Contacts of the helix formed by residues 57 - 71 (chain O) in PDB entry 5LN3
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 57 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55O GLY 5.2 0.4 - - - +
56O LEU* 1.3 73.9 - - - +
58O LYS* 1.4 86.2 + - + +
59O LEU 3.4 1.5 - - - +
60O TYR* 4.0 17.4 + - + -
61O GLU* 3.7 16.6 + - - +
80O ILE 5.5 0.2 - - - +
83O VAL* 3.9 40.4 - - + +
84O VAL* 4.4 12.6 - - + +
87O MET* 3.8 33.2 - - + -
89O ASP* 4.2 12.6 - - - +
92O VAL* 4.6 19.8 - - + +
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Residues in contact with LYS 58 (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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57O ILE* 1.4 89.2 - - + +
59O LEU* 1.4 68.6 + - + +
61O GLU* 3.3 22.2 + - + +
62O ASN* 3.5 11.5 + - - +
89O ASP* 5.0 4.4 + - - -
92O VAL* 3.6 31.1 - - + +
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Residues in contact with LEU 59 (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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22O TRP* 3.5 31.5 - - + -
25O LEU* 5.2 6.7 - - + -
29O TYR* 4.4 21.8 - - + +
36O GLN* 3.9 17.9 - - + +
37O LEU* 4.8 0.9 - - - -
56O LEU* 4.2 36.8 - - + -
57O ILE 3.4 1.2 - - - +
58O LYS* 1.4 86.1 - - + +
60O TYR* 1.3 58.5 + - - +
62O ASN* 3.3 20.0 + - - +
63O PHE* 3.9 1.4 + - - +
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Residues in contact with TYR 60 (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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36O GLN* 3.7 30.8 - - - +
37O LEU* 4.3 9.6 - - + -
38O THR* 3.5 29.5 + - - -
39O LEU* 5.3 0.3 - - - -
43O ASP* 3.5 21.1 + - - -
48O PRO* 6.4 2.5 - - + -
56O LEU 5.1 0.4 - - - +
57O ILE* 4.1 25.1 - - + +
59O LEU* 1.3 74.7 - - - +
61O GLU* 1.3 59.2 + - - +
63O PHE* 3.0 22.7 + + + +
64O ILE* 2.8 52.5 + - + +
67O PHE* 5.6 6.1 - - - +
79O ILE 4.8 2.1 + - - -
80O ILE* 4.2 26.9 - - + +
83O VAL* 5.2 13.2 - - + -
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Residues in contact with GLU 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57O ILE 3.7 10.6 + - - +
58O LYS* 3.3 15.9 + - + +
60O TYR* 1.3 76.4 - - - +
62O ASN* 1.4 83.1 + - - +
64O ILE* 3.0 38.9 + - + +
65O SER* 3.4 18.2 + - - -
92O VAL* 6.5 2.2 - - + -
95O THR* 6.4 2.7 - - + -
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Residues in contact with ASN 62 (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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22O TRP* 3.8 22.9 - - + -
58O LYS 3.5 9.9 + - - +
59O LEU* 3.3 20.4 - - - +
60O TYR 3.2 0.8 - - - -
61O GLU* 1.4 94.0 + - - +
63O PHE* 1.4 61.8 + - - +
65O SER* 3.5 13.1 + - - -
66O GLU* 3.6 10.3 + - - +
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Residues in contact with PHE 63 (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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18O GLN* 3.9 28.5 - - + -
22O TRP* 4.2 19.3 - + + -
37O LEU* 3.7 44.2 - - + -
38O THR 3.6 17.9 - - - -
39O LEU* 4.2 10.8 - - + -
59O LEU 4.3 0.9 - - - +
60O TYR* 3.0 29.8 + + - +
62O ASN* 1.4 77.6 - - - +
64O ILE* 1.4 61.9 + - - +
66O GLU* 3.1 16.9 + - + +
67O PHE* 3.0 23.0 + + + +
70O ARG* 3.2 31.9 - - - -
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Residues in contact with ILE 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60O TYR* 2.8 57.7 + - + +
61O GLU* 3.0 34.8 + - + +
63O PHE* 1.4 71.5 - - - +
65O SER* 1.3 61.6 + - - +
67O PHE* 3.3 23.0 - - + +
68O GLU* 3.7 11.8 - - - +
73O PRO* 5.4 2.8 - - + +
