Contacts of the helix formed by residues 70 - 89 (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 SER 70 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37O PHE 6.0 1.1 - - - -
67O ASP 3.0 15.5 + - - -
68O GLU 2.9 4.4 + - - -
69O SER* 1.3 83.6 - - - +
71O PRO* 1.3 61.1 - - - +
72O TYR* 2.7 20.7 + - - +
73O ALA 3.0 11.1 + - - -
74O ALA 3.6 2.1 + - - -
111O GLY* 4.6 2.0 - - - -
86z U 4.5 8.5 + - - -
335z G 3.2 38.6 + - - -
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Residues in contact with PRO 71 (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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70O SER* 1.3 88.7 - - - +
72O TYR* 1.3 57.7 + - - +
73O ALA 3.4 0.2 - - - -
74O ALA* 3.3 3.4 + - + +
75O MET* 2.9 22.9 + - - +
110O PRO* 4.3 10.3 - - + +
111O GLY* 3.7 30.9 - - - +
114O SER* 3.3 30.8 + - - +
86z U 6.1 0.4 - - - +
335z G 3.7 21.8 - - + +
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Residues in contact with TYR 72 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62O VAL* 4.4 15.5 - - + -
68O GLU 5.6 0.9 - - - +
70O SER* 2.7 11.7 + - - +
71O PRO* 1.3 78.2 - - - +
73O ALA* 1.3 56.1 + - - +
75O MET* 3.0 17.3 + - + +
76O LEU* 2.9 64.2 + - + +
85z A 5.2 0.7 - - - -
86z U 3.1 95.1 + + + +
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Residues in contact with ALA 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58O GLY* 3.3 11.8 - - - +
61O LYS* 5.3 3.1 - - + +
62O VAL* 4.7 8.1 - - + -
68O GLU* 3.1 46.8 + - + +
69O SER* 4.4 1.1 - - - -
70O SER 3.0 5.0 + - - +
72O TYR* 1.3 79.1 - - - +
74O ALA* 1.3 60.7 + - - +
75O MET 3.2 0.2 - - - -
76O LEU* 4.3 6.3 - - - +
77O ALA* 2.9 34.6 + - + +
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Residues in contact with ALA 74 (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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40O THR* 4.1 15.3 - - + +
42O VAL* 5.7 2.7 - - + -
58O GLY* 5.0 2.6 + - - -
69O SER 4.9 1.0 + - - -
70O SER 3.6 3.4 + - - +
71O PRO* 3.3 11.4 + - + +
72O TYR 3.2 0.6 - - - -
73O ALA* 1.3 78.8 - - - +
75O MET* 1.3 50.6 + - - +
77O ALA* 4.8 1.3 - - - -
78O ALA* 2.5 42.3 + - - +
111O GLY 3.2 27.1 - - - +
115O ALA* 3.9 21.3 - - + +
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Residues in contact with MET 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71O PRO 2.9 12.7 + - - +
72O TYR* 3.0 23.3 + - + +
74O ALA* 1.3 75.5 - - - +
76O LEU* 1.3 66.3 + - + +
78O ALA* 3.6 1.6 - - - +
79O GLN* 2.9 53.4 + - + +
114O SER* 4.3 9.6 + - - +
117O ARG* 6.2 3.4 - - - -
118O ALA* 3.6 25.1 - - + -
121O ARG* 4.8 16.8 - - + +
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Residues in contact with LEU 76 (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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61O LYS* 4.6 18.8 - - + -
62O VAL* 4.4 14.1 - - + -
72O TYR* 2.9 58.4 + - + +
73O ALA* 4.3 4.3 - - - +
75O MET* 1.3 80.0 - - + +
77O ALA* 1.3 58.7 + - - +
79O GLN* 2.9 26.1 + - + +
80O ASP* 2.9 11.8 + - - +
86z U 5.7 0.9 - - - +
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Residues in contact with ALA 77 (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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42O VAL* 5.6 3.6 - - + -
56O VAL* 3.9 12.4 - - + +
57O THR 3.7 23.8 - - - +
58O GLY* 4.3 6.7 - - - -
60O MET* 5.7 0.2 - - + -
61O LYS* 5.0 12.4 - - + +
73O ALA* 2.9 23.2 + - + +
74O ALA* 4.8 1.6 - - - +
76O LEU* 1.3 73.9 - - - +
78O ALA* 1.3 57.0 + - - +
80O ASP* 3.2 11.2 + - - +
81O VAL* 2.9 32.2 + - - +
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Residues in contact with ALA 78 (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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42O VAL* 5.0 4.2 - - + +
74O ALA* 2.5 26.0 + - - +
75O MET 3.6 0.2 - - - +
76O LEU 3.1 0.2 - - - -
77O ALA* 1.3 78.1 - - - +
79O GLN* 1.3 58.7 + - - +
81O VAL* 3.4 5.3 + - - +
82O ALA* 2.9 27.4 + - - +
115O ALA* 3.9 11.0 - - + +
118O ALA* 3.5 22.4 - - + -
119O LEU* 3.6 24.7 - - + +
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Residues in contact with GLN 79 (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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75O MET* 2.9 37.4 + - + +
76O LEU* 2.9 15.7 + - + +
78O ALA* 1.3 75.7 - - - +
80O ASP* 1.3 59.3 + - - +
82O ALA* 3.3 7.8 + - - +
83O GLN* 2.9 27.9 + - - +
118O ALA* 3.5 29.6 - - - +
121O ARG* 5.0 3.0 - - - +
122O SER* 4.3 16.0 + - - -
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Residues in contact with ASP 80 (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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56O VAL* 3.8 26.3 - - + +
