Contacts of the helix formed by residues 88 - 104 (chain A) in PDB entry 2B2T
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 MSE 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ILE* 4.9 2.2 - - - +
77A GLU* 4.5 4.5 - - + +
80A LEU* 3.9 31.2 - - - +
81A LYS* 3.3 45.1 - - + +
85A VAL* 3.6 25.6 - - + +
86A ARG 3.4 0.6 - - - -
87A GLY* 1.3 76.5 - - - +
89A LYS* 1.3 62.9 + - - +
91A LEU* 3.0 33.9 + - + +
92A ASP* 3.3 14.2 - - - +
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Residues in contact with LYS 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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87A GLY* 3.0 2.8 + - - +
88A MSE 1.3 78.7 - - - +
90A LYS* 1.3 63.4 + - + +
92A ASP* 3.0 34.4 + - + +
93A ASN* 3.1 32.7 + - - +
96A LYS* 5.8 5.0 - - - +
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Residues in contact with LYS 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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15A THR* 5.1 2.6 - - - +
16A ILE* 3.0 28.5 + - + +
17A GLU* 3.7 23.0 + - - +
18A ARG* 5.2 0.9 - - - -
19A PHE* 3.3 20.2 - - + -
87A GLY* 2.8 24.9 + - - +
89A LYS* 1.3 77.2 - - + +
91A LEU* 1.3 58.0 + - - +
93A ASN* 3.3 12.2 + - - +
94A TYR* 2.9 31.4 + - - +
65B LYS* 5.4 14.4 - - - +
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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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19A PHE* 3.3 34.8 - - + -
60A TYR* 3.6 32.1 - - + -
77A GLU* 3.3 46.2 - - + +
80A LEU* 4.5 9.4 - - + -
87A GLY 4.1 0.4 + - - -
88A MSE 3.0 24.8 + - + +
90A LYS* 1.3 78.2 - - - +
92A ASP* 1.3 67.8 + - - +
94A TYR* 3.7 1.5 - - + +
95A LYS* 3.0 34.4 + - + +
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Residues in contact with ASP 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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88A MSE 3.3 14.3 - - - +
89A LYS* 3.0 31.9 + - + +
91A LEU* 1.3 84.3 - - - +
93A ASN* 1.3 62.4 + - - +
95A LYS* 3.8 9.2 + - - +
96A LYS* 3.0 40.3 + - + +
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Residues in contact with ASN 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 LYS* 3.1 41.6 + - - +
90A LYS* 3.3 11.6 + - - +
92A ASP* 1.3 73.9 - - - +
94A TYR* 1.3 61.5 + - - +
96A LYS* 3.3 17.0 + - - +
97A LYS* 2.9 32.4 + - - +
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Residues in contact with TYR 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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19A PHE* 3.6 33.0 - + + -
20A MSE 3.3 25.6 + - - -
21A ASP* 4.0 2.9 + - - -
22A CYS* 3.9 21.7 + - + +
60A TYR* 4.0 35.2 - + - -
90A LYS 2.9 19.1 + - - +
91A LEU* 3.7 4.3 - - - +
93A ASN* 1.3 77.3 - - - +
95A LYS* 1.3 60.9 + - + +
97A LYS* 3.7 5.9 - - + +
98A ASP* 2.8 46.8 + - + +
161B SER* 4.6 20.5 - - - -
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Residues in contact with LYS 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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58A ILE* 5.9 1.8 - - - -
60A TYR* 3.6 28.9 - - + +
77A GLU* 2.7 30.1 + - - -
91A LEU* 3.0 35.5 + - + +
92A ASP* 3.8 8.2 + - - +
94A TYR* 1.3 77.0 - - + +
96A LYS* 1.3 64.4 + - + +
98A ASP* 3.5 7.3 + - - +
99A GLN* 3.1 29.6 + - + +
