Contacts of the helix formed by residues 94 - 101 (chain B) in PDB entry 1Z0X
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 CYS 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B LEU* 4.0 20.6 - - + -
22B PRO* 3.6 36.7 - - - +
23B THR 3.8 0.2 - - - -
24B LEU* 3.6 29.4 - - + -
92B PHE 3.7 0.8 + - - -
93B PRO* 1.3 74.5 - - - +
95B ALA* 1.3 64.3 + - - +
96B VAL 3.1 2.9 - - - -
97B ALA* 3.0 10.2 + - + -
98B ILE* 2.8 25.9 + - + +
221B CL 4.5 4.9 - - - -
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 3.9 26.6 - - + +
89B TYR* 3.6 33.7 - - + +
92B PHE* 3.5 20.1 + - + +
93B PRO 3.0 3.8 + - - -
94B CYS* 1.3 76.1 - - - +
96B VAL* 1.3 63.4 + - + +
98B ILE* 3.3 3.4 + - - +
99B GLU* 3.1 29.1 + - - +
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B TYR* 4.5 12.1 - - + -
94B CYS 3.1 0.6 - - - -
95B ALA* 1.3 72.3 - - + +
97B ALA* 1.3 67.6 + - - +
99B GLU* 2.9 8.4 + - - +
100B ILE* 2.8 29.1 + - + +
142B PHE* 3.4 37.0 - - + +
145B ILE* 3.3 42.8 - - + -
146B MSE 3.1 34.5 - - + -
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 3.7 17.7 - - + -
94B CYS* 3.0 11.0 + - - +
96B VAL* 1.3 78.7 - - - +
98B ILE* 1.3 57.0 + - - +
100B ILE* 3.6 8.0 - - - +
101B GLN* 2.9 44.3 + - - +
146B MSE 4.4 10.8 - - + +
221B CL 3.8 26.7 - - + -
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PHE* 3.9 28.5 - - + -
18B LEU* 4.3 4.3 - - + -
24B LEU* 3.9 23.1 - - + -
54B LEU* 4.0 11.7 - - + +
57B MSE 4.2 15.5 - - + -
58B ALA* 3.6 36.8 - - + +
61B ILE* 4.0 10.3 - - + -
93B PRO 3.9 10.3 - - - +
94B CYS 2.8 18.1 + - - +
95B ALA* 3.5 7.0 - - - +
97B ALA* 1.3 73.9 - - - +
99B GLU* 1.3 63.0 + - - +
101B GLN* 3.5 1.3 + - - -
102B THR* 2.9 34.8 + - + +
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Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ALA* 4.6 3.7 - - - +
61B ILE* 4.1 18.5 - - - +
62B GLU* 4.3 3.1 - - - +
89B TYR* 3.4 29.3 - - + +
95B ALA 3.1 16.5 + - - +
96B VAL* 2.9 8.0 + - - +
98B ILE* 1.3 75.8 - - - +
100B ILE* 1.3 63.6 + - - +
102B THR* 3.2 23.9 + - - +
106B TYR* 3.8 14.0 + - - -
109B ARG* 2.8 38.8 + - - +
142B PHE* 4.1 17.7 - - + -
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A MSE 4.3 11.7 - - + +
147A ASP* 4.7 22.0 - - - +
150A GLU* 3.0 47.2 - - + +
154A LEU* 4.5 4.3 - - - +
96B VAL* 2.8 46.6 + - + +
97B ALA* 3.6 9.4 - - - +
99B GLU* 1.3 79.6 - - - +
101B GLN* 1.3 61.2 + - + +
102B THR 3.4 6.4 + - - +
142B PHE* 3.6 33.9 - - + -
146B MSE 4.4 12.1 - - + -
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLU* 3.8 23.6 + - - +
154A LEU* 4.4 13.5 - - - +
24B LEU* 3.3 33.3 - - + +
25B GLU* 3.7 23.5 + - - +
50B LYS* 5.9 0.7 - - - -
51B GLN* 3.0 22.7 + - - +
54B LEU* 3.9 19.2 - - + +
97B ALA* 2.9 24.3 + - - +
98B ILE 3.5 2.2 + - - +
99B GLU 3.3 0.2 - - - -
100B ILE* 1.3 80.2 - - + +
102B THR* 1.3 59.8 + - - +
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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