Contacts of the helix formed by residues 96 - 110 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A SER* 5.8 2.1 - - - -
87B GLY 4.2 2.7 - - - +
90B LEU* 3.6 11.7 + - + -
91B LYS* 3.4 51.8 - - + +
94B PHE* 3.7 9.2 - - - -
95B SER* 1.3 83.1 + - - +
97B GLU* 1.3 69.9 + - - +
98B ASN 3.0 2.8 + - - -
99B ILE* 3.1 11.1 + - + +
100B GLU* 2.9 51.5 + - - +
134B LYS* 5.5 4.7 - - - +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B PHE 3.6 9.8 - - - +
95B SER* 3.4 25.7 + - - -
96B GLU* 1.3 86.6 + - - +
98B ASN* 1.3 69.6 + - - +
100B GLU* 4.2 11.2 - - - -
101B PHE* 2.8 32.7 + - - +
127B PHE* 3.8 3.3 - - + -
134B LYS* 3.6 43.5 - - + +
135B GLN 3.9 14.4 - - - +
136B ILE* 4.3 4.2 - - + -
137B ASN 5.7 0.5 + - - -
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Residues in contact with ASN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 5.0 1.1 - - + +
95B SER* 3.2 25.4 + - - +
96B GLU 3.0 1.0 - - - -
97B GLU* 1.3 86.9 + - - +
99B ILE* 1.3 58.6 + - - +
101B PHE* 3.8 1.5 - - - +
102B TRP* 3.0 27.4 + - - +
136B ILE* 4.1 8.0 - - - +
137B ASN* 4.7 4.0 + - - +
165B ILE* 3.5 44.6 - - + +
168B LEU* 4.9 13.1 - - - +
169B MET* 3.8 22.3 - - + +
173B SER* 5.5 2.6 + - - -
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Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LEU* 3.9 28.9 - - + -
83B GLN* 3.6 26.5 - - - +
86B PHE* 4.0 11.4 - - + -
87B GLY* 4.2 13.5 - - - +
90B LEU* 3.8 21.9 - - + +
96B GLU* 3.1 16.7 + - + +
98B ASN* 1.3 76.7 - - - +
100B GLU* 1.3 65.9 + - + +
102B TRP* 4.2 5.2 - - + -
103B LEU* 2.9 51.7 + - + +
169B MET* 4.0 8.0 - - - -
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LYS* 3.9 16.0 + - - -
96B GLU* 2.9 42.1 + - + +
97B GLU* 3.9 10.6 - - - +
99B ILE* 1.3 81.1 - - + +
101B PHE* 1.3 56.3 + - - +
103B LEU* 3.9 6.7 - - + +
104B ALA* 3.0 29.1 + - - +
127B PHE* 4.0 19.9 - - + -
134B LYS* 4.5 10.6 - - - +
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Residues in contact with PHE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU 2.8 23.4 + - - +
98B ASN 3.8 1.6 - - - +
100B GLU* 1.3 71.5 - - - +
102B TRP* 1.3 68.0 + - - +
104B ALA* 3.3 1.4 + - - +
105B CYS* 3.0 49.8 + - - -
123B ILE* 3.7 17.3 - - + -
127B PHE* 3.7 33.1 - + + -
128B VAL* 4.2 7.9 - - + -
136B ILE* 3.5 33.0 - - + -
158B PHE* 4.3 5.6 - + + -
161B ALA* 3.8 17.7 - - + -
162B GLN* 3.8 15.0 - - - -
165B ILE* 3.6 29.2 - - + -
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Residues in contact with TRP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LEU* 3.7 46.7 - - + -
83B GLN* 4.6 3.4 - - - -
98B ASN 3.0 19.3 + - - +
99B ILE* 3.7 5.6 - - + +
101B PHE* 1.3 79.8 - - - +
103B LEU* 1.3 92.5 + - + +
105B CYS* 3.2 3.2 + - - -
106B GLU* 3.0 50.8 + - + +
162B GLN* 3.3 44.1 + - + +
165B ILE* 5.0 2.2 - - + -
166B TYR* 3.5 37.0 - + + +
169B MET* 4.2 13.5 - - + -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLN* 3.5 42.8 - - + +
99B ILE* 2.9 43.0 + - + +
100B GLU* 4.0 5.8 - - + +
102B TRP* 1.3 98.0 - - + +
104B ALA* 1.3 57.8 + - - +
106B GLU* 3.4 7.7 + - + +
107B ASP* 3.1 33.6 + - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B GLU 3.0 20.0 + - - +
101B PHE 3.5 6.1 - - - +
102B TRP 3.3 0.2 - - - -
103B LEU* 1.3 72.8 - - - +
105B CYS* 1.3 55.9 + - - +
107B ASP* 3.4 8.6 + - - +
108B TYR* 2.7 35.2 + - - +
119B LYS* 6.0 0.2 - - - +
123B ILE* 3.8 25.1 - - + +
127B PHE* 4.3 13.2 - - + -
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Residues in contact with CYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE* 3.0 55.5 + - - -
102B TRP 3.5 8.1 - - - +
104B ALA* 1.3 72.5 - - - +
106B GLU* 1.3 67.2 - - - +
108B TYR* 3.6 8.9 - - - +
109B LYS* 3.0 30.0 + - - +
123B ILE* 5.0 2.0 - - - -
158B PHE* 3.5 24.2 - - + -
162B GLN* 3.5 24.5 - - + +
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TRP* 3.0 52.6 + - + +
103B LEU* 3.5 10.8 - - + +
105B CYS* 1.3 78.6 - - - +
107B ASP* 1.3 63.1 + - - +
109B LYS* 3.3 33.5 + - - +
110B LYS* 3.1 35.9 + - - +
162B GLN* 2.8 22.0 + - - +
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Residues in contact with ASP 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 3.1 18.1 + - - +
104B ALA* 3.6 10.0 - - - +
106B GLU* 1.3 75.3 - - - +
108B TYR* 1.3 59.2 + - - +
110B LYS* 3.2 18.8 + - - +
111B THR* 2.8 23.5 + - - +
119B LYS* 6.5 0.9 - - + -
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Residues in contact with TYR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ALA 2.7 22.3 + - - +
105B CYS* 3.3 7.6 + - - +
107B ASP* 1.3 71.8 - - - +
109B LYS* 1.3 63.6 + - + +
111B THR* 3.1 23.6 + - - -
116B LEU* 3.5 49.6 - - + +
119B LYS* 3.7 22.6 - - + +
120B ALA* 3.7 7.9 - - + -
123B ILE* 3.6 18.6 - - + -
153B PRO* 3.3 22.0 - - - +
154B THR 2.7 30.9 + - - -
155B PRO* 3.7 16.2 - - + -
157B CYS* 3.6 4.4 - - + +
158B PHE* 3.6 25.8 - + + -
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Residues in contact with LYS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B CYS* 3.0 15.3 + - - +
106B GLU* 3.3 36.0 + - - +
108B TYR* 1.3 78.3 - - + +
110B LYS* 1.3 62.8 + - + +
111B THR 3.4 2.9 + - - +
116B LEU* 5.7 0.2 - - - +
155B PRO* 3.6 41.3 - - + +
156B THR* 6.1 0.9 - - + -
159B ASP* 3.5 16.9 + - - +
162B GLN* 2.9 28.1 + - - -
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLU* 3.1 45.5 + - - +
107B ASP* 3.2 13.1 + - - +
109B LYS* 1.3 81.7 - - + +
111B THR* 1.3 59.4 + - - +
112B GLU 3.9 1.2 + - - -
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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