Contacts of the strand formed by residues 55 - 58 (chain Y) in PDB entry 5FLX
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 ILE 55 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Y ARG* 2.7 46.2 + - + +
44Y LEU* 3.8 20.9 - - + +
45Y ALA* 3.6 34.5 - - + +
48Y TYR* 4.7 1.1 - - + -
50Y THR* 3.6 20.0 - - - +
51Y THR 4.1 2.7 - - - +
52Y PRO 3.2 7.0 + - - +
54Y VAL* 1.3 89.7 - - + +
56Y PHE* 1.3 70.2 + - - +
57Y VAL* 5.8 0.9 - - + -
74Y MET 3.5 9.6 - - - +
75Y ILE* 3.7 32.1 - - + -
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Residues in contact with PHE 56 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Y LYS* 4.9 3.1 - - - +
41Y ARG* 4.6 1.8 - - - +
44Y LEU* 5.4 0.3 - - - +
53Y ASP 3.9 16.8 - - - -
54Y VAL 4.7 3.1 - - - -
55Y ILE* 1.3 90.2 - - - +
57Y VAL* 1.3 61.1 + - - +
73Y GLY* 3.6 0.7 - - - -
74Y MET* 2.5 52.3 + - + +
76Y TYR* 4.4 7.6 - + - -
79Y LEU* 6.5 0.7 - - + -
82Y ALA* 3.8 22.4 - - + -
83Y LYS* 6.0 1.3 - - + -
86Y GLU* 3.6 35.0 - - + -
90Y ARG* 4.2 23.3 - - + -
91Y LEU* 4.6 12.3 - - + -
94Y HIS* 3.4 38.4 - + - -
96Y LEU* 6.6 0.4 - - + -
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Residues in contact with VAL 57 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Y ILE* 4.8 11.2 - - + -
37Y LYS* 3.2 48.8 + - + +
40Y ILE* 5.4 9.9 - - + -
41Y ARG* 5.1 10.8 - - + -
44Y LEU* 5.9 2.5 - - + -
55Y ILE* 5.8 1.6 - - + -
56Y PHE* 1.3 78.8 - - - +
58Y PHE* 1.3 69.3 + - - +
59Y GLY 5.0 0.4 - - - +
60Y PHE* 4.6 23.5 - - + -
71Y GLY* 5.1 2.2 - - - -
72Y PHE 3.4 23.1 - - - +
73Y GLY* 4.0 4.7 - - - -
74Y MET 4.4 0.2 - - - +
90Y ARG* 5.7 2.0 - - - +
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Residues in contact with PHE 58 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5721 U 4.7 1.1 - - - -
56E LEU* 3.5 33.7 - - + -
57Y VAL* 1.3 78.0 - - - +
59Y GLY* 1.3 69.3 + - - +
60Y PHE* 5.1 1.3 - - - -
72Y PHE* 3.0 59.3 + + + +
74Y MET* 3.5 25.4 - - + -
90Y ARG* 3.2 48.0 - - + +
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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