Contacts of the helix formed by residues 85 - 93 (chain B) in PDB entry 4CZ8
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 ASN 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LEU* 3.2 13.4 + - - +
82B LEU 3.0 7.2 + - - -
84B LYS* 1.3 92.2 - - - +
86B MSE 1.3 63.5 + - - +
87B PRO* 3.5 7.1 - - - -
88B THR* 3.6 9.0 + - - +
89B ILE* 3.4 23.8 + - + +
146B ASP* 2.5 37.5 + - - +
149B THR* 5.0 5.3 - - + +
150B VAL* 3.6 21.0 - - + +
348B TRP* 4.5 6.0 - - + -
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Residues in contact with MSE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 2.7 23.0 + - + +
83B LYS* 3.3 56.1 - - + +
84B LYS 3.4 1.4 - - - -
85B ASN* 1.3 73.4 - - - +
87B PRO* 1.3 71.6 - - + +
89B ILE* 3.4 4.0 + - - +
90B VAL* 2.9 44.5 + - + +
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Residues in contact with PRO 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LYS 5.2 0.2 - - - +
84B LYS 4.9 3.1 - - - +
85B ASN* 3.5 4.5 - - - -
86B MSE 1.3 94.3 - - + +
88B THR* 1.3 67.8 + - - +
90B VAL* 3.7 5.8 - - + +
91B THR* 2.9 31.5 + - + +
347B TRP* 3.8 28.9 - - + -
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Residues in contact with THR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASN* 3.8 10.9 + - - +
86B MSE 3.4 0.2 - - - -
87B PRO* 1.3 81.3 - - - +
89B ILE* 1.3 59.4 + - - +
91B THR* 2.3 28.0 + - - -
92B LEU* 2.9 22.2 + - + +
150B VAL* 3.7 27.6 - - + -
344B LEU* 4.3 12.1 - - + -
347B TRP* 4.8 7.1 - - - +
348B TRP* 2.4 50.4 + - + +
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Residues in contact with ILE 89 (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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81B LEU 5.7 0.2 - - - +
82B LEU* 3.9 26.0 - - + +
85B ASN* 3.4 19.0 + - + +
86B MSE 3.4 6.6 + - - +
87B PRO 3.3 0.4 - - - -
88B THR* 1.3 74.9 - - - +
90B VAL* 1.3 65.9 + - + +
92B LEU* 2.9 9.2 + - + +
93B ASP* 2.9 44.3 + - - +
150B VAL* 3.3 46.0 - - + +
153B THR* 3.8 26.2 - - + -
154B GLU* 4.0 3.1 - - - +
157B PHE* 4.4 5.2 - - + -
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 6.0 1.8 - - + -
86B MSE 2.9 44.4 + - + +
87B PRO* 3.7 6.5 - - + +
89B ILE* 1.3 78.4 - - + +
91B THR* 1.3 59.9 + - + +
93B ASP* 3.1 4.1 + - - +
94B THR* 2.5 48.4 + - + +
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Residues in contact with THR 91 (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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87B PRO 2.9 16.3 + - - +
88B THR* 2.3 31.5 + - - -
90B VAL* 1.3 77.4 - - + +
92B LEU* 1.3 59.3 + - - +
94B THR* 4.8 0.4 - - - -
95B ILE* 2.9 41.2 + - + +
96B GLY 3.0 9.8 + - - -
343B PRO* 5.7 12.3 - - + +
344B LEU* 3.8 14.6 - - - +
347B TRP* 3.8 26.2 - - + -
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Residues in contact with LEU 92 (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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88B THR* 2.9 20.7 + - + +
89B ILE* 2.9 11.2 + - + +
91B THR* 1.3 81.4 + - - +
93B ASP* 1.3 61.9 + - - +
94B THR 3.6 0.2 - - - -
96B GLY* 4.2 8.0 - - - +
97B LEU* 3.5 22.1 + - - +
150B VAL* 3.6 30.3 - - + -
154B GLU* 3.5 50.9 - - + +
158B ASN* 5.5 0.3 - - - +
337B ARG* 5.1 2.9 - - - +
341B THR* 4.6 12.3 - - + -
344B LEU* 3.6 31.0 - - + -
356B ILE* 5.0 3.8 - - + -
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Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 2.9 32.9 + - - +
90B VAL* 4.1 2.7 - - - +
92B LEU* 1.3 83.4 - - - +
94B THR* 1.3 64.1 + - - +
97B LEU* 4.7 11.4 - - - +
98B ILE* 6.0 0.5 - - - +
154B GLU* 3.2 26.3 - - - +
157B PHE* 3.1 29.6 - - + +
158B ASN* 3.9 8.3 - - - +
161B LEU* 3.4 30.1 - - + +
199B PHE* 5.0 6.4 - - - -
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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