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Residues in contact with LYS 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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89A LYS* 5.8 5.5 - - - +
92A ASP* 3.0 32.0 + - - +
93A ASN* 3.8 15.1 + - - +
95A LYS* 1.3 76.2 - - + +
97A LYS* 1.3 60.1 + - - +
99A GLN* 3.2 7.8 + - - +
100A GLU* 2.9 28.2 + - - +
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Residues in contact with LYS 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 ASN 2.9 18.8 + - - +
94A TYR* 3.8 6.5 - - + +
96A LYS* 1.3 73.6 - - - +
98A ASP* 1.3 60.9 + - - +
100A GLU* 3.2 14.3 + - - +
101A THR* 2.9 34.8 + - - +
152B TYR* 3.1 31.9 - - - +
161B SER* 3.5 33.4 + - - +
162B GLU* 4.7 0.8 - - - +
163B CYS 3.1 24.4 + - - +
164B SER* 5.2 1.1 - - - +
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Residues in contact with ASP 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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22A CYS* 5.5 8.6 - - - +
94A TYR* 2.8 37.1 + - + +
95A LYS* 3.6 8.9 - - - +
97A LYS* 1.3 78.8 - - - +
99A GLN* 1.3 62.6 + - - +
101A THR* 3.4 6.6 + - - +
102A LYS* 2.9 67.9 + - - +
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Residues in contact with GLN 99 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LYS* 3.1 20.3 + - + +
96A LYS* 3.5 9.9 - - - +
97A LYS 3.2 0.2 - - - -
98A ASP* 1.3 80.6 + - + +
100A GLU* 1.3 65.9 + - - +
102A LYS* 3.7 11.4 - - - +
103A ARG* 2.8 26.4 + - - +
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Residues in contact with GLU 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 LYS 2.9 13.6 + - - +
97A LYS* 3.6 19.9 - - - +
99A GLN* 1.3 75.4 - - - +
101A THR* 1.3 62.5 + - - +
103A ARG* 3.3 12.5 + - - +
104A TRP* 3.2 47.3 + - + +
152B TYR* 3.9 16.2 - - - +
165B TRP* 3.0 33.7 + - - -
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Residues in contact with THR 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 LYS* 2.9 20.8 + - - +
98A ASP* 3.5 8.2 - - - +
100A GLU* 1.3 74.2 - - - +
102A LYS* 1.3 83.2 + - - +
104A TRP* 3.1 25.6 + - - +
105A LEU* 4.7 1.2 - - - +
116A TYR* 4.4 21.8 - - + +
152B TYR* 4.2 11.1 + - - -
160B TYR* 3.9 28.8 + - + +
161B SER* 5.1 1.2 + - - -
163B CYS* 5.4 0.5 - - - -
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Residues in contact with LYS 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 ASP* 2.9 57.2 + - - +
99A GLN* 3.2 13.7 + - - +
101A THR* 1.3 93.6 - - - +
103A ARG* 1.3 62.3 + - - +
105A LEU* 3.1 44.5 + - + +
106A LYS 4.6 0.2 + - - -
116A TYR* 4.1 14.6 + - - -
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Residues in contact with ARG 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 GLN 2.8 17.7 + - - +
100A GLU* 3.6 9.0 - - - +
101A THR 3.1 0.4 - - - -
102A LYS* 1.3 76.7 - - - +
104A TRP* 1.3 77.5 + - + +
105A LEU 3.2 2.2 + - - -
106A LYS* 3.3 51.0 + - - +
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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 GLU* 3.2 47.7 + - + +
101A THR* 3.1 12.9 + - - +
103A ARG* 1.3 103.1 - - + +
105A LEU* 1.3 58.9 + - - +
106A LYS* 3.3 17.9 - - + +
108A ALA* 4.4 10.0 - - - +
137B ILE* 4.4 21.3 - - + +
138B ALA* 4.3 17.4 - - + +
152B TYR* 4.0 30.9 - + - -
165B TRP* 4.0 16.4 - + - -
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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