Contacts of the helix formed by residues 78 - 88 (chain H) in PDB entry 1ZGL
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 TYR 78 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7G ILE* 5.5 1.9 - - - +
9G GLN* 3.5 24.4 + - - +
24G PHE* 3.9 6.7 - + - -
13H TYR* 3.8 7.9 + - + +
15H CYS* 4.3 10.6 - - - -
26H PHE* 3.6 35.0 - + - -
74H ALA* 2.8 21.6 + - + +
76H ASP 3.0 0.4 + - - -
77H THR* 1.3 76.2 - - - +
79H CYS* 1.3 60.4 - - - +
80H ARG 3.6 0.9 - - - -
81H HIS* 3.7 2.4 + - - +
82H ASN* 2.6 60.4 + - - +
5I LYS* 4.3 20.4 - - + +
6I ASN 4.6 0.7 - - - -
7I ILE* 3.2 44.9 - - + +
100T VAL* 4.0 11.7 - - + -
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Residues in contact with CYS 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H GLU 3.7 0.4 - - - -
15H CYS* 2.0 55.9 - - + -
17H PHE* 3.1 20.2 - - + -
24H VAL* 3.7 14.8 - - + -
26H PHE* 3.6 34.3 - - - -
74H ALA 3.1 3.8 + - - -
75H VAL 3.3 14.1 - - - +
78H TYR* 1.3 77.3 - - - +
80H ARG* 1.3 64.8 + - - +
82H ASN* 4.3 0.9 - - - +
83H TYR 3.2 12.1 + - - -
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Residues in contact with ARG 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H PHE* 4.7 1.1 - - - -
21H THR* 3.2 27.3 + - - +
22H GLU 3.9 9.9 + - - -
24H VAL* 3.2 46.0 + - + +
75H VAL* 3.1 32.1 + - - +
76H ASP* 3.0 29.0 + - - +
79H CYS* 1.3 73.1 - - - +
81H HIS* 1.3 67.0 + - - +
83H TYR* 3.1 7.6 + - - +
84H GLY* 2.8 22.3 + - - -
29S TYR* 3.0 30.8 + - + +
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Residues in contact with HIS 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76H ASP 3.4 0.4 + - - +
77H THR 3.9 8.5 - - - +
78H TYR* 3.7 7.6 - - - +
79H CYS 3.3 0.2 - - - -
80H ARG* 1.3 75.6 - - - +
82H ASN* 1.3 65.2 + - - +
84H GLY* 3.0 12.2 + - - -
85H VAL* 3.1 24.9 + - + +
2I HIS 5.7 0.4 + - - -
3I PHE 4.0 11.2 + - - -
5I LYS* 2.9 47.2 + - + +
27S THR* 4.6 7.9 - - - +
28S GLY* 3.5 26.0 + - - -
29S TYR* 3.0 30.1 + - + -
94S GLY 3.4 15.9 - - - -
98S GLY 3.9 10.4 + - - -
99S ASP* 5.7 0.4 - - - -
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Residues in contact with ASN 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ILE* 5.3 11.6 - - + +
24G PHE* 3.6 18.2 - - + -
15H CYS* 5.4 2.1 - - - -
78H TYR* 2.6 51.4 + - - +
79H CYS* 4.3 3.4 - - - +
81H HIS* 1.3 76.8 - - - +
83H TYR* 1.3 65.1 + - - +
85H VAL* 3.4 7.1 + - - +
86H GLY* 3.0 22.0 + - - -
4I PHE* 3.2 23.0 - - + -
5I LYS* 2.6 31.4 + - - +
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Residues in contact with TYR 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G HIS* 4.7 6.5 - + + -
7G ILE* 5.4 5.8 - - - +
17H PHE* 3.3 44.2 - + + -
20H GLY* 2.8 44.4 + - - -
21H THR* 4.0 17.5 - - + -
79H CYS 3.2 17.1 + - - +
80H ARG* 3.1 6.9 + - - +
82H ASN* 1.3 74.4 - - - +
84H GLY* 1.3 71.7 + - - +
86H GLY 5.4 0.4 - - - -
87H GLU* 2.9 45.7 + - + +
91H VAL* 4.1 26.8 - - + +
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Residues in contact with GLY 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H ARG 2.8 14.4 + - - -
81H HIS* 3.0 4.9 + - - -
83H TYR* 1.3 80.7 - - - +
85H VAL* 1.3 65.9 + - - +
86H GLY 3.0 0.2 + - - -
87H GLU* 3.1 24.4 + - - +
88H SER* 4.6 1.2 + - - -
27S THR 6.1 0.7 - - - -
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Residues in contact with VAL 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G PHE 4.9 4.8 - - - +
52G ALA* 3.9 25.4 - - + -
81H HIS* 3.1 26.4 + - + +
82H ASN* 3.4 10.5 - - - +
84H GLY* 1.3 74.0 - - - +
86H GLY* 1.3 61.4 + - - +
88H SER* 3.6 13.7 + - - -
89H PHE* 4.2 5.0 - - - -
2I HIS* 4.4 10.3 - - - +
3I PHE 3.6 31.9 - - - +
4I PHE* 4.2 15.3 - - + +
27S THR* 5.1 12.5 + - + +
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Residues in contact with GLY 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82H ASN 3.0 10.7 + - - -
83H TYR* 3.7 2.0 - - - -
85H VAL* 1.3 81.2 - - - +
87H GLU* 1.3 55.4 + - - +
88H SER 3.3 1.6 - - - -
89H PHE* 3.7 21.4 + - - -
90H THR* 2.4 42.6 + - - +
4I PHE* 4.4 6.9 - - - -
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Residues in contact with GLU 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H TYR* 2.9 41.9 + - + +
84H GLY* 3.1 20.4 + - - +
86H GLY* 1.3 72.5 - - - +
88H SER* 1.3 75.1 + - - +
89H PHE 2.9 1.6 + - - -
90H THR* 3.1 17.2 + - - -
91H VAL* 4.4 4.0 - - + +
92H GLN* 2.6 44.0 + - - +
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Residues in contact with SER 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G PHE* 4.9 10.7 + - - -
84H GLY 4.6 1.0 + - - -
85H VAL 3.6 13.0 + - - -
87H GLU* 1.3 84.1 - - - +
89H PHE* 1.3 68.5 + - - +
92H GLN* 3.5 26.3 - - - +
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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