Contacts of the strand formed by residues 46 - 53 (chain B) in PDB entry 3FPK
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 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B GLU* 3.4 5.7 - - - +
43B ILE* 2.7 41.4 + - - +
44B ASP 3.3 7.8 - - - +
45B GLY* 1.3 81.6 - - - +
47B ARG* 1.3 65.5 + - - +
48B VAL* 3.6 6.3 + - + +
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Residues in contact with ARG 47 (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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40B GLY* 3.4 3.6 + - - -
41B LEU* 3.3 26.4 + - - +
42B GLU* 3.7 33.4 + - - +
46B GLU* 1.3 75.4 - - - +
48B VAL* 1.3 63.1 + - - +
49B GLN* 4.4 0.6 + - - -
89B GLN* 3.3 51.9 + - - +
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Residues in contact with VAL 48 (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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40B GLY* 3.2 2.4 - - - -
41B LEU 2.9 31.9 + - - -
43B ILE* 3.9 29.8 - - + +
46B GLU* 4.0 12.6 - - + +
47B ARG* 1.3 78.8 - - - +
49B GLN* 1.3 65.0 + - - +
50B ARG* 3.8 23.1 - - - +
74B LYS* 4.0 28.0 - - + -
75B LEU* 4.1 16.4 - - + +
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Residues in contact with GLN 49 (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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2B ALA* 4.8 10.2 - - - +
4B TRP* 6.0 0.3 - - - +
38B LYS* 3.5 34.8 - - + +
39B LEU 3.2 15.8 - - - +
40B GLY* 3.9 6.3 - - - -
47B ARG 4.4 1.1 + - - +
48B VAL* 1.3 77.1 - - - +
50B ARG* 1.3 85.8 + - - +
75B LEU* 3.9 1.6 - - - -
89B GLN* 5.5 6.1 - - - +
91B VAL* 3.7 21.5 - - - +
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Residues in contact with ARG 50 (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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38B LYS* 3.2 7.8 - - - -
39B LEU 2.9 28.9 + - - -
48B VAL* 3.8 15.7 - - - +
49B GLN* 1.3 91.9 + - - +
51B ALA* 1.3 59.6 + - - +
52B TYR* 3.2 31.5 - - + +
74B LYS* 3.6 19.6 - - - +
75B LEU* 3.5 18.1 - - + +
301B FAD 2.9 63.1 + - - +
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B PHE* 3.6 21.8 - - + -
37B THR 3.2 7.6 - - - -
38B LYS* 3.9 11.6 - - + +
50B ARG* 1.3 72.2 - - - +
52B TYR* 1.3 65.7 + - - +
301B FAD 2.7 66.3 + - + +
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Residues in contact with TYR 52 (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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36B PHE* 3.6 3.4 - - - -
37B THR 2.9 29.3 + - - +
39B LEU* 3.6 27.4 - - + -
50B ARG* 3.2 49.6 - - + +
51B ALA* 1.3 77.7 - - - +
53B SER* 1.3 64.4 - - - +
54B TYR 3.7 0.2 + - - -
65B PHE* 3.8 27.1 - - + -
67B LEU* 3.5 29.4 - - + +
75B LEU* 4.0 3.1 - - + +
76B SER* 4.3 4.9 + - - -
79B LEU* 3.6 29.8 - - + +
301B FAD 2.8 48.6 + + - +
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Residues in contact with SER 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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34B GLY 5.0 0.3 + - - -
35B GLN 3.8 4.5 - - - -
36B PHE* 3.7 9.4 - - - +
52B TYR* 1.3 71.8 - - - +
54B TYR* 1.3 65.1 + - - +
55B VAL* 3.4 5.9 + - - +
64B GLU 3.7 1.4 - - - +
65B PHE* 3.4 16.9 - - - -
119B GLY* 4.7 2.2 - - - -
120B PRO* 3.5 26.7 - - - +
245B GLU* 4.0 4.5 + - - -
247B TYR* 2.7 34.1 + - - -
301B FAD 3.1 20.7 + - - +
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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