Contacts of the helix formed by residues 96 - 110 (chain A) in PDB entry 2BV1
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 GLU 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A GLY* 4.3 4.3 - - - +
90A LEU* 3.6 13.5 + - + -
91A LYS* 3.6 58.4 + - + +
94A PHE* 3.8 8.5 - - - -
95A SER* 1.3 79.8 + - - +
97A GLU* 1.3 66.8 + - - +
98A ASN 3.0 6.4 + - - -
99A ILE* 3.2 7.1 + - + +
100A GLU* 3.1 45.9 + - - +
134A LYS* 5.2 7.6 - - - +
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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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94A PHE 3.7 8.9 - - - +
95A SER* 3.1 26.4 - - - -
96A GLU* 1.3 78.2 + - - +
98A ASN* 1.3 67.9 + - - +
100A GLU* 4.4 8.3 - - - -
101A PHE* 2.9 33.7 + - - +
127A PHE* 4.0 4.4 - - + -
134A LYS* 3.1 46.7 - - + +
135A GLN 4.3 7.5 - - - +
136A ILE* 3.9 15.1 - - + +
137A ASN* 4.6 11.4 + - - -
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Residues in contact with ASN 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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90A LEU* 4.9 1.8 - - + +
95A SER* 3.2 24.9 + - - +
96A GLU 3.0 0.8 - - - -
97A GLU* 1.3 93.8 + - - +
99A ILE* 1.3 58.4 + - - +
101A PHE* 3.8 1.1 - - - +
102A TRP* 3.0 23.0 + - - +
136A ILE* 4.3 2.6 - - - +
137A ASN* 4.7 6.7 + - - +
165A ILE* 3.3 48.6 - - + +
168A LEU* 4.6 16.8 - - - +
169A MET* 3.8 21.1 - - + +
173A SER* 5.4 3.0 + - - -
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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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77A LEU* 4.0 20.2 - - + -
83A GLN* 3.6 28.3 - - + +
86A PHE* 4.0 19.1 - - + -
87A GLY* 4.1 12.8 - - - +
90A LEU* 3.7 20.8 - - + +
96A GLU* 3.2 13.6 + - + +
98A ASN* 1.3 77.1 - - - +
100A GLU* 1.3 71.7 + - + +
102A TRP* 3.2 4.2 + - + +
103A LEU* 2.8 55.8 + - + +
169A MET* 3.9 11.4 - - + -
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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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91A LYS* 4.2 12.2 + - - +
96A GLU* 3.1 36.4 + - + +
97A GLU* 4.5 2.8 - - - -
99A ILE* 1.3 80.3 - - + +
101A PHE* 1.3 59.2 + - - +
103A LEU* 3.8 10.3 - - + +
104A ALA* 2.9 30.1 + - - +
127A PHE* 3.9 25.5 - - + -
134A LYS* 4.7 7.6 - - - +
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Residues in contact with PHE 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 2.9 20.5 + - - +
98A ASN 3.8 2.9 - - - +
100A GLU* 1.3 76.1 - - - +
102A TRP* 1.3 66.3 + - - +
104A ALA* 3.1 2.9 + - - +
105A CYS* 2.9 49.5 + - - -
123A ILE* 3.6 20.2 - - + -
127A PHE* 3.7 34.1 - + + -
128A VAL* 3.9 13.2 - - + -
136A ILE* 3.7 27.4 - - + -
158A PHE* 4.1 8.3 - + + -
161A ALA* 3.8 34.8 - - + -
162A GLN* 3.9 3.1 - - - -
165A ILE* 3.7 20.0 - - + -
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Residues in contact with TRP 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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77A LEU* 4.0 44.0 - - + -
83A GLN* 4.7 4.0 - - - -
98A ASN 3.0 19.4 + - - +
99A ILE* 3.2 6.0 + - + +
101A PHE* 1.3 81.4 - - - +
103A LEU* 1.3 84.5 + - + +
105A CYS* 3.2 6.6 + - - +
106A GLU* 3.2 50.1 + - + +
162A GLN* 3.2 42.0 + - + +
165A ILE* 4.9 2.0 - - + -
166A TYR* 3.5 30.1 - + + +
169A MET* 4.0 14.4 - - + -
