Contacts of the helix formed by residues 78 - 88 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7J ILE* 5.7 1.4 - - + +
9J GLN* 2.8 42.4 + - - +
24J PHE* 3.8 5.2 - + - -
13K TYR* 3.5 15.5 + - + +
15K CYS* 3.8 15.3 - - - -
26K PHE* 3.2 37.0 - + - -
74K ALA* 2.7 23.0 + - + +
76K ASP 3.2 0.2 - - - -
77K THR* 1.3 77.5 - - - +
79K CYS* 1.3 63.4 + - - +
80K ARG 3.7 0.4 - - - -
81K HIS 4.0 1.6 - - - -
82K ASN* 3.1 58.7 + - - -
5L LYS* 3.9 11.7 - - + +
6L ASN* 4.3 8.7 - - - -
7L ILE* 3.7 22.7 - - + -
100V VAL* 4.1 10.8 - - + -
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Residues in contact with CYS 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K CYS* 2.0 53.3 - - - -
17K PHE* 3.0 16.5 - - + -
24K VAL* 3.4 25.1 - - + -
26K PHE* 3.6 32.1 - - - -
74K ALA 3.0 5.5 + - - -
75K VAL* 3.4 7.6 - - - +
78K TYR* 1.3 76.2 - - - +
80K ARG* 1.3 65.7 + - - +
82K ASN* 4.1 1.4 - - - +
83K TYR 3.0 14.6 + - - -
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Residues in contact with ARG 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K PHE* 4.1 3.1 - - + -
21K THR* 3.5 22.8 + - + +
22K GLU 3.7 14.1 + - - -
23K ARG* 4.4 0.2 - - - +
24K VAL* 2.9 53.4 + - + +
75K VAL* 3.3 23.3 + - - +
76K ASP* 2.6 43.7 + - - +
79K CYS* 1.3 77.2 - - - +
81K HIS* 1.3 69.3 + - - +
83K TYR* 3.5 6.3 - - - +
84K GLY* 2.9 17.5 + - - -
29U TYR* 3.3 31.1 + - + +
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Residues in contact with HIS 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76K ASP 3.7 2.4 + - - -
77K THR 3.7 17.2 + - - +
78K TYR 3.9 3.8 - - - +
79K CYS 3.2 0.8 - - - -
80K ARG* 1.3 82.7 - - - +
82K ASN* 1.3 63.0 + - - +
84K GLY* 2.9 13.7 + - - -
85K VAL* 3.0 27.1 + - + +
3L PHE 3.8 14.9 + - - -
5L LYS* 3.5 26.7 + - + +
27U THR* 4.3 5.4 - - + +
28U GLY* 3.3 30.5 + - - -
29U TYR* 3.6 21.8 + - + -
94U GLY 3.2 27.5 + - - -
98U GLY* 4.2 7.4 - - - -
99U ASP 4.6 3.0 + - - -
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Residues in contact with ASN 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ILE* 5.2 11.5 - - + +
24J PHE* 4.0 10.2 - - + -
15K CYS* 5.6 1.7 - - - -
78K TYR* 3.1 52.0 + - - +
79K CYS* 4.1 2.0 - - - +
81K HIS* 1.3 78.3 - - - +
83K TYR* 1.3 71.0 + - - +
85K VAL* 3.1 2.5 + - - +
86K GLY* 3.0 17.2 + - - -
4L PHE* 3.2 33.0 - - + -
5L LYS* 2.6 36.0 + - - +
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Residues in contact with TYR 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J HIS* 4.3 8.1 - + + -
7J ILE* 5.3 10.5 - - + +
26J PHE* 6.3 1.1 - + - -
17K PHE* 3.5 40.8 - + + -
20K GLY* 3.1 33.5 + - - -
21K THR* 4.2 16.2 - - + -
79K CYS 3.0 19.6 + - - +
80K ARG* 3.5 5.4 - - - +
82K ASN* 1.3 75.3 - - - +
84K GLY* 1.3 64.2 + - - +
86K GLY* 3.6 0.9 - - - -
87K GLU* 2.8 62.0 + - + -
91K VAL* 3.7 33.2 - - + +
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Residues in contact with GLY 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80K ARG 2.9 9.6 + - - -
81K HIS 2.9 10.3 + - - -
83K TYR* 1.3 81.7 - - - +
85K VAL* 1.3 62.4 + - - +
87K GLU* 3.4 29.4 - - - +
88K SER* 4.6 2.3 + - - -
27U THR* 6.5 0.2 - - - -
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Residues in contact with VAL 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J PHE 5.1 2.9 - - - +
52J ALA* 3.8 8.6 - - + +
81K HIS* 3.0 33.8 + - + +
82K ASN* 3.1 7.8 + - - +
84K GLY* 1.3 76.4 - - - +
86K GLY* 1.3 60.5 + - - +
88K SER* 3.9 11.1 + - - -
89K PHE* 4.2 6.6 - - - -
1L VAL 4.0 9.4 - - - +
2L HIS* 3.8 31.6 - - - +
3L PHE 3.6 12.8 - - - +
4L PHE* 3.7 25.8 - - + -
27U THR* 4.6 5.8 - - + +
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Residues in contact with GLY 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K ASN 3.0 11.4 + - - -
83K TYR* 3.6 1.8 - - - -
85K VAL* 1.3 77.7 - - - +
87K GLU* 1.3 60.0 + - - +
88K SER 3.3 2.9 + - - -
89K PHE* 3.4 12.1 + - - -
90K THR* 2.6 36.6 + - - +
4L PHE* 3.7 21.3 - - - -
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Residues in contact with GLU 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K TYR* 2.8 47.7 + - + +
84K GLY* 3.4 26.3 - - - +
86K GLY* 1.3 68.8 - - - +
88K SER* 1.3 67.3 + - - +
89K PHE 2.6 15.6 + - - -
90K THR* 2.8 20.8 + - - -
91K VAL* 4.4 7.0 - - + +
92K GLN* 3.5 30.3 + - + +
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Residues in contact with SER 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J PHE* 5.1 11.4 - - - -
84K GLY 4.6 1.6 + - - -
85K VAL 3.9 12.7 + - - -
87K GLU* 1.3 82.2 - - - +
89K PHE* 1.3 69.5 + - - +
92K GLN* 3.7 29.6 - - - +
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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