Contacts of the helix formed by residues 89 - 97 (chain A) in PDB entry 5Z66
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 ASP 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A SER 3.6 5.3 + - - +
88A PHE* 1.3 76.2 - - - +
90A LEU* 1.3 68.4 + - - +
91A ARG* 3.2 12.6 - - - +
92A HIS* 3.0 56.4 + - + +
93A PHE* 3.0 21.5 + - - +
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Residues in contact with LEU 90 (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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47A LEU* 4.1 15.3 - - + -
50A ASP* 4.3 12.3 - - + +
51A VAL* 4.2 17.9 - - + +
54A ALA* 4.3 9.9 - - + -
56A LEU* 3.7 27.6 - - + -
79A TYR* 4.0 31.2 - - + +
88A PHE* 3.9 18.9 + - + -
89A ASP* 1.3 72.5 + - - +
91A ARG* 1.3 62.3 + - - +
93A PHE* 3.3 2.6 + - + +
94A VAL* 3.0 34.6 + - + +
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Residues in contact with ARG 91 (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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55A LYS 4.9 1.0 + - - -
56A LEU* 2.8 64.4 + - + +
57A PHE* 4.4 16.7 - - + -
89A ASP* 3.2 13.5 + - - +
90A LEU* 1.3 79.8 - - - +
92A HIS* 1.3 61.0 + - + +
94A VAL* 3.4 2.3 + - - +
95A GLU* 3.0 54.3 + - + +
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Residues in contact with HIS 92 (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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89A ASP* 3.0 40.2 + - + +
91A ARG* 1.3 82.0 - - + +
93A PHE* 1.3 61.0 + - - +
95A GLU* 3.3 17.4 + - - +
96A MET* 2.9 41.6 + - + +
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Residues in contact with PHE 93 (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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47A LEU* 3.9 23.3 - - + -
75A ILE* 3.5 18.6 - - + -
78A ASP* 4.2 3.1 - - + -
79A TYR* 3.4 51.1 - + + -
82A GLN* 3.6 29.8 - - - -
88A PHE* 3.6 28.7 - + + -
89A ASP 3.0 6.0 + - - +
90A LEU* 3.6 7.0 - - + +
92A HIS* 1.3 77.4 - - - +
94A VAL* 1.3 67.6 + - + +
96A MET* 3.2 9.8 + - + +
97A ASN* 2.9 55.9 + - + +
98A PHE* 4.8 0.9 - + - -
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Residues in contact with VAL 94 (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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47A LEU* 5.0 0.9 - - + -
51A VAL* 3.9 20.0 - - + -
56A LEU* 3.7 18.6 - - + -
57A PHE* 3.8 26.0 - - + -
63A PHE* 4.0 21.1 - - + -
90A LEU* 3.0 26.6 + - + +
91A ARG 3.7 4.5 - - - +
93A PHE* 1.3 80.7 - - + +
95A GLU* 1.3 58.5 + - - +
97A ASN 3.1 0.7 + - - -
98A PHE* 2.8 41.1 + - + +
100A LEU* 4.1 10.5 - - + -
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Residues in contact with GLU 95 (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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57A PHE* 5.9 1.9 - - + -
69A LYS* 3.2 17.7 + - - -
91A ARG* 3.0 39.9 + - + +
92A HIS* 3.3 15.1 + - - +
94A VAL* 1.3 77.2 - - + +
96A MET* 1.3 61.5 + - + +
98A PHE 3.5 8.4 - - - +
100A LEU* 4.3 21.2 - - + +
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Residues in contact with MET 96 (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 LYS* 3.2 20.6 + - - +
82A GLN* 3.8 25.8 - - - +
92A HIS* 2.9 24.2 + - + +
93A PHE* 3.6 23.3 - - + +
95A GLU* 1.3 79.3 - - - +
97A ASN* 1.3 65.1 + - - +
98A PHE 3.6 0.2 - - - -
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Residues in contact with ASN 97 (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 LYS* 2.8 32.0 + - - +
70A SER* 4.5 4.9 + - - -
75A ILE* 3.6 24.8 - - + +
78A ASP* 4.7 9.5 - - - +
82A GLN* 5.3 1.4 - - - +
93A PHE* 2.9 58.4 + - + +
96A MET* 1.3 89.7 - - - +
98A PHE* 1.3 78.2 + - + +
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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