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Residues in contact with LEU 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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83A GLN* 3.3 37.9 - - + +
99A ILE* 2.8 45.9 + - + +
100A GLU* 3.8 9.0 - - + +
102A TRP* 1.3 88.7 - - + +
104A ALA* 1.3 65.4 + - - +
106A GLU* 3.3 6.9 + - + +
107A ASP* 3.1 23.4 + - - +
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Residues in contact with ALA 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 2.9 21.4 + - - +
101A PHE* 3.1 5.1 + - - +
103A LEU* 1.3 72.1 - - - +
105A CYS* 1.3 53.4 + - - +
107A ASP* 3.3 15.9 + - - +
108A TYR* 2.7 35.0 + - - +
119A LYS* 5.5 0.9 - - - -
122A GLU* 6.1 0.4 - - - +
123A ILE* 3.6 24.7 - - + +
127A PHE* 4.1 15.9 - - + -
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Residues in contact with CYS 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 PHE* 2.9 56.7 + - - -
102A TRP 3.2 8.3 + - - +
104A ALA* 1.3 77.1 - - - +
106A GLU* 1.3 62.0 - - - +
108A TYR* 3.2 9.5 + - - +
109A LYS* 3.1 29.6 + - - +
123A ILE* 4.8 1.6 - - - -
158A PHE* 3.6 22.9 - - + -
162A GLN* 3.6 24.9 - - - +
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Residues in contact with GLU 106 (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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102A TRP* 3.2 47.3 + - + +
103A LEU* 3.6 11.0 - - + +
105A CYS* 1.3 75.0 - - - +
107A ASP* 1.3 61.6 + - - +
109A LYS* 2.8 41.7 + - - +
110A LYS* 3.6 33.3 + - - +
162A GLN* 2.7 22.6 + - - -
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Residues in contact with ASP 107 (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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103A LEU 3.1 13.6 + - - +
104A ALA* 3.4 14.6 - - - +
106A GLU* 1.3 75.3 - - - +
108A TYR* 1.3 61.7 + - - +
109A LYS 3.4 0.2 + - - -
110A LYS* 3.4 18.2 + - - +
111A THR* 2.8 21.3 + - - -
119A LYS* 3.2 29.1 - - - -
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Residues in contact with TYR 108 (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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104A ALA 2.7 19.9 + - - +
105A CYS* 3.2 9.2 + - - +
107A ASP* 1.3 74.0 - - - +
109A LYS* 1.3 58.7 + - + +
111A THR* 3.0 27.7 + - - -
116A LEU* 3.6 34.0 - - + +
119A LYS* 3.7 22.7 - - + -
120A ALA* 3.8 19.7 - - + -
123A ILE* 3.6 10.8 - - + -
153A PRO* 3.2 22.3 - - - +
154A THR 2.6 31.2 + - - -
155A PRO* 3.7 20.4 - - + +
157A CYS* 3.6 7.9 - - + +
158A PHE* 3.8 28.0 - + + -
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Residues in contact with LYS 109 (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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105A CYS* 3.1 17.1 + - - +
106A GLU* 2.8 40.9 + - - +
107A ASP 3.3 0.4 - - - -
108A TYR* 1.3 79.8 - - + +
110A LYS* 1.3 61.2 + - + +
111A THR 3.3 3.1 + - - +
155A PRO* 3.5 33.2 - - + +
159A ASP* 4.2 14.8 + - - +
162A GLN* 2.9 23.3 + - - -
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Residues in contact with LYS 110 (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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106A GLU* 3.7 35.8 + - - +
107A ASP* 3.4 11.9 + - - +
108A TYR 3.2 0.6 - - - -
109A LYS* 1.3 79.4 - - + +
111A THR* 1.3 59.9 + - - +
112A GLU 4.0 0.7 + - - -
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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