Contacts of the helix formed by residues 72 - 87 (chain O) in PDB entry 5GJQ
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 ASN 72 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71O VAL* 1.3 77.7 - - - +
73O PRO* 1.3 59.8 - - - +
74O LEU* 4.1 6.7 - - + +
75O SER* 3.0 28.7 + - - +
76O LEU* 2.9 25.5 + - - +
14W GLU* 5.8 0.6 + - - -
81W LYS* 4.4 13.5 - - + +
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Residues in contact with PRO 73 (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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68O GLU 5.8 2.9 - - - +
71O VAL 4.2 5.6 - - - +
72O ASN* 1.3 69.6 - - - +
74O LEU* 1.3 61.0 + - - +
76O LEU* 4.0 7.4 - - + +
77O VAL* 2.8 33.4 + - - +
104O VAL* 6.3 0.9 - - + -
107O SER* 4.1 17.9 - - - +
109O GLU* 4.5 8.1 - - + -
110O ALA* 3.0 33.8 - - + +
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Residues in contact with LEU 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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72O ASN* 3.2 7.5 - - + +
73O PRO* 1.3 78.1 - - - +
75O SER* 1.3 56.6 + - - +
77O VAL* 4.1 3.9 - - - +
78O GLU* 2.9 31.4 + - - +
109O GLU* 5.4 3.9 - - + +
110O ALA* 4.7 2.7 - - - +
113O LEU* 4.8 14.2 - - + +
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Residues in contact with SER 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O THR* 5.1 4.5 - - - -
42O LEU* 4.8 19.9 - - - +
71O VAL* 4.0 15.8 - - - +
72O ASN* 3.0 28.1 + - - +
74O LEU* 1.3 82.5 - - - +
76O LEU* 1.3 64.4 + - - +
78O GLU* 3.2 15.8 + - - +
79O ILE* 3.5 11.2 - - - +
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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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64O ILE* 6.1 5.4 - - + -
67O PHE 5.0 0.7 - - - +
68O GLU* 4.3 30.7 - - + +
70O ARG* 5.2 0.2 - - + -
71O VAL* 3.5 26.7 - - + +
72O ASN 2.9 24.1 + - - +
73O PRO* 4.0 7.9 - - + +
75O SER* 1.3 72.5 - - - +
77O VAL* 1.3 62.4 + - - +
79O ILE* 3.1 25.8 + - - +
80O ILE* 3.6 8.1 + - - +
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Residues in contact with VAL 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 PRO 2.8 19.3 + - - +
74O LEU 4.1 1.8 - - - +
76O LEU* 1.3 71.7 - - - +
78O GLU* 1.3 67.1 + - - +
79O ILE 3.0 2.6 + - - -
80O ILE* 3.1 11.9 + - - +
81O LEU* 2.9 21.0 + - - +
110O ALA* 5.1 4.5 - - + +
113O LEU* 4.3 21.1 - - + -
114O CYS* 4.6 20.6 - - - -
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Residues in contact with GLU 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 LEU* 6.6 0.2 - - - -
45O VAL* 6.5 1.1 - - + -
46O GLN* 6.0 5.6 - - + -
74O LEU 2.9 19.7 + - - +
75O SER* 3.4 9.2 - - - +
77O VAL* 1.3 75.1 - - - +
79O ILE* 1.3 65.1 + - + +
81O LEU* 3.1 9.8 + - + +
82O HIS* 2.9 26.7 + - + +
113O LEU* 5.4 2.6 - - - +
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Residues in contact with ILE 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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41O VAL* 5.7 5.6 - - + +
42O LEU* 6.1 6.3 - - + -
45O VAL* 4.9 24.5 - - + +
64O ILE* 4.9 17.7 - - + -
75O SER 3.5 12.1 - - - +
76O LEU* 3.1 17.7 - - - +
77O VAL 3.0 0.6 - - - -
78O GLU* 1.3 75.8 - - + +
80O ILE* 1.3 69.0 + - + +
81O LEU 3.1 0.3 + - - -
82O HIS* 3.3 1.3 + - - +
83O VAL* 2.8 27.7 + - - +
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Residues in contact with ILE 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 LEU 3.6 8.3 + - - +
77O VAL* 3.1 11.7 + - - +
79O ILE* 1.3 77.3 - - + +
81O LEU* 1.3 57.9 + - - +
83O VAL* 4.1 6.1 - - - -
84O VAL* 2.8 42.0 + - + +
96O PHE* 5.6 11.7 - - + +
97O LEU* 6.4 2.2 - - - -
100O THR* 5.3 13.7 - - - -
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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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77O VAL 2.9 13.5 + - - +
78O GLU* 3.2 15.5 - - + +
79O ILE 3.1 0.2 - - - -
80O ILE* 1.3 76.3 - - - +
82O HIS* 1.3 59.3 + - - +
84O VAL* 3.6 1.8 - - - +
85O ARG* 2.8 29.5 + - - +
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Residues in contact with HIS 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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45O VAL* 5.2 12.3 - - + +
46O GLN* 6.3 0.9 - - - -
49O CYS* 4.9 17.8 - - + +
78O GLU* 2.9 17.0 + - + +
79O ILE* 4.2 2.9 - - - +
81O LEU* 1.3 75.9 - - - +
83O VAL* 1.3 64.2 + - - +
85O ARG* 3.2 20.7 - - - +
86O GLN* 4.4 1.0 + - - +
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Residues in contact with VAL 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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45O VAL* 6.1 1.5 - - + +
57O ILE* 3.0 37.9 - - + -
61O GLU* 5.3 0.2 - - + -
79O ILE 2.8 21.6 + - - +
80O ILE* 3.7 6.1 - - - +
82O HIS* 1.3 79.7 - - - +
84O VAL* 1.3 68.6 + - + +
85O ARG 3.1 1.4 + - - -
86O GLN* 3.8 12.6 + - - +
87O MET* 4.4 1.6 + - - +
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Residues in contact with VAL 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 ILE* 2.8 32.4 + - + +
81O LEU* 3.6 2.5 - - - +
83O VAL* 1.3 78.5 - - + +
85O ARG* 1.3 65.7 + - - +
86O GLN 3.4 0.4 - - - -
87O MET* 2.9 28.5 + - + +
93O ALA* 4.4 33.0 - - + +
96O PHE* 5.1 11.4 - - + -
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Residues in contact with ARG 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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81O LEU 2.8 12.6 + - - +
82O HIS* 3.2 20.2 - - - +
83O VAL 3.1 0.8 - - - -
84O VAL* 1.3 76.8 - - - +
86O GLN* 1.3 65.2 + - - +
87O MET 4.0 3.6 - - - +
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Residues in contact with GLN 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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52O GLN* 6.1 2.9 - - + +
54O ASP* 6.5 0.9 - - - -
82O HIS 4.4 0.8 + - - +
83O VAL 3.8 9.0 + - - +
84O VAL 3.4 0.2 - - - -
85O ARG* 1.3 81.1 - - - +
87O MET* 1.3 66.1 + - - +
88O THR* 3.1 11.8 + - - -
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Residues in contact with MET 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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83O VAL 4.4 1.7 + - - +
84O VAL* 2.9 32.5 + - + +
85O ARG 4.0 2.8 - - - +
86O GLN* 1.3 79.5 - - - +
88O THR* 1.3 59.0 + - - +
89O ASP* 3.0 39.3 - - + +
90O PRO* 5.3 4.0 - - - +
92O VAL* 4.6 10.8 - - + -
93O ALA* 4.7 8.3 - - + +
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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