Contacts of the strand formed by residues 41 - 45 (chain O) 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 PHE 41 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9571 A 3.7 21.3 - - - -
9581 G 5.1 0.4 - - - -
9731 C 3.9 17.3 - - - -
9741 C 3.4 46.9 - - - +
32O HIS 5.4 0.7 - - - +
33O ILE* 3.3 27.1 - - - +
34O PHE* 3.1 45.5 + + + +
39O ASP* 3.0 29.6 - - - -
40O THR* 1.3 84.9 - - - +
42O VAL* 1.3 66.9 + - - +
43O HIS* 4.2 2.0 - - + +
55O ARG* 4.2 2.7 - - - -
57O THR* 3.9 26.9 - - + -
58O GLY 4.5 0.4 - - - +
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Residues in contact with VAL 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O CYS* 4.2 17.0 - - - -
32O HIS 3.9 2.2 - - - -
33O ILE* 4.4 4.7 - - + -
40O THR* 5.2 4.5 - - + -
41O PHE* 1.3 79.4 - - - +
43O HIS* 1.3 61.0 + - - +
44O VAL* 4.2 1.0 + - + +
55O ARG* 4.1 2.6 - - - +
56O VAL 3.2 38.2 + - - +
58O GLY* 5.0 2.4 - - - +
74O ALA* 5.4 2.9 - - - +
77O ALA* 5.6 3.1 - - + +
78O ALA* 5.0 9.4 - - + +
81O VAL* 3.6 36.9 - - + +
115O ALA* 3.7 29.8 - - + -
119O LEU* 4.9 7.9 - - + -
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Residues in contact with HIS 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9521 G 3.1 22.0 + - - -
9741 C 3.8 22.4 + - + +
9751 G 3.9 19.4 + - - +
31O CYS* 3.3 2.0 - - - -
32O HIS* 2.5 58.6 + - + +
41O PHE* 5.6 2.9 - - + -
42O VAL* 1.3 75.9 - - - +
44O VAL* 1.3 60.5 + - - +
45O THR* 2.9 28.9 + - + -
52O THR* 3.2 27.6 - - + +
54O CYS 3.9 1.3 - - - -
55O ARG* 3.4 32.5 - - + -
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Residues in contact with VAL 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O VAL 3.5 7.0 - - - +
31O CYS* 4.3 12.1 - - - +
42O VAL* 4.9 0.4 - - + -
43O HIS* 1.3 73.6 + - - +
45O THR* 1.3 69.9 + - - +
52O THR* 3.5 6.1 - - - +
53O ILE* 3.1 46.0 + - + -
54O CYS* 2.7 30.0 + - + +
81O VAL* 3.6 31.4 - - + -
85O CYS* 3.7 17.9 - - - -
90O ILE* 5.0 1.1 - - + -
93O LEU* 4.2 17.9 - - + -
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Residues in contact with THR 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9751 G 3.9 3.4 - - - +
30O VAL* 2.4 47.2 + - - -
32O HIS* 3.1 16.6 - - - +
43O HIS* 2.9 30.7 + - - -
44O VAL* 1.3 71.1 - - - +
46O ASP* 1.3 72.4 + - - +
49O GLY* 3.4 29.6 - - - +
50O LYS 3.8 1.8 - - - +
51O GLU 3.2 18.4 - - - +
52O THR* 4.7 0.2 - - - -
53O ILE* 3.7 11.9 - - - +
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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