Contacts of the strand formed by residues 46 - 53 (chain I) in PDB entry 5FUR
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 VAL 46 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35I ILE* 3.5 4.3 - - - -
36I ASN* 3.1 38.7 + - + +
37I ASN* 4.0 22.4 - - + +
39I ASN* 5.8 2.9 - - + -
44I SER* 3.7 13.0 - - - +
45I VAL* 1.3 85.9 - - - +
47I GLY* 1.3 59.2 + - - +
149I ASN* 5.8 0.4 - - - +
150I PHE* 3.4 13.0 - - - +
151I SER* 3.6 23.3 - - - +
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Residues in contact with GLY 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I CYS 3.6 6.1 - - - -
36I ASN* 4.8 3.4 - - - -
46I VAL* 1.3 76.4 - - - +
48I PHE* 1.3 78.0 + - - -
149I ASN* 3.4 6.6 + - - +
150I PHE* 2.8 45.7 + - - -
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Residues in contact with PHE 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I VAL 4.0 0.7 - - - +
33I VAL* 3.7 0.7 - - - -
34I CYS* 2.8 49.2 + - + +
36I ASN* 5.6 8.5 - - - -
47I GLY* 1.3 84.8 - - - -
49I VAL* 1.3 63.1 + - - +
50I GLU* 3.9 11.1 + - + +
76I ARG* 6.1 2.2 - - - -
147I HIS* 5.5 7.2 - - + -
148I ILE 3.3 10.5 - - - +
149I ASN* 3.3 43.5 - - + -
150I PHE* 3.8 3.3 - - - -
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Residues in contact with VAL 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I GLN* 2.8 27.8 - - + +
32I VAL 3.8 4.3 - - - +
33I VAL* 4.2 11.7 - - + -
48I PHE* 1.3 72.1 - - - +
50I GLU* 1.4 63.9 + - - +
51I LEU* 2.7 37.5 - - + -
146I ILE 3.3 2.9 - - - +
147I HIS* 3.7 1.9 - - - -
148I ILE* 3.2 42.6 + - + +
150I PHE* 3.7 12.1 - - + -
190I PHE* 3.9 16.2 - - + -
191I PRO* 3.9 13.7 - - + +
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Residues in contact with GLU 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I HIS* 4.0 0.5 - - - +
31I GLN* 3.3 4.9 - - - -
32I VAL* 2.7 51.1 + - + +
34I CYS* 6.5 1.8 - - + -
48I PHE* 4.8 11.1 - - + +
49I VAL* 1.4 76.1 - - - +
51I LEU* 1.3 61.4 + - - +
52I THR* 3.5 3.0 + - - -
76I ARG* 5.5 1.9 + - - -
145I LYS* 5.3 10.5 + - + +
146I ILE 3.6 3.6 - - - -
147I HIS* 3.5 33.0 + - + +
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Residues in contact with LEU 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I LEU* 3.7 30.6 - - + +
31I GLN* 3.2 24.2 - - + +
49I VAL* 2.7 50.7 - - + +
50I GLU* 1.3 69.8 - - - +
52I THR* 1.3 62.2 + - - +
53I ILE 3.4 0.5 + - - -
65I LEU* 3.4 33.2 - - + -
144I LEU 2.9 5.2 - - - +
145I LYS* 4.2 1.8 - - - -
146I ILE* 2.8 50.9 + - + +
148I ILE* 4.4 4.3 - - + -
191I PRO 3.8 6.1 - - - +
192I CYS* 4.5 0.7 - - - -
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Residues in contact with THR 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I LEU* 3.4 5.9 - - - +
29I THR* 3.2 25.3 + - - +
30I HIS* 3.0 35.0 + - + +
50I GLU 3.5 3.9 + - - -
51I LEU* 1.3 70.8 - - - +
53I ILE* 1.3 59.9 + - - +
54I PHE* 3.2 33.7 - - + -
143I VAL* 3.4 18.2 - - + -
144I LEU 3.4 6.1 - - - +
145I LYS* 4.2 17.8 - - + +
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Residues in contact with ILE 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I LYS* 3.7 24.2 - - - +
28I LEU* 3.4 22.9 - - + -
51I LEU 4.5 0.2 - - - +
52I THR* 1.3 74.9 - - - +
54I PHE* 1.3 63.9 + - - +
55I PRO* 3.2 21.2 - - + +
60I LEU* 5.2 3.8 - - + -
63I ILE* 3.6 41.1 - - + -
142I LYS 3.4 1.7 - - - +
143I VAL* 3.5 0.9 - - - -
144I LEU* 3.0 45.8 + - + +
146I ILE* 4.2 13.2 - - + -
193I VAL* 6.2 0.2 - - + -
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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