Contacts of the helix formed by residues 66 - 83 (chain I) 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 GLU 66 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65I LEU* 1.3 77.4 - - - +
67I ARG* 1.3 51.9 + - - +
69I LYS* 3.0 13.6 + - + +
70I ASP* 2.4 39.5 + - + +
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Residues in contact with ARG 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I LEU 3.0 9.5 - - - +
66I GLU* 1.3 76.9 - - - +
68I ILE* 1.3 52.4 + - - +
70I ASP* 3.0 9.3 + - - +
71I TYR* 2.6 37.9 + - - +
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Residues in contact with ILE 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I LEU* 2.9 14.1 + - - +
67I ARG* 1.3 77.4 - - - +
69I LYS* 1.3 62.7 + - - +
71I TYR* 3.0 8.5 + - - +
72I LEU* 2.9 27.1 + - - +
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Residues in contact with LYS 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H ASP* 6.5 0.9 - - + -
53H GLN* 6.1 4.7 - - + -
65I LEU 3.5 2.6 + - - +
66I GLU* 3.0 18.2 + - + +
68I ILE* 1.3 78.0 - - - +
70I ASP* 1.3 57.5 + - - +
72I LEU* 4.3 4.4 - - - +
73I LEU* 3.1 28.4 + - - +
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Residues in contact with ASP 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I GLU* 2.4 30.2 + - + +
67I ARG* 3.3 10.3 - - - +
69I LYS* 1.3 68.3 - - - +
71I TYR* 1.3 59.9 + - - +
73I LEU* 3.2 7.7 - - - +
74I MET* 2.9 27.4 + - - +
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Residues in contact with TYR 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I ARG 2.6 19.8 + - - +
68I ILE* 3.4 7.9 - - - +
70I ASP* 1.3 72.4 - - - +
72I LEU* 1.3 51.1 + - - +
74I MET* 2.9 12.7 + - - +
75I GLU* 2.7 32.8 + - - +
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Residues in contact with LEU 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I ILE 2.9 18.0 + - - +
69I LYS* 4.3 4.9 - - - +
71I TYR* 1.3 69.4 - - - +
73I LEU* 1.3 56.1 + - - +
75I GLU* 3.3 10.4 - - + +
76I GLU* 2.5 39.6 + - - +
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Residues in contact with LEU 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I LYS 3.1 22.0 + - - +
70I ASP* 3.2 9.4 - - - +
72I LEU* 1.3 74.4 - - - +
74I MET* 1.3 63.1 + - - +
76I GLU* 3.3 5.6 + - - +
77I GLU* 2.9 25.2 + - - +
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Residues in contact with MET 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I ASP 2.9 12.8 + - - +
71I TYR* 3.1 14.8 - - - +
73I LEU* 1.3 73.3 - - - +
75I GLU* 1.3 61.4 + - - +
77I GLU* 3.4 9.1 - - - +
78I PHE* 3.1 19.2 + - - +
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Residues in contact with GLU 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71I TYR 2.7 15.6 + - - +
72I LEU* 2.9 15.3 + - - +
74I MET* 1.3 71.3 - - - +
76I GLU* 1.3 60.3 + - - +
78I PHE* 2.8 26.4 + - - +
79I ILE* 3.0 11.3 + - - +
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Residues in contact with GLU 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H LYS* 5.5 11.4 - - + -
72I LEU 2.5 20.5 + - - +
73I LEU* 3.8 5.6 - - - +
75I GLU* 1.3 72.4 - - - +
77I GLU* 1.3 61.2 + - - +
79I ILE* 3.2 10.6 + - - +
80I ARG* 3.1 23.4 + - - +
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Residues in contact with GLU 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I LEU 2.9 14.7 + - - +
74I MET* 3.4 13.7 - - - +
76I GLU* 1.3 73.0 - - - +
78I PHE* 1.3 65.4 + - - +
79I ILE 3.4 0.2 + - - -
80I ARG* 3.4 5.4 + - - +
81I ASN* 2.9 25.7 + - - +
606Z VAL* 5.7 11.2 - - + +
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Residues in contact with PHE 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I MET 3.1 8.9 + - - +
75I GLU* 2.8 16.8 + - - +
77I GLU* 1.3 78.9 - - - +
79I ILE* 1.4 54.6 + - - +
81I ASN* 3.3 7.5 + - - +
82I GLN* 2.8 31.6 + - - +
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Residues in contact with ILE 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I GLU 3.0 10.1 + - - +
76I GLU* 3.2 13.0 + - - +
78I PHE* 1.4 75.7 - - - +
80I ARG* 1.3 51.8 + - - +
82I GLN* 3.0 9.4 + - - +
83I GLU* 2.6 35.5 + - - +
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Residues in contact with ARG 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H GLU* 5.9 7.9 - - - -
76I GLU 3.1 14.9 + - - +
77I GLU* 3.9 5.4 - - - +
79I ILE* 1.3 74.5 - - - +
81I ASN* 1.3 64.9 + - - +
83I GLU* 2.9 25.0 + - - +
84I GLN 3.7 2.1 + - - -
614Z HIS* 5.2 1.4 - - - +
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Residues in contact with ASN 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I GLU 2.9 20.0 + - - +
78I PHE* 3.3 8.1 - - - +
80I ARG* 1.3 79.0 - - - +
82I GLN* 1.3 62.2 + - - +
83I GLU 3.2 0.2 + - - -
84I GLN* 3.2 9.4 + - - +
606Z VAL 5.4 0.9 - - - +
610Z GLN* 4.3 32.8 - - + +
611Z GLN* 5.2 4.0 - - - +
614Z HIS* 3.4 17.6 - - - +
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Residues in contact with GLN 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I PHE 2.8 20.0 + - - +
79I ILE* 3.5 7.2 - - - +
81I ASN* 1.3 67.9 - - - +
83I GLU* 1.3 57.2 + - - +
84I GLN* 3.0 18.5 + - - +
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Residues in contact with GLU 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H SER* 5.8 4.2 - - - -
79I ILE 2.6 16.9 + - - +
80I ARG* 2.9 22.8 + - - +
82I GLN* 1.3 72.0 - - - +
84I GLN* 1.3 60.6 + - - +
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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