80O ILE* 3.7 29.2 - - + -
96O PHE* 4.8 13.0 - - + -
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Residues in contact with SER 65 (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 GLU* 3.4 22.0 + - - -
62O ASN* 3.8 9.0 - - - -
63O PHE 3.3 0.4 - - - -
64O ILE* 1.3 79.8 - - - +
66O GLU* 1.4 61.1 + - - +
67O PHE 3.5 0.3 + - - -
68O GLU* 3.6 30.9 + - - +
69O HIS 4.9 0.5 + - - -
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Residues in contact with GLU 66 (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 PRO* 4.5 10.8 - - + +
17O GLY 2.7 25.9 - - - +
18O GLN* 3.7 7.1 - - - -
19O PRO* 3.9 17.6 - - + +
62O ASN 3.6 8.6 + - - +
63O PHE* 3.1 20.3 + - + +
65O SER* 1.4 75.1 - - - +
67O PHE* 1.4 65.5 + - - +
68O GLU 3.2 0.5 + - - -
69O HIS* 3.8 12.3 + - - +
70O ARG* 3.0 33.9 + - - +
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Residues in contact with PHE 67 (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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12O GLN* 4.9 2.0 - - - -
38O THR 5.5 0.4 - - - -
39O LEU* 3.9 11.7 - - + -
40O GLN* 3.8 17.7 - - + -
43O ASP* 4.6 2.2 - - - -
60O TYR* 5.6 6.3 - - + +
63O PHE* 3.0 16.2 + + + +
64O ILE* 3.3 20.6 - - + +
65O SER 3.3 0.2 - - - -
66O GLU* 1.4 76.3 - - - +
68O GLU* 1.4 62.2 + - - +
70O ARG* 2.9 44.0 + - - +
71O VAL* 3.1 57.6 + - + +
72O ASN 4.2 9.4 - - - -
73O PRO* 4.3 17.7 - - + -
76O LEU* 3.8 27.4 - - + -
80O ILE* 5.9 2.9 - - + -
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Residues in contact with GLU 68 (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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64O ILE 3.7 9.4 - - - +
65O SER* 3.6 28.7 + - - +
66O GLU 3.2 1.8 + - - -
67O PHE* 1.4 74.0 - - - +
69O HIS* 1.3 58.7 + - - +
70O ARG 3.6 0.3 + - - -
71O VAL* 3.7 18.0 - - - -
72O ASN* 3.8 14.2 + - + +
73O PRO* 4.2 19.3 - - + -
99O LYS* 4.1 26.4 + - - -
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Residues in contact with HIS 69 (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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14O SER* 4.1 5.1 - - - -
15O GLY 4.6 0.4 + - - -
16O PRO* 3.6 40.1 - - + +
65O SER 4.9 0.4 + - - -
66O GLU* 3.8 10.6 + - - +
68O GLU* 1.3 77.8 - - - +
70O ARG* 1.3 68.7 + - + +
18W ASN* 5.2 1.2 - - - -
19W GLY* 3.1 42.8 + - - -
23W PRO 6.0 0.9 - - - -
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Residues in contact with ARG 70 (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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9O GLN* 4.2 6.7 - - - +
12O GLN* 3.0 33.7 - - - +
14O SER* 3.6 28.4 + - - +
16O PRO* 5.8 0.2 - - + -
17O GLY* 3.6 24.3 + - - +
18O GLN* 4.0 12.3 - - - +
39O LEU* 3.4 23.7 - - - +
63O PHE* 3.2 33.1 - - - -
66O GLU* 3.0 37.3 + - - +
67O PHE* 2.9 36.7 + - + +
69O HIS* 1.3 80.7 - - + +
71O VAL* 1.3 63.4 + - + +
18W ASN* 3.2 18.0 + - - +
19W GLY 4.9 0.3 + - - -
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Residues in contact with VAL 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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12O GLN* 3.5 25.4 - - - +
40O GLN* 4.0 16.8 - - + +
67O PHE* 3.1 49.6 - - + +
68O GLU 3.7 4.5 - - - -
70O ARG* 1.3 82.7 - - - +
72O ASN* 1.4 69.9 + - - +
75O SER* 5.8 2.7 - - - +
76O LEU* 5.3 3.4 - - + -
14W GLU 5.4 1.3 - - - +
17W ARG* 4.9 12.3 - - - +
18W ASN* 4.0 19.7 - - - +
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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