Contacts of the helix formed by residues 84 - 95 (chain A) in PDB entry 2Z17
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 THR 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A SER* 4.3 0.2 - - - -
48A MET* 4.7 7.6 - - - -
82A GLY 4.5 4.5 - - - +
83A PHE* 1.3 77.0 - - - +
85A TYR* 1.3 64.7 + - - +
86A LYS* 3.6 8.6 + - - +
87A GLN* 2.7 49.1 + - + +
88A VAL* 3.2 10.3 + - - +
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Residues in contact with TYR 85 (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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32A GLU* 5.1 5.0 + - - -
33A ILE* 3.4 48.1 + - + +
34A GLN* 3.9 6.7 - - - -
35A SER* 3.5 39.9 + - - +
48A MET* 5.7 0.2 - - - -
50A THR* 5.2 0.4 - - + -
84A THR* 1.3 71.5 - - - +
86A LYS* 1.3 60.9 + - + +
88A VAL* 3.3 10.1 + - - +
89A VAL* 3.0 48.4 + - + +
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Residues in contact with LYS 86 (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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84A THR* 3.1 8.4 + - - +
85A TYR* 1.3 81.9 - - + +
87A GLN* 1.3 58.2 + - + +
89A VAL* 3.6 6.8 - - + +
90A ASP* 2.7 74.5 + - - +
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Residues in contact with GLN 87 (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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82A GLY 3.7 4.4 + - - -
83A PHE* 3.3 32.5 - - + +
84A THR* 2.7 51.2 + - - +
86A LYS* 1.3 73.5 - - + +
88A VAL* 1.3 59.0 + - - +
90A ASP* 3.1 7.7 + - - +
91A LEU* 2.7 37.4 + - - +
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Residues in contact with VAL 88 (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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33A ILE* 3.3 24.5 - - + -
50A THR* 3.9 22.7 - - + +
72A LEU* 4.6 5.6 - - + -
75A ILE* 4.1 21.9 - - + +
80A THR* 5.0 5.8 - - + -
83A PHE* 3.8 28.2 - - + -
84A THR 3.2 13.9 + - - +
85A TYR* 3.4 8.7 - - - +
87A GLN* 1.3 77.9 - - - +
89A VAL* 1.3 57.0 + - - +
91A LEU* 3.4 4.4 + - - +
92A ILE* 3.0 38.8 + - + +
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Residues in contact with VAL 89 (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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33A ILE* 4.1 13.2 - - + -
85A TYR* 3.0 41.7 + - + +
86A LYS* 3.7 9.6 - - + +
87A GLN 3.1 0.2 - - - -
88A VAL* 1.3 75.0 - - - +
90A ASP* 1.3 68.1 + - - +
92A ILE* 3.3 9.0 + - + +
93A ARG* 2.9 40.4 + - + +
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Residues in contact with ASP 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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86A LYS* 2.7 66.4 + - - +
87A GLN* 3.6 6.9 - - - +
89A VAL* 1.3 75.5 - - - +
91A LEU* 1.3 64.2 + - - +
93A ARG* 3.2 13.5 + - - +
94A SER* 2.8 22.4 + - - -
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Residues in contact with LEU 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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75A ILE* 3.8 35.9 - - + +
76A ASN* 4.2 12.1 - - + +
78A VAL* 3.9 35.9 - - + -
80A THR* 5.0 0.2 - - + -
83A PHE* 3.9 18.2 - - + -
87A GLN 2.7 20.2 + - - +
88A VAL 3.8 4.5 - - - +
90A ASP* 1.3 73.6 - - - +
92A ILE* 1.3 55.4 + - - +
94A SER* 2.4 44.9 + - - +
95A SER* 3.3 3.5 + - - +
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Residues in contact with ILE 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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29A PHE* 4.0 30.1 - - + -
31A PHE* 3.9 28.9 - - + -
33A ILE* 4.7 7.9 - - + -
72A LEU* 5.2 2.0 - - + -
75A ILE* 4.3 16.8 - - + -
88A VAL* 3.0 36.4 + - + +
89A VAL* 3.7 7.2 - - + +
91A LEU* 1.3 76.6 - - - +
93A ARG* 1.3 63.1 + - + +
95A SER* 3.1 18.7 + - - -
96A GLY 4.3 1.2 + - - +
99A LEU* 4.1 20.0 - - + +
101A ILE* 6.1 0.4 - - + -
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Residues in contact with ARG 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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89A VAL* 2.9 37.4 + - + +
90A ASP* 3.7 11.9 - - - +
92A ILE* 1.3 73.8 - - + +
94A SER* 1.3 61.3 + - - +
95A SER 3.0 6.3 + - - -
96A GLY* 3.6 9.5 + - - +
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Residues in contact with SER 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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90A ASP 2.8 12.0 + - - -
91A LEU* 2.4 37.0 + - - +
93A ARG* 1.3 77.9 - - - +
95A SER* 1.3 59.1 + - - +
96A GLY 3.5 1.1 + - - -
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Residues in contact with SER 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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76A ASN* 2.4 28.6 + - - -
91A LEU* 3.5 10.0 + - - +
92A ILE 3.1 11.2 + - - -
93A ARG 3.0 2.4 - - - -
94A SER* 1.3 79.9 + - - +
96A GLY* 1.3 66.0 + - - +
98A LEU* 2.8 34.5 + - - +
99A LEU* 3.7 9.7 - - - +
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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