Contacts of the helix formed by residues 101 - 112 (chain B) in PDB entry 2BWJ
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 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B LEU* 5.0 3.1 - - - +
72B SER* 3.5 8.7 + - - -
99B PRO* 3.3 8.4 - - - +
100B ARG* 1.3 119.5 + - + +
102B VAL* 1.3 65.7 + - - +
103B LYS* 4.1 17.2 - - - +
104B GLN* 3.3 14.8 + - + -
105B GLY 3.2 15.9 + - - -
159B ALA 5.4 0.2 - - - -
162B PRO* 6.2 1.8 - - - -
163B VAL* 3.8 10.1 - - - -
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Residues in contact with VAL 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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99B PRO* 5.4 1.3 - - - -
101B GLU* 1.3 73.4 - - - +
103B LYS* 1.3 60.5 + - + +
105B GLY* 3.1 3.9 + - - -
106B GLU* 2.9 39.8 + - - +
162B PRO* 3.3 43.7 - - + +
163B VAL* 4.0 4.2 - - - +
166B TYR* 3.5 40.2 - - + -
167B TYR* 6.2 0.2 - - - -
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Residues in contact with LYS 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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101B GLU* 3.4 13.5 + - - +
102B VAL* 1.3 79.5 - - + +
104B GLN* 1.3 61.5 + - - +
106B GLU* 3.7 20.1 - - - +
107B GLU* 3.1 23.6 + - - +
110B ARG* 4.7 2.4 + - - +
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Residues in contact with GLN 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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66A ARG 5.1 0.6 + - - -
42B THR* 5.2 1.0 - - - +
72B SER* 3.6 28.0 + - - +
75B VAL* 3.8 21.8 - - - +
76B LEU* 5.4 0.4 - - + +
98B TYR* 3.5 31.2 + - + +
99B PRO* 3.2 6.4 - - - +
100B ARG* 2.8 61.4 + - - +
101B GLU* 3.3 17.7 + - + +
102B VAL 3.2 0.4 - - - -
103B LYS* 1.3 74.5 - - - +
105B GLY* 1.3 61.4 + - - +
107B GLU* 3.4 8.0 + - - +
108B PHE* 2.9 28.1 + - - +
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Residues in contact with GLY 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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15B PHE* 5.2 1.0 - - - -
98B TYR* 5.1 0.7 - - - -
99B PRO* 3.6 15.1 - - - +
101B GLU 3.2 5.3 + - - -
102B VAL* 3.1 7.0 + - - -
104B GLN* 1.3 79.2 - - - +
106B GLU* 1.3 55.8 + - - +
108B PHE* 3.3 8.5 + - - +
109B GLY* 3.0 24.8 + - - -
166B TYR* 5.3 2.2 - - - -
167B TYR* 3.6 25.3 + - - -
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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
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102B VAL* 2.9 26.8 + - - +
103B LYS* 3.7 25.2 - - - +
104B GLN 3.3 0.2 - - - -
105B GLY* 1.3 74.6 - - - +
107B GLU* 1.3 58.3 + - - +
109B GLY* 3.1 3.6 + - - +
110B ARG* 3.0 52.2 + - - +
166B TYR* 3.5 38.1 + - + +
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Residues in contact with GLU 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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72B SER* 3.4 32.4 - - - -
73B GLY* 4.4 10.4 - - - -
76B LEU* 3.9 22.9 - - + +
103B LYS 3.1 15.1 + - - +
104B GLN* 3.7 5.9 - - - +
106B GLU* 1.3 75.7 - - - +
108B PHE* 1.3 60.5 + - - +
110B ARG* 3.4 24.0 + - - +
111B ARG* 2.9 47.0 + - + +
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Residues in contact with PHE 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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13B ILE* 4.1 11.4 - - + -
15B PHE* 3.7 20.0 - + + -
76B LEU* 3.8 18.9 - - + +
79B LEU* 4.2 8.3 - - + -
83B MET* 4.1 5.8 - - - -
95B ILE* 3.8 29.4 - - + -
98B TYR* 3.5 33.2 - + + +
104B GLN 2.9 14.8 + - - +
105B GLY* 3.3 10.5 + - - +
107B GLU* 1.3 76.1 - - - +
109B GLY* 1.3 58.9 + - - +
112B ILE* 2.9 60.9 + - + -
113B GLY 2.9 38.5 + - - -
115B PRO* 4.7 1.1 - - + -
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Residues in contact with GLY 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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9B ARG* 2.5 34.9 + - - -
105B GLY 3.0 13.8 + - - -
106B GLU* 3.1 4.9 + - - -
108B PHE* 1.3 79.8 - - - +
110B ARG* 1.3 51.3 + - - +
113B GLY 3.4 11.7 + - - -
114B ASP* 3.3 24.0 - - - -
115B PRO* 5.4 1.8 - - - -
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Residues in contact with ARG 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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9B ARG* 3.0 16.9 + - - +
103B LYS* 4.7 2.4 + - - +
106B GLU* 3.0 49.6 + - - +
107B GLU* 3.4 32.3 - - - +
108B PHE 3.4 0.2 - - - -
109B GLY* 1.3 76.1 - - - +
111B ARG* 1.3 93.4 + - - +
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Residues in contact with ARG 111 (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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9B ARG* 4.8 0.9 - - - -
76B LEU* 3.9 25.1 - - + -
80B LYS* 4.5 15.0 + - + +
107B GLU* 2.9 35.9 + - + +
110B ARG* 1.3 116.9 + - + +
112B ILE* 1.3 65.1 + - + +
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Residues in contact with ILE 112 (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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5B MET 4.5 2.8 - - - +
8B LEU* 4.2 17.2 - - + +
9B ARG* 3.6 30.2 + - - +
13B ILE* 4.6 2.7 - - + -
76B LEU* 3.7 29.8 - - + -
79B LEU* 4.4 1.1 - - + -
80B LYS* 4.0 42.8 - - + +
83B MET* 3.8 22.4 - - + -
108B PHE* 2.9 37.9 + - + +
109B GLY 4.2 0.9 - - - -
110B ARG 3.6 0.4 - - - -
111B ARG* 1.3 85.9 - - + +
113B GLY* 1.3 60.1 + - - +
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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