Contacts of the helix formed by residues 69 - 83 (chain A) in PDB entry 1G24
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 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLY 3.6 2.4 + - - -
68A LEU* 1.3 76.8 - - - +
70A LYS* 1.3 64.5 - - - +
71A SER* 3.1 11.0 + - - -
72A GLU* 2.8 40.9 + - - +
73A LYS* 3.0 23.3 + - - +
117A LYS* 4.5 5.4 - - - -
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Residues in contact with LYS 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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69A SER* 1.3 74.3 - - - +
71A SER* 1.3 58.6 + - - +
73A LYS* 3.3 10.4 + - - +
74A GLU* 3.0 61.3 + - + +
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Residues in contact with SER 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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69A SER* 3.1 11.5 + - - -
70A LYS* 1.3 77.0 - - - +
72A GLU* 1.3 62.4 + - - +
74A GLU* 3.4 14.9 + - - +
75A ALA* 3.0 26.9 + - - +
106A LYS* 6.0 2.9 - - - -
110A LEU* 3.6 30.8 - - - +
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Residues in contact with GLU 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* 3.4 11.3 - - + -
69A SER* 2.8 45.5 + - - +
71A SER* 1.3 73.6 - - - +
73A LYS* 1.3 66.1 + - - +
75A ALA* 3.2 8.1 + - - +
76A ILE* 3.1 28.8 + - - +
110A LEU* 4.3 20.3 - - + +
113A LYS* 4.5 7.4 - - - +
114A SER* 3.7 38.6 + - - -
117A LYS* 2.9 27.5 + - - +
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Residues in contact with LYS 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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63A TYR* 3.1 32.2 + - - +
68A LEU* 3.9 40.8 + - + +
69A SER 3.0 17.0 + - - +
70A LYS* 3.7 10.3 - - - +
72A GLU* 1.3 78.3 - - - +
74A GLU* 1.3 57.0 + - - +
76A ILE* 3.1 6.5 + - - +
77A VAL* 2.9 33.3 + - + +
206A ILE* 3.9 18.5 - - + +
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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 LYS* 3.0 54.8 + - + +
71A SER* 3.8 15.2 - - - +
72A GLU 3.3 0.2 - - - -
73A LYS* 1.3 76.6 - - + +
75A ALA* 1.3 57.6 + - - +
77A VAL* 3.3 9.3 + - - +
78A SER* 2.8 30.2 + - - -
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Residues in contact with ALA 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 SER 3.0 15.0 + - - +
72A GLU* 3.4 9.9 - - - +
73A LYS 3.2 0.2 - - - -
74A GLU* 1.3 76.7 - - - +
76A ILE* 1.3 56.5 + - - +
78A SER* 3.3 7.4 + - - -
79A TYR* 2.9 27.2 + - - +
107A GLN* 3.9 31.4 - - + +
110A LEU* 3.9 16.8 - - + -
111A LEU* 4.3 11.0 - - + +
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Residues in contact with ILE 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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68A LEU* 3.8 15.0 - - + -
72A GLU 3.1 15.5 + - - +
73A LYS* 3.1 7.2 + - - +
75A ALA* 1.3 75.0 - - - +
77A VAL* 1.3 67.2 + - - +
79A TYR* 3.1 9.1 + - + +
80A THR* 3.0 24.4 + - + +
111A LEU* 3.7 21.3 - - + -
114A SER* 4.5 4.7 - - - +
118A MET* 4.3 14.8 - - + -
203A ILE* 3.6 43.1 - - + -
206A ILE* 3.8 32.5 - - + -
207A SER* 5.3 0.7 - - - -
216A LEU* 5.5 1.3 - - + -
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Residues in contact with VAL 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 LYS* 2.9 20.9 + - + +
74A GLU* 3.6 10.1 - - - +
76A ILE* 1.3 76.5 - - - +
78A SER* 1.3 63.4 + - - +
80A THR* 2.6 23.8 + - - -
81A LYS* 3.2 36.9 + - - +
206A ILE* 3.4 27.8 - - + +
207A SER* 4.1 14.4 - - - +
209A PHE* 5.7 0.2 - - + -
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Residues in contact with SER 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 2.8 17.4 + - - -
75A ALA* 3.5 7.6 - - - -
77A VAL* 1.3 79.7 - - - +
79A TYR* 1.3 62.4 + - - +
81A LYS* 3.1 19.2 + - - +
82A SER* 3.1 18.2 + - - -
86A ILE* 4.5 2.4 - - - +
107A GLN* 3.1 28.2 + - - -
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Residues in contact with TYR 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 ALA 2.9 14.6 + - - +
76A ILE* 3.4 8.7 - - - +
78A SER* 1.3 75.7 - - - +
80A THR* 1.3 68.2 + - + +
82A SER 3.1 0.2 + - - -
83A ALA* 2.7 60.5 + - + +
86A ILE* 3.9 23.7 - - + +
87A ASN* 3.2 23.9 + - - -
111A LEU* 4.0 25.1 - - + -
172A TYR* 3.8 27.6 + + + +
174A SER* 2.9 23.8 + - - -
203A ILE* 4.8 1.6 - - + -
214A GLU* 4.2 6.1 - - - -
216A LEU* 3.6 33.5 - - + +
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Residues in contact with THR 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 ILE* 3.0 14.2 + - + +
77A VAL 2.6 18.0 + - - -
79A TYR* 1.3 82.0 - - + +
81A LYS* 1.3 60.8 + - - +
82A SER 3.7 0.2 + - - -
83A ALA* 4.3 7.0 + - - +
203A ILE* 3.9 26.5 - - + -
207A SER* 2.7 33.6 + - - -
209A PHE* 3.8 26.4 - - - +
210A ALA* 4.0 8.3 - - - -
214A GLU* 4.9 2.2 - - - +
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Residues in contact with LYS 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 VAL* 3.5 34.5 - - + +
78A SER* 3.1 12.3 + - - +
80A THR* 1.3 77.2 + - - +
82A SER* 1.3 64.7 + - - +
83A ALA 3.8 0.4 - - - -
209A PHE* 4.0 36.1 - - + -
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Residues in contact with SER 82 (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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78A SER* 3.1 15.4 + - - -
79A TYR 3.4 1.8 - - - -
81A LYS* 1.3 86.1 + - - +
83A ALA* 1.3 63.2 + - - +
84A SER* 3.3 2.9 - - - -
85A GLU* 3.1 26.5 + - - +
86A ILE* 2.9 33.2 + - - +
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Residues in contact with ALA 83 (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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79A TYR* 2.7 53.1 + - + +
80A THR* 4.3 6.9 + - - +
81A LYS 3.8 1.0 - - - -
82A SER* 1.3 71.9 - - - +
84A SER* 1.3 64.2 + - - +
86A ILE* 4.6 0.4 - - - +
87A ASN* 2.9 34.2 + - - +
174A SER* 5.3 1.3 - - - +
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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