Contacts of the helix formed by residues 65 - 81 (chain A) in PDB entry 5ZRV
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 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A THR 3.4 6.5 + - - -
64A LEU* 1.3 74.2 - - - +
66A LYS* 1.3 66.1 + - - +
67A GLU 3.2 2.9 - - - +
68A LEU* 3.1 6.3 + - - +
69A HIS* 3.1 19.6 + - - -
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A SER* 1.3 71.5 - - - +
67A GLU* 1.3 56.1 + - - +
69A HIS* 4.6 1.1 - - - +
70A SER* 2.9 29.8 + - - -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A SER* 3.2 1.6 - - - +
66A LYS* 1.3 76.5 - - - +
68A LEU* 1.3 54.9 + - - +
70A SER* 4.4 3.2 + - - +
71A GLU 5.0 2.4 + - - -
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A SER* 3.1 13.2 + - - +
66A LYS 3.1 0.6 - - - -
67A GLU* 1.3 76.2 - - - +
69A HIS* 1.3 59.9 + - - +
70A SER 3.2 1.8 - - - -
71A GLU* 3.2 4.5 + - - -
72A PHE* 2.9 22.0 + - - -
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Residues in contact with HIS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A SER 3.1 13.6 + - - -
66A LYS* 3.9 1.8 - - - +
68A LEU* 1.3 76.0 - - - +
70A SER* 1.3 56.0 + - - +
71A GLU 3.1 0.2 - - - -
72A PHE* 3.9 6.1 - - - +
73A SER* 2.9 28.1 + - - +
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LYS 2.9 17.5 + - - -
67A GLU* 5.0 3.4 - - - +
68A LEU 3.2 1.2 - - - -
69A HIS* 1.3 74.6 - - - +
71A GLU* 1.3 55.5 + - - +
73A SER* 4.6 1.3 - - - -
74A GLU 5.2 2.1 + - - -
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A THR 5.2 11.9 - - - +
67A GLU 5.0 2.4 + - - -
68A LEU* 3.2 5.9 + - - +
69A HIS 3.1 0.2 - - - -
70A SER* 1.3 77.7 - - - +
72A PHE* 1.3 62.7 + - - +
73A SER 3.1 2.3 + - - -
74A GLU 3.5 11.6 + - - +
75A VAL* 3.8 8.3 + - - -
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Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU 2.9 16.3 + - - -
69A HIS* 3.2 6.0 + - - +
71A GLU* 1.3 75.0 - - - +
73A SER* 1.3 64.4 + - - +
75A VAL* 4.1 4.5 + - - +
76A MET* 4.2 5.9 + - - -
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Residues in contact with SER 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A HIS 2.9 15.1 + - - -
70A SER 5.4 0.7 - - - -
71A GLU* 3.1 0.6 - - - +
72A PHE* 1.3 80.1 - - - +
74A GLU* 1.3 57.7 + - - +
75A VAL 2.9 7.6 + - - -
76A MET* 3.5 8.3 + - - -
77A ASN* 3.9 6.8 + - - -
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A SER 5.2 1.6 + - - -
71A GLU* 3.5 10.5 + - - +
73A SER* 1.3 71.3 - - - +
75A VAL* 1.3 57.5 + - - +
77A ASN* 4.7 3.8 - - - +
78A GLU* 4.6 6.1 + - - -
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLU 3.8 8.9 + - - -
72A PHE 4.1 1.7 + - - -
73A SER 2.9 4.6 + - - -
74A GLU* 1.3 77.3 - - - +
76A MET* 1.3 58.8 + - - +
77A ASN 3.2 1.8 - - - -
78A GLU* 3.0 5.7 + - - -
79A ILE* 2.9 22.0 + - - -
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Residues in contact with MET 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE 4.2 6.2 + - - -
73A SER 3.5 5.2 + - - -
75A VAL* 1.3 74.9 - - - +
77A ASN* 1.3 52.2 + - - +
79A ILE* 3.2 5.1 + - - +
80A TRP* 2.6 30.5 + - - -
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Residues in contact with ASN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A SER 3.9 9.5 + - - -
74A GLU* 5.4 1.8 - - - +
75A VAL 3.2 1.0 - - - +
76A MET* 1.3 77.4 - - - +
78A GLU* 1.3 50.4 + - - +
80A TRP* 3.0 4.5 + - - +
81A ALA* 2.5 31.7 + - - -
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLU 4.6 6.8 + - - -
75A VAL 3.0 9.4 + - - -
77A ASN* 1.3 71.7 - - - +
79A ILE* 1.3 59.8 + - - +
81A ALA* 3.1 4.8 + - - +
82A SER* 3.0 24.1 + - - -
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Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL 2.9 13.7 + - - -
76A MET* 3.2 6.5 + - - +
78A GLU* 1.3 76.2 - - - +
80A TRP* 1.3 58.5 + - - +
82A SER* 3.3 16.2 + - - +
85A ILE 5.5 1.7 - - - +
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Residues in contact with TRP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A MET 2.6 17.9 + - - -
77A ASN* 3.0 6.9 + - - +
79A ILE* 1.3 73.2 - - - +
81A ALA* 1.3 58.0 + - - +
82A SER 3.3 5.3 + - - +
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASN 2.5 17.7 + - - -
78A GLU* 3.1 9.2 + - - +
80A TRP* 1.3 74.2 - - - +
82A SER* 1.3 58.4 + - - +
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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