Contacts of the strand formed by residues 52 - 57 (chain B) in PDB entry 3D87
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 THR 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B VAL* 4.0 16.0 - - + +
26B LEU 2.9 12.6 - - - -
27B THR* 3.6 14.8 - - + +
38B TRP* 3.8 3.4 - - - -
49B SER 3.4 12.1 - - - +
50B GLY* 3.0 2.0 - - - -
51B LYS* 1.3 94.9 - - + +
53B LEU* 1.3 58.4 + - - +
54B THR* 4.1 6.8 + - - -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 3.2 1.2 - - - -
26B LEU* 2.5 63.3 + - + +
38B TRP* 3.4 39.9 - - + +
47B LEU* 3.3 37.2 - - + +
48B GLY* 3.8 11.2 - - - +
49B SER 5.2 0.4 - - - +
52B THR* 1.3 75.2 - - - +
54B THR* 1.3 69.4 + - - +
55B ILE* 3.6 18.4 - - + -
66B TYR* 4.0 13.0 - - + -
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Residues in contact with THR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B MET* 3.9 27.8 - - + -
24B VAL 3.3 12.6 - - - +
25B VAL* 3.5 27.8 - - + +
52B THR* 4.1 7.5 + - - -
53B LEU* 1.3 81.0 - - - +
55B ILE* 1.3 66.3 + - - +
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Residues in contact with ILE 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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23B MET* 3.3 11.0 - - - +
24B VAL* 2.6 49.3 + - + +
26B LEU* 3.7 16.4 - - + -
47B LEU* 5.7 4.5 - - + +
53B LEU* 3.6 25.6 - - + -
54B THR* 1.3 81.5 - - - +
56B GLN* 1.3 64.1 + - - +
57B VAL* 4.0 19.1 - - + -
62B ASP 4.1 1.1 - - - +
66B TYR* 3.2 39.0 - - + +
80B LEU* 4.7 3.4 - - + -
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Residues in contact with GLN 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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20B PRO* 3.0 37.2 + - - +
22B GLU 3.3 7.2 - - - +
23B MET* 4.5 2.9 - - + +
55B ILE* 1.3 79.1 - - - +
57B VAL* 1.3 71.2 + - - +
58B LYS* 3.9 24.0 - - + +
62B ASP* 3.6 15.0 - - - +
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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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11B VAL* 4.0 13.0 - - + -
13B LEU* 3.5 9.6 - - + +
21B GLY* 3.4 4.9 - - - -
22B GLU 2.7 32.5 + - - +
24B VAL* 3.5 30.3 - - + -
55B ILE* 4.0 17.5 - - + -
56B GLN* 1.3 82.0 - - - +
58B LYS* 1.3 62.6 + - - +
59B GLU 4.5 0.9 - - - +
62B ASP* 3.2 20.9 - - + +
63B ALA* 5.2 0.7 - - + -
80B LEU* 5.0 4.0 - - + -
82B LEU* 3.7 29.6 - - + -
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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