Contacts of the helix formed by residues 100 - 112 (chain B) in PDB entry 2BME
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 ALA 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B ASN* 3.3 35.0 - - - +
96B GLU* 3.2 7.8 + - + +
97B THR 3.7 11.2 - - - +
98B TYR 3.0 0.8 - - - -
99B ASN* 1.3 76.2 - - - +
101B LEU* 1.3 63.9 + - - +
102B THR 3.2 2.0 - - - -
103B ASN* 2.9 27.3 + - + +
104B TRP* 3.3 15.5 + - + -
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Residues in contact with LEU 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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88B LEU* 3.6 36.5 - - + +
89B VAL 4.4 4.5 - - - +
90B TYR* 3.8 16.6 - - + -
97B THR 3.9 11.0 - - - +
98B TYR* 3.0 43.5 + - + +
99B ASN 3.2 0.4 - - - -
100B ALA* 1.3 78.3 - - - +
102B THR* 1.3 62.6 + - - +
104B TRP* 3.1 9.0 + - + +
105B LEU* 2.9 27.2 + - - +
120B LEU* 3.8 22.4 - - + -
141B PHE* 3.8 25.6 - - + -
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Residues in contact with THR 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 ASN 4.1 7.7 + - - -
100B ALA 3.2 0.8 - - - -
101B LEU* 1.3 78.2 - - - +
103B ASN* 1.3 64.1 + - - +
105B LEU* 3.4 7.8 + - - +
106B THR* 2.9 40.4 + - - +
109B ARG* 5.0 4.0 + - - +
141B PHE* 3.7 22.7 - - - -
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Residues in contact with ASN 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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73B ARG* 5.7 7.4 - - - +
99B ASN 4.9 2.8 + - - -
100B ALA* 2.9 20.2 + - + +
102B THR* 1.3 81.4 - - - +
104B TRP* 1.3 65.2 + - + +
106B THR* 3.4 8.4 + - - -
107B ASP* 3.1 28.8 + - - +
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Residues in contact with TRP 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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16B ILE* 3.9 19.9 - - + +
17B GLY* 3.3 42.0 - - - -
18B ASN* 2.8 27.9 + - - +
66B THR* 5.3 0.4 - - - -
67B ALA 4.6 6.3 - - - -
68B GLY 4.4 0.4 - - - -
73B ARG* 3.5 50.1 - - - +
76B THR* 4.0 18.8 - - + -
80B TYR* 3.6 25.2 + - - -
88B LEU* 3.6 22.2 - - + -
97B THR 5.5 0.7 - - - -
100B ALA* 3.3 27.2 + - + +
101B LEU* 3.1 10.9 + - + +
103B ASN* 1.3 76.9 - - + +
105B LEU* 1.4 62.7 + - - +
107B ASP* 3.1 10.4 + - - +
108B ALA* 3.0 22.3 + - - +
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Residues in contact with LEU 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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88B LEU* 3.8 20.9 - - + -
101B LEU 2.9 16.2 + - - +
102B THR* 3.8 6.3 - - + +
104B TRP* 1.4 78.1 - - - +
106B THR* 1.3 56.4 + - - +
108B ALA* 3.3 3.4 + - - +
109B ARG* 2.8 46.4 + - + +
118B ILE* 4.1 22.9 - - + -
141B PHE* 3.8 33.2 - - + -
145B ASN* 3.9 22.2 - - + +
147B LEU* 4.1 20.2 - - + -
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Residues in contact with THR 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 THR* 2.9 24.3 + - - +
103B ASN* 3.6 10.1 + - - -
105B LEU* 1.3 75.0 - - - +
107B ASP* 1.3 65.8 + - - +
109B ARG* 3.2 28.8 + - - +
110B MET* 3.1 25.6 + - + +
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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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73B ARG* 4.2 13.9 + - - -
77B ARG* 2.9 49.0 + - - +
80B TYR* 3.8 19.5 + - + +
103B ASN 3.1 19.7 + - - +
104B TRP* 3.5 10.5 - - - +
106B THR* 1.3 81.1 - - - +
108B ALA* 1.3 53.3 + - - +
110B MET* 3.2 4.2 + - - -
111B LEU* 2.8 46.1 + - + +
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Residues in contact with ALA 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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16B ILE* 5.2 2.5 - - + -
80B TYR* 4.0 27.5 - - + -
104B TRP 3.0 12.3 + - - +
105B LEU* 3.3 8.5 + - + +
107B ASP* 1.3 74.9 - - - +
109B ARG* 1.3 64.9 + - + +
112B ALA* 2.9 32.2 + - + +
113B SER 5.0 1.0 - - - +
116B ILE* 5.2 3.2 - - + +
118B ILE* 3.8 28.7 - - + -
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Residues in contact with ARG 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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102B THR* 5.0 4.4 + - - +
105B LEU* 2.8 34.4 + - + +
106B THR* 3.2 36.4 + - - +
108B ALA* 1.3 73.7 - - + +
110B MET* 1.3 62.8 + - - +
112B ALA 4.3 2.9 - - - +
114B GLN* 3.6 25.4 + - - +
145B ASN* 5.8 1.8 + - - -
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Residues in contact with MET 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 THR* 3.1 18.7 + - + +
107B ASP* 3.7 4.5 - - - +
109B ARG* 1.3 80.3 - - - +
111B LEU* 1.3 74.0 + - + +
112B ALA 4.7 1.9 - - - +
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Residues in contact with LEU 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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77B ARG* 3.7 37.5 - - + +
80B TYR* 3.6 36.5 - - + +
81B ARG* 4.1 12.8 + - - +
107B ASP* 2.8 28.0 + - + +
110B MET* 1.3 88.9 - - + +
112B ALA* 1.3 60.5 + - - +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B TYR* 4.0 26.7 - - + +
83B ALA 5.3 0.2 - - - +
108B ALA* 2.9 19.9 + - - +
109B ARG 4.3 7.8 - - - +
110B MET 4.7 1.4 - - - +
111B LEU* 1.3 80.5 + - - +
113B SER* 1.3 72.0 + - - +
114B GLN* 3.5 4.5 + - - +
116B ILE* 3.8 30.5 - - + -
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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