Contacts of the helix formed by residues 52 - 57 (chain B) in PDB entry 3DOY
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 GLU 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B LYS* 2.8 33.3 + - - -
47B ASN 3.6 0.3 - - - +
48B ILE* 3.4 6.8 - - - +
49B THR* 2.9 48.8 + - + +
50B PHE 2.7 11.6 + - - +
51B ASN* 1.3 74.4 - - - +
53B ASP* 1.3 66.1 + - - +
54B VAL* 4.3 5.8 - - + +
55B PHE* 3.1 31.7 + - + +
56B ASN 4.3 0.7 + - - -
65B PHE* 4.1 8.6 - - - -
25F TYR* 3.5 6.7 - - - -
49F THR* 3.7 4.7 - - + -
51F ASN* 2.9 37.7 - - - +
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Residues in contact with ASP 53 (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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25A TYR* 4.1 14.8 + - - -
26A PRO* 3.4 25.5 - - + +
53A ASP* 3.9 16.2 - - - +
25B TYR* 3.9 17.2 + - + +
26B PRO* 5.8 4.0 - - + -
52B GLU* 1.3 72.1 - - - +
54B VAL* 1.3 63.1 + - + +
56B ASN* 2.8 46.2 + - - +
25F TYR* 3.5 27.1 + - - +
51F ASN* 4.8 1.8 + - - -
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Residues in contact with VAL 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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26A PRO* 4.1 12.2 - - + +
27A MET* 3.8 15.3 - - + +
26B PRO* 6.0 1.6 - - + +
52B GLU* 4.3 11.9 - - + +
53B ASP* 1.3 74.2 - - + +
55B PHE* 1.3 67.0 + - + +
56B ASN 3.2 1.2 + - - -
57B GLY 3.2 11.1 + - - -
58B HIS* 3.3 10.9 + - - +
65B PHE* 4.9 6.5 - - + -
66B PRO* 3.6 37.0 - - + -
69B LEU* 3.8 18.2 - - + -
51F ASN* 3.9 21.1 - - - +
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Residues in contact with PHE 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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48B ILE* 3.6 25.8 - - + -
49B THR 2.8 31.9 - - - -
50B PHE* 3.7 35.9 - + + +
52B GLU* 3.1 22.8 + - + +
53B ASP 3.1 0.2 + - - -
54B VAL* 1.3 77.9 - - + +
56B ASN* 1.3 64.7 + - - +
57B GLY 3.1 1.1 + - - -
58B HIS* 3.8 11.4 + - + +
59B PHE 4.0 13.0 + - - +
60B PRO* 4.9 1.2 - - - +
63B PRO* 3.9 12.9 - - + +
64B ILE 3.6 17.7 - - - -
65B PHE* 3.5 37.5 - + - -
66B PRO* 5.1 1.3 - - + -
115B PRO* 3.9 8.7 - - + -
25F TYR* 6.2 0.2 - - + -
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Residues in contact with ASN 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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24A ARG* 4.4 2.4 - - - +
25A TYR* 3.4 15.9 - - + +
26A PRO* 4.3 1.1 - - + -
52B GLU 4.3 0.2 + - - -
53B ASP* 2.8 41.5 + - - +
55B PHE* 1.3 78.9 - - - +
57B GLY* 1.3 57.7 + - - +
60B PRO* 3.6 19.4 - - - +
25F TYR* 3.5 38.3 - - - +
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Residues in contact with GLY 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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23A HIS* 3.6 9.0 - - - +
24A ARG* 3.0 47.8 + - - +
25A TYR 3.1 8.9 + - - -
26A PRO 4.4 0.2 - - - -
27A MET* 4.1 4.3 - - - +
54B VAL 3.2 5.5 + - - -
56B ASN* 1.3 80.1 - - - +
58B HIS* 1.3 59.5 + - - +
59B PHE* 3.5 9.0 - - - -
60B PRO* 3.9 2.1 - - - +
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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