Contacts of the helix formed by residues 92 - 106 (chain A) in PDB entry 1B0N
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 LYS 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ASP* 3.0 13.9 + - - -
91A SER* 1.3 73.7 - - - +
93A LYS* 1.3 57.8 + - - +
95A PHE* 3.2 2.4 + - - +
96A ARG* 2.9 53.6 + - - +
1003A ZN 2.1 37.7 - - - -
12B ASP* 3.6 13.8 + - - -
14B GLU* 3.8 21.7 - - + +
15B TRP* 3.6 34.7 - - + +
18B LEU* 4.1 10.5 - - + +
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Residues in contact with LYS 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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91A SER* 3.2 9.3 + - - +
92A LYS* 1.3 79.3 - - - +
94A GLN* 1.3 63.0 + - + +
96A ARG* 3.2 22.6 + - + +
97A GLU* 3.1 44.0 + - + +
1002A ZN 4.2 6.3 - - - -
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Residues in contact with GLN 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLY 4.3 2.6 - - - +
90A VAL* 3.5 11.0 - - + -
91A SER* 2.9 42.9 + - - +
93A LYS* 1.3 76.9 - - + +
95A PHE* 1.4 58.1 + - - +
97A GLU* 3.1 20.6 + - - +
98A PHE 2.9 22.3 + - - -
1002A ZN 4.5 7.2 - - - -
35B TYR* 3.2 24.0 + - - +
39B ASN* 3.2 30.4 + - - +
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Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 4.3 1.1 - - + +
91A SER 3.0 6.8 + - - +
92A LYS 3.2 7.2 + - - +
94A GLN* 1.4 72.8 - - - +
96A ARG* 1.4 64.6 + - - +
98A PHE* 3.1 35.0 + + - +
99A LEU* 2.8 34.6 + - + +
15B TRP* 3.6 29.6 - + + -
18B LEU* 3.9 41.1 - - + -
19B MET* 3.7 32.5 - - + -
22B ALA* 4.4 3.4 - - + -
32B ILE* 4.2 14.4 - - + -
35B TYR* 4.1 17.0 - + - -
36B LEU* 4.4 8.3 - - + -
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Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER* 4.3 8.1 + - - -
92A LYS* 2.9 27.8 + - - +
93A LYS* 3.4 34.2 - - + +
95A PHE* 1.4 75.7 - - - +
97A GLU* 1.3 59.5 + - + +
99A LEU* 3.4 12.3 + - + +
100A ASP* 3.0 31.7 + - - +
14B GLU* 2.8 42.4 + - - +
18B LEU* 3.6 22.7 - - + +
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Residues in contact with GLU 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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93A LYS* 3.1 35.2 + - + +
94A GLN* 3.2 14.2 - - - +
96A ARG* 1.3 76.0 - - + +
98A PHE* 1.3 58.9 - - - +
100A ASP* 3.2 8.3 + - - +
101A TYR* 2.8 31.7 + - - +
1002A ZN 1.9 37.6 - - - -
35B TYR* 5.4 0.5 + - - -
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Residues in contact with PHE 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 GLN 2.9 6.6 + - - +
95A PHE* 3.1 38.3 + + - +
97A GLU* 1.3 76.1 - - - +
99A LEU* 1.3 58.3 + - + +
101A TYR* 3.2 10.6 + + - +
102A GLN* 2.9 69.9 + - + +
27B ILE* 4.0 13.9 - - + -
31B GLU* 3.8 28.3 - - + -
32B ILE* 3.9 15.3 - - + -
35B TYR* 3.4 56.1 + + + -
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Residues in contact with LEU 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 PHE* 2.8 28.9 + - + +
96A ARG* 3.4 10.5 - - + +
97A GLU 3.3 0.2 - - - -
98A PHE* 1.3 73.0 - - + +
100A ASP* 1.3 64.7 + - - +
102A GLN* 3.6 1.6 + - - +
103A LYS* 3.1 40.0 + - - +
18B LEU* 3.9 38.1 - - + +
21B GLU* 4.3 13.5 - - + +
22B ALA* 3.4 40.8 - - + +
25B ALA* 5.4 1.8 - - + -
27B ILE* 3.5 15.6 - - + +
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Residues in contact with ASP 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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96A ARG 3.0 16.2 + - - +
97A GLU* 3.3 11.7 - - - +
99A LEU* 1.3 79.3 - - - +
101A TYR* 1.3 60.0 + - - +
103A LYS* 3.4 13.2 + - - +
104A TRP* 2.9 30.0 + - - +
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Residues in contact with TYR 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 GLU 2.8 17.3 + - - +
98A PHE* 3.5 12.1 - + - +
100A ASP* 1.3 79.2 - - - +
102A GLN* 1.3 78.6 + - - +
104A TRP* 3.2 25.8 + + - +
105A ARG* 2.8 71.3 + - + +
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Residues in contact with GLN 102 (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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98A PHE* 2.9 55.8 + - + +
99A LEU 4.0 0.2 - - - +
101A TYR* 1.3 94.0 - - + +
103A LYS* 1.4 56.5 + - - +
105A ARG* 3.3 10.9 + - - +
106A LYS* 2.9 50.0 + - - +
27B ILE* 3.5 29.2 - - + +
31B GLU* 3.8 23.4 + - - +
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Residues in contact with LYS 103 (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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99A LEU* 3.1 31.0 + - - +
100A ASP* 3.7 12.6 + - - +
102A GLN* 1.4 75.1 - - + +
104A TRP* 1.3 58.1 + - - +
106A LYS* 3.5 8.7 + - - +
107A SER* 3.0 28.6 + - - -
21B GLU* 4.2 23.4 + - - +
25B ALA* 3.8 31.6 - - + -
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Residues in contact with TRP 104 (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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100A ASP 2.9 17.4 + - - +
101A TYR* 3.2 27.3 + + - +
103A LYS* 1.3 74.3 - - - +
105A ARG* 1.3 95.9 + - + +
107A SER* 2.7 26.3 + - - -
108A GLN* 3.1 49.2 + - + +
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Residues in contact with ARG 105 (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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101A TYR* 2.8 62.0 + - + +
102A GLN* 3.7 13.2 - - - +
104A TRP* 1.3 88.9 - - + +
106A LYS* 1.3 64.2 + - + +
108A GLN* 3.2 24.4 + - - +
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN* 2.9 32.0 + - - +
103A LYS* 3.8 6.5 - - - +
105A ARG* 1.3 77.5 - - + +
107A SER* 1.3 59.7 + - - +
108A GLN 3.4 7.1 + - - +
25B ALA* 3.6 19.1 - - + +
26B ASN* 3.0 33.3 + - + +
27B ILE* 4.2 16.0 - - - +
28B SER 5.0 1.6 - - - +
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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