Contacts of the helix formed by residues 90 - 101 (chain A) in PDB entry 4BT9
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 SER 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A TYR* 3.7 15.7 - - - -
32A GLU* 5.2 0.9 - - - -
88A ASP* 2.7 22.2 + - - -
89A MET* 1.3 78.3 - - - +
91A ASP* 1.3 59.6 + - - +
92A GLY 3.3 3.3 + - - -
93A PHE* 3.4 4.0 + - - +
94A ILE* 2.9 29.9 + - - +
85B VAL* 3.6 32.2 + - - -
86B LEU* 3.9 19.1 - - - +
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Residues in contact with ASP 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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88A ASP* 3.9 17.6 + - - +
89A MET 3.5 2.2 - - - -
90A SER* 1.3 80.1 + - - +
92A GLY* 1.3 56.6 + - - +
94A ILE* 4.6 4.4 - - - +
95A SER* 2.7 50.9 + - - -
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Residues in contact with GLY 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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24A SER* 5.1 0.7 - - - -
89A MET 4.8 3.0 + - - -
90A SER 3.3 0.4 - - - -
91A ASP* 1.3 81.7 + - - +
93A PHE* 1.3 61.0 + - - +
95A SER* 3.7 5.3 - - - -
96A ASN* 3.1 23.2 + - - +
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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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21A LEU* 3.9 12.8 - - + -
24A SER* 3.4 27.1 - - - +
25A LEU* 3.7 35.4 - - + -
28A TYR* 3.8 24.7 - - + -
89A MET 5.4 0.6 + - - -
90A SER* 3.4 5.9 + - - +
92A GLY* 1.3 73.3 - - - +
94A ILE* 1.3 83.0 + - + +
96A ASN* 3.2 4.2 + - - +
97A LEU* 2.9 46.3 + - + +
78B TRP* 3.9 23.1 - + - -
81B LEU* 4.5 4.5 - - + -
82B GLU* 5.2 0.9 - - - -
85B VAL* 4.1 26.2 - - + -
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Residues in contact with ILE 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 SER* 2.9 27.7 + - - +
91A ASP* 4.2 4.3 - - - +
93A PHE* 1.3 97.0 - - + +
95A SER* 1.3 54.6 + - - +
97A LEU* 3.4 4.9 + - + +
98A THR* 2.6 47.0 + - - +
82B GLU* 3.7 37.9 - - + +
85B VAL* 3.9 13.0 - - + -
86B LEU* 3.8 27.1 - - + -
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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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91A ASP* 2.7 41.2 + - - -
92A GLY* 3.7 5.6 - - - -
94A ILE* 1.3 77.0 - - - +
96A ASN* 1.3 62.7 + - - +
98A THR* 3.4 6.1 + - - -
99A ILE* 3.1 33.7 + - - +
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Residues in contact with ASN 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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20A ASP* 5.0 4.2 + - - +
21A LEU* 4.0 11.0 - - + +
24A SER* 3.3 30.4 + - - +
92A GLY 3.1 11.4 + - - +
93A PHE 3.2 8.9 + - - +
95A SER* 1.3 76.3 - - - +
97A LEU* 1.3 66.4 + - - +
99A ILE* 3.2 9.6 + - - +
100A GLN* 3.0 41.3 + - - +
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Residues in contact with LEU 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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21A LEU* 3.8 33.1 - - + +
93A PHE* 2.9 37.7 + - + +
94A ILE* 3.8 5.2 - - + +
96A ASN* 1.3 77.0 - - - +
98A THR* 1.3 64.3 + - - +
100A GLN* 3.2 1.8 + - - +
101A ARG* 3.0 55.0 + - - +
104A PHE* 4.1 13.2 - - + -
78B TRP* 4.1 20.4 - - + +
82B GLU* 3.7 26.0 - - + +
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Residues in contact with THR 98 (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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94A ILE* 2.6 36.3 + - - +
95A SER* 3.5 8.4 - - - -
97A LEU* 1.3 79.1 - - - +
99A ILE* 1.3 65.3 + - + +
101A ARG* 3.4 23.0 + - - +
102A GLN* 4.1 2.4 + - - +
82B GLU* 4.6 6.2 + - - -
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Residues in contact with ILE 99 (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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95A SER* 3.1 20.0 + - - +
96A ASN* 3.2 9.6 + - - +
98A THR* 1.3 80.3 - - + +
100A GLN* 1.3 79.6 + - - +
102A GLN* 3.2 33.9 + - - +
103A TYR* 4.4 3.7 - - + -
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Residues in contact with GLN 100 (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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17A THR* 3.6 34.4 + - + +
21A LEU* 4.0 21.3 - - + -
96A ASN* 3.0 36.2 + - - +
97A LEU 3.2 4.5 + - - +
99A ILE* 1.3 85.0 - - - +
101A ARG* 1.3 57.0 + - - +
102A GLN 3.0 5.6 - - - -
103A TYR* 2.9 41.2 + - - +
104A PHE* 3.5 12.3 - - + -
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Residues in contact with ARG 101 (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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97A LEU* 3.0 46.8 + - - +
98A THR* 3.7 16.8 + - - +
99A ILE 3.2 0.8 - - - -
100A GLN* 1.3 74.0 - - - +
102A GLN* 1.3 64.0 + - - +
103A TYR 3.0 0.2 - - - -
104A PHE* 3.0 45.6 + - + +
74B LEU 5.2 1.0 + - - -
78B TRP* 3.7 14.8 + - - +
79B SER* 3.6 24.5 + - - +
82B GLU* 2.7 34.2 + - - -
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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