Contacts of the helix formed by residues 74 - 86 (chain O) in PDB entry 5G04
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 THR 74 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73O ILE* 1.3 79.1 - - - +
75O LEU* 1.3 65.0 + - - +
76O SER* 3.9 10.9 + - - -
77O LYS* 3.3 23.0 + - - +
78O LEU* 3.2 19.2 + - - +
161O TYR* 4.3 4.9 - - - -
164O ASN* 5.3 17.7 - - + +
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Residues in contact with LEU 75 (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 ALA* 4.2 1.1 - - + -
74O THR* 1.3 72.3 - - - +
76O SER* 1.3 51.2 + - - +
78O LEU* 3.2 26.1 + - + -
79O TYR* 2.7 39.0 + - + +
93O VAL* 5.6 8.5 - - + -
94O GLN* 5.8 8.5 - - + -
97O ILE* 4.0 44.0 - - + -
161O TYR* 3.5 42.7 + - + +
162O PHE* 4.4 18.8 - - + +
165O GLY* 4.6 7.6 - - - -
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Residues in contact with SER 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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74O THR* 3.2 10.4 - - - -
75O LEU* 1.3 73.0 - - - +
77O LYS* 1.4 62.9 + - - +
79O TYR* 3.2 10.0 + - - +
80O LYS* 3.1 41.1 + - - +
164O ASN 4.3 2.5 - - - -
165O GLY* 3.7 26.4 + - - -
168O LYS* 3.2 26.4 - - - +
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Residues in contact with LYS 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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73O ILE* 4.2 26.9 - - + +
74O THR* 3.3 19.2 + - - +
75O LEU 3.3 0.2 - - - -
76O SER* 1.4 81.1 - - - +
78O LEU* 1.3 60.8 + - - +
80O LYS* 3.2 13.4 + - + +
81O LEU* 3.0 39.0 + - + +
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Residues in contact with LEU 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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33O TYR* 4.4 3.8 - - + -
36O ALA* 4.1 16.2 - - + +
37O VAL* 4.3 17.9 - - + -
40O LEU* 4.5 8.5 - - + -
63O LEU* 6.5 0.4 - - + -
67O LEU* 4.4 22.2 - - + -
73O ILE* 3.8 18.0 - - + +
74O THR 3.2 13.0 + - - +
75O LEU* 3.6 27.8 - - + +
77O LYS* 1.3 74.5 - - - +
79O TYR* 1.4 61.4 + - - +
81O LEU* 3.2 6.9 + - + +
82O ILE* 2.8 44.7 + - + +
93O VAL* 6.3 2.0 - - + -
161O TYR* 4.0 12.3 - - - +
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Residues in contact with TYR 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75O LEU* 2.7 23.7 + - + +
76O SER* 3.2 10.5 + - - +
78O LEU* 1.4 72.7 - - - +
80O LYS* 1.4 54.3 + - + +
82O ILE* 3.4 11.3 - - + +
83O GLU* 2.6 54.4 + - + +
90O ALA* 5.2 4.7 - - + +
93O VAL* 5.9 4.3 - - + -
94O GLN* 6.3 4.3 - - + -
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Residues in contact with LYS 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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76O SER* 3.1 33.1 + - - +
77O LYS* 3.2 15.4 + - + +
79O TYR* 1.4 75.9 - - + +
81O LEU* 1.3 57.8 + - + +
83O GLU* 3.4 16.2 + - - +
84O GLU* 2.9 31.5 + - - +
168O LYS* 5.4 3.0 - - - +
169O THR 6.3 0.8 - - - -
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Residues in contact with LEU 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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63O LEU* 3.7 27.2 - - + +
67O LEU* 4.5 16.2 - - + -
73O ILE* 3.9 27.8 - - + -
77O LYS* 3.0 26.9 + - + +
78O LEU* 3.6 7.9 - - + +
80O LYS* 1.3 77.1 - - + +
82O ILE* 1.3 60.0 - - - +
84O GLU* 3.5 16.0 + - - +
85O SER* 3.3 17.3 + - - -
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Residues in contact with ILE 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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40O LEU* 3.7 44.0 - - + -
60O LEU* 5.4 8.1 - - + -
63O LEU* 4.3 13.2 - - + +
78O LEU* 2.8 31.0 + - + +
79O TYR* 3.4 19.3 - - - +
81O LEU* 1.3 72.5 - - - +
83O GLU* 1.3 51.4 + - - +
85O SER* 3.4 3.8 + - - -
86O CYS* 2.8 37.6 + - + +
89O LEU* 4.4 23.3 - - + +
90O ALA* 3.9 15.7 - - + -
93O VAL* 4.5 15.5 - - + -
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Residues in contact with GLU 83 (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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79O TYR* 2.6 33.1 + - - +
80O LYS* 3.6 17.3 - - - +
82O ILE* 1.3 68.5 - - - +
84O GLU* 1.3 67.7 + - - +
86O CYS 3.2 23.4 - - - +
87O PRO* 3.2 15.6 - - + +
90O ALA* 3.1 26.2 - - + +
91O ASN* 5.6 3.1 + - - -
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Residues in contact with GLU 84 (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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80O LYS 2.9 17.4 + - - +
81O LEU* 3.6 16.0 - - - +
82O ILE 3.4 0.2 - - - -
83O GLU* 1.3 78.3 - - - +
85O SER* 1.3 63.9 + - - +
87O PRO* 5.2 1.6 - - - +
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Residues in contact with SER 85 (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 GLU* 4.2 4.3 - - - +
59O ARG* 3.8 36.0 + - - +
60O LEU* 5.0 4.3 - - - -
63O LEU* 3.3 35.5 - - - +
81O LEU 3.3 6.4 + - - -
82O ILE* 3.8 7.6 - - - -
84O GLU* 1.3 84.4 - - - +
86O CYS* 1.3 74.0 + - - +
87O PRO* 4.5 1.8 - - - +
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Residues in contact with CYS 86 (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 GLU* 3.4 49.8 - - - +
60O LEU* 4.6 12.8 - - - -
82O ILE* 2.8 25.5 + - - +
83O GLU* 3.2 8.9 + - - -
85O SER* 1.3 89.2 - - - +
87O PRO* 1.3 70.0 - - - +
88O GLN 3.3 0.8 + - - +
89O LEU* 3.8 28.1 + - + +
90O ALA 3.9 3.5 + - - -
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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