP* 3.6 7.0 + - - +
57B VAL* 3.5 31.4 + - + +
60B LYS* 5.2 14.6 + - - -
77B LEU* 4.2 16.0 - - + +
80B ASP* 3.6 29.6 + - - +
81B ILE* 4.8 2.2 - - + +
95B CYS* 4.5 5.6 - - - -
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LYS* 5.6 2.9 - - - -
32B LEU* 3.9 26.0 - - + +
35B MET* 3.9 27.1 - - + -
36B LYS* 3.5 36.3 - - + -
43B LEU* 3.7 27.6 - - + -
52B ASN* 3.1 17.5 - - - +
53B TYR* 1.3 75.6 - - - +
55B ALA* 1.3 66.6 + - - +
56B ASP* 3.1 2.0 + - - -
57B VAL* 3.3 20.8 - - + +
58B PHE 4.9 0.5 + - - -
59B GLU* 5.3 0.3 - - - +
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LYS* 5.1 3.3 + - - -
52B ASN* 2.7 30.4 + - + +
53B TYR 3.1 0.8 + - - -
54B LEU* 1.3 77.2 - - - +
56B ASP* 1.3 65.7 + - + +
59B GLU* 3.6 9.5 - - - +
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Residues in contact with ASP 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASN 4.8 1.2 - - - +
53B TYR* 3.7 8.1 - - - +
54B LEU 4.0 0.2 - - - -
55B ALA* 1.3 83.5 - - + +
57B VAL* 1.3 57.7 + - - +
58B PHE 3.2 3.6 - - - -
59B GLU* 2.9 18.6 + - + +
60B LYS* 2.6 67.0 + - + +
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 4.0 15.7 - - + -
32B LEU* 4.0 15.0 - - + -
35B MET* 5.1 4.7 - - + -
53B TYR* 3.5 22.8 + - + +
54B LEU* 3.3 35.4 - - + +
56B ASP* 1.3 80.7 + - - +
58B PHE* 1.3 70.6 + - - +
60B LYS* 3.2 10.6 + - - +
61B LYS* 2.9 27.5 + - + +
77B LEU* 4.0 28.7 - - + -
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Residues in contact with PHE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE 3.8 1.3 - - - -
27B ASP 3.6 5.4 - - - -
28B LYS* 3.3 56.3 - - + -
31B LEU* 3.7 24.7 - - + -
32B LEU* 5.1 2.7 - - + -
54B LEU 4.9 0.8 + - - +
56B ASP 3.2 0.6 - - - -
57B VAL* 1.3 82.8 - - + +
59B GLU* 1.3 79.5 + - - +
61B LYS* 3.1 2.8 + - - +
62B ASP* 2.9 37.8 + - + +
67B LYS* 3.5 53.6 - - + -
68B LYS* 3.6 7.4 - - - -
69B ILE* 3.4 21.2 - - + +
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LYS* 2.7 41.4 + - - +
54B LEU 5.3 0.2 - - - +
55B ALA 3.6 5.4 - - - +
56B ASP* 2.9 28.3 + - + +
58B PHE* 1.3 86.4 - - - +
60B LYS* 1.3 62.4 + - - +
61B LYS 3.2 0.7 + - - -
62B ASP* 3.6 12.9 + - - +
67B LYS* 3.7 16.7 + - - +
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B TYR* 5.2 16.0 + - - -
56B ASP* 2.6 51.3 + - + +
57B VAL* 3.5 11.5 - - - +
59B GLU* 1.3 72.8 - - - +
61B LYS* 1.3 77.0 + - + +
62B ASP 3.9 0.3 + - - -
63B LYS* 4.7 8.5 + - - +
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 5.8 0.7 - - + -
57B VAL* 2.9 27.9 + - + +
58B PHE* 4.1 2.0 - - - +
60B LYS* 1.3 94.8 + - + +
62B ASP* 1.3 58.9 + - - +
63B LYS* 2.7 15.8 + - - +
69B ILE* 3.7 13.7 - - + -
73B GLU* 3.4 28.1 - - - +
76B SER* 3.3 24.5 + - - -
77B LEU* 4.0 25.4 - - + +
80B ASP* 2.5 38.5 + - - +
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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