60O MET* 4.5 10.0 - - - +
61O LYS* 4.7 13.7 + - - -
76O LEU 2.9 11.1 + - - +
77O ALA* 3.4 12.8 - - - +
79O GLN* 1.3 73.8 - - - +
81O VAL* 1.3 60.3 + - - +
83O GLN* 3.1 10.2 + - - +
84O ARG* 2.9 30.5 + - - +
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Residues in contact with VAL 81 (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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42O VAL* 3.6 32.5 - - + +
44O VAL* 3.6 30.7 - - + -
54O CYS* 4.7 10.1 - - - +
55O ARG* 5.9 0.2 - - - -
56O VAL* 3.6 26.7 - - + +
77O ALA 2.9 21.2 + - - +
78O ALA 3.7 5.6 - - - +
80O ASP* 1.3 73.8 - - - +
82O ALA* 1.3 57.4 + - - +
84O ARG* 3.4 0.7 + - - +
85O CYS* 2.9 40.5 + - - -
119O LEU* 4.9 10.3 - - + -
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Residues in contact with ALA 82 (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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78O ALA 2.9 18.5 + - - +
79O GLN* 3.6 16.2 - - - +
80O ASP 3.2 0.2 - - - -
81O VAL* 1.3 76.8 - - - +
83O GLN* 1.3 61.0 + - - +
85O CYS* 4.1 4.1 - - - +
86O LYS* 3.1 40.0 + - - +
119O LEU* 5.0 9.8 - - + +
122O SER* 5.0 8.5 - - - +
124O MET* 4.7 18.6 - - + -
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Residues in contact with GLN 83 (chain O).
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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79O GLN 2.9 14.2 + - - +
80O ASP* 3.1 13.7 + - - +
82O ALA* 1.3 74.1 - - - +
84O ARG* 1.3 60.8 + - - +
86O LYS* 3.1 11.1 + - - +
87O GLU* 2.4 64.1 + - + +
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Residues in contact with ARG 84 (chain O).
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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23B ASP* 4.7 5.7 + - - -
25B PHE* 3.2 42.0 - - - +
53O ILE 5.3 0.7 - - - +
54O CYS* 3.6 34.8 - - + -
56O VAL* 5.9 0.4 - - + -
80O ASP* 2.9 20.2 + - - +
81O VAL 4.1 0.2 - - - +
83O GLN* 1.3 76.5 - - - +
85O CYS* 1.3 62.3 + - - +
87O GLU* 3.2 35.8 + - - +
88O LEU* 3.4 31.4 + - + +
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Residues in contact with CYS 85 (chain O).
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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44O VAL* 3.7 35.0 - - - -
53O ILE* 5.4 3.4 - - - -
54O CYS* 4.7 6.7 - - - -
81O VAL* 2.9 29.8 + - - +
82O ALA* 4.1 3.1 - - - +
84O ARG* 1.3 78.5 - - - +
86O LYS* 1.3 56.7 + - - +
88O LEU* 3.4 3.3 + - - -
89O GLY 3.1 19.9 + - - -
90O ILE* 3.3 43.5 + - + +
91O THR 4.7 0.2 + - - -
93O LEU* 4.8 5.4 - - - -
119O LEU* 6.3 0.2 - - - -
124O MET* 4.3 12.1 - - - -
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Residues in contact with LYS 86 (chain O).
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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82O ALA* 3.1 23.2 + - - +
83O GLN* 3.1 13.5 + - - +
85O CYS* 1.3 74.4 - - - +
87O GLU* 1.3 65.7 + - - +
89O GLY* 3.5 11.5 + - - +
90O ILE 5.3 0.2 - - - +
91O THR 5.9 0.2 - - - +
122O SER* 3.3 42.4 + - - -
123O GLY* 4.1 8.3 - - - +
124O MET* 3.7 26.0 - - + -
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Residues in contact with GLU 87 (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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16O SER 5.3 3.6 - - - +
83O GLN* 2.4 49.9 + - + +
84O ARG* 3.2 34.7 + - - +
86O LYS* 1.3 80.4 - - - +
88O LEU* 1.3 62.3 + - - +
89O GLY 3.7 0.2 + - - -
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Residues in contact with LEU 88 (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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25B PHE* 4.2 33.7 - - + -
30B TRP* 5.8 7.6 - - + -
16O SER 5.1 11.2 - - - +
17O LEU 4.4 14.4 - - - +
18O GLY* 5.3 0.5 - - - -
19O PRO* 4.8 8.5 - - - +
53O ILE* 4.0 27.1 - - + +
84O ARG* 3.4 38.1 + - + +
85O CYS 3.4 4.8 + - - +
86O LYS 3.3 0.2 - - - -
87O GLU* 1.3 80.2 - - - +
89O GLY* 1.3 62.7 + - - +
90O ILE* 4.1 15.0 - - + +
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Residues in contact with GLY 89 (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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19O PRO* 5.8 3.3 - - - +
21O VAL* 5.7 6.1 - - - +
27O VAL* 4.5 9.2 - - - +
85O CYS 3.1 5.5 + - - -
86O LYS* 3.5 9.6 + - - -
87O GLU 3.3 3.4 - - - -
88O LEU* 1.3 80.4 - - - +
90O ILE* 1.3 62.9 + - - +
91O THR* 3.3 16.1 + - - +
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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