Contacts of the helix formed by residues 100 - 118 (chain B) in PDB entry 3BRU
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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98B SER 4.4 0.4 + - - -
99B LEU* 1.3 76.9 - - - +
101B PRO* 1.3 72.3 - - + +
102B LEU 3.4 0.9 - - - -
103B ALA* 3.2 13.7 + - + +
104B ARG* 3.0 16.1 + - - +
166B CYS* 5.9 0.7 - - - -
168B GLU* 3.2 23.8 - - - +
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Residues in contact with PRO 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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100B ALA* 1.3 84.2 - - + +
102B LEU* 1.3 59.9 + - - +
104B ARG* 3.1 30.4 + - + +
105B LEU 3.3 4.7 + - - -
159B LEU* 3.6 26.9 - - + +
162B GLU* 3.9 31.0 - - + +
163B ALA* 3.9 25.1 - - + +
166B CYS* 4.0 10.8 - - - -
168B GLU* 3.0 20.9 - - - +
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Residues in contact with LEU 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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101B PRO* 1.3 72.3 - - - +
103B ALA* 1.3 65.6 + - - +
105B LEU* 3.2 16.9 + - + +
106B ARG* 3.1 50.4 + - + +
163B ALA* 5.0 3.5 - - + +
168B GLU* 3.0 32.5 + - + +
210B GLY* 5.6 1.3 - - - +
213B PHE* 3.6 57.4 - - + -
214B VAL 5.9 1.6 - - - +
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Residues in contact with ALA 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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99B LEU* 4.1 24.1 - - + +
100B ALA* 3.2 21.7 + - + +
102B LEU* 1.3 77.6 - - - +
104B ARG* 1.3 56.8 + - - +
106B ARG* 3.5 27.8 + - - +
107B LEU* 3.0 27.0 + - - +
168B GLU* 5.1 0.2 + - - -
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Residues in contact with ARG 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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93B ALA* 3.3 28.1 - - - +
94B PHE* 3.1 26.2 + - - -
95B LEU 5.4 0.2 - - - -
96B ASP 2.9 28.7 + - - -
97B GLY* 4.3 7.5 + - - -
99B LEU* 2.5 37.6 + - + -
100B ALA* 3.0 15.9 - - - +
101B PRO* 3.1 20.6 + - - +
103B ALA* 1.3 75.0 - - - +
105B LEU* 1.3 58.4 + - - +
107B LEU* 3.4 7.0 + - - +
108B PHE* 3.0 26.3 + - - +
159B LEU* 3.7 15.9 - - + +
162B GLU* 2.5 41.4 + - - -
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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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94B PHE* 4.2 22.9 - - + -
101B PRO 3.3 4.0 + - - +
102B LEU* 3.2 20.4 + - + +
104B ARG* 1.3 78.2 - - - +
106B ARG* 1.3 58.4 + - + +
108B PHE* 3.2 7.2 + - + +
109B THR* 3.0 30.1 + - + +
156B THR* 4.5 7.0 - - + -
159B LEU* 4.0 15.6 - - + +
160B PHE* 3.8 25.8 - - + -
182B PHE* 3.9 41.5 - - + -
209B PHE* 4.9 2.7 - - + -
213B PHE* 4.4 14.8 - - + -
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Residues in contact with ARG 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 LEU* 3.1 52.2 + - + +
103B ALA* 3.8 30.1 - - - +
105B LEU* 1.3 74.8 - - + +
107B LEU* 1.3 59.6 + - - +
109B THR* 3.4 9.1 + - - +
110B ARG* 3.0 30.5 + - - +
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Residues in contact with LEU 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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92B GLN* 4.7 4.7 - - + +
93B ALA* 4.4 16.8 - - + +
96B ASP* 4.3 10.3 - - - +
99B LEU* 3.6 25.6 - - + -
103B ALA 3.0 18.0 + - - +
104B ARG 3.6 5.6 - - - +
106B ARG* 1.3 75.4 - - - +
108B PHE* 1.3 58.4 + - - +
110B ARG* 3.3 14.8 + - - +
111B MSE 2.8 60.3 + - + +
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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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86B PHE* 3.7 33.0 - + - -
89B LEU* 4.4 22.2 - - + -
90B LEU* 3.8 17.7 - - + -
93B ALA* 3.8 13.6 - - + +
94B PHE* 4.0 12.6 - + + -
104B ARG 3.0 14.1 + - - +
105B LEU* 3.2 11.0 + - + +
107B LEU* 1.3 76.5 - - - +
109B THR* 1.3 69.6 + - + +
111B MSE 3.2 10.1 + - + +
112B ALA* 2.8 35.5 + - + +
182B PHE* 4.2 11.7 - + - -
183B TRP* 3.8 17.5 - + - -
186B TRP* 3.7 30.3 - + - -
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Residues in contact with THR 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 LEU* 3.0 14.6 + - + +
106B ARG* 3.4 13.0 + - - +
108B PHE* 1.3 89.3 - - + +
110B ARG* 1.3 62.8 + - - +
112B ALA* 3.9 1.4 - - - +
113B GLU* 3.1 24.9 + - - +
182B PHE* 3.8 21.5 - - + -
186B TRP* 3.7 33.0 - - + -
202B LEU* 6.0 0.2 - - - +
206B THR* 4.0 20.6 + - + +
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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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106B ARG 3.0 19.3 + - - +
107B LEU* 3.7 14.6 - - - +
109B THR* 1.3 79.1 + - - +
111B MSE 1.3 63.4 + - + +
113B GLU* 3.3 13.1 + - - +
114B GLU* 3.1 42.7 + - + +
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Residues in contact with MSE 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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89B LEU* 3.8 35.9 - - + +
92B GLN* 4.3 24.0 - - + -
93B ALA* 3.4 37.7 - - + +
107B LEU* 2.8 46.8 + - + +
108B PHE* 3.8 5.4 - - + +
110B ARG* 1.3 72.8 - - + +
112B ALA* 1.3 64.0 + - - +
114B GLU* 3.3 19.4 + - - +
115B GLY* 3.1 19.9 + - - -
118B ARG* 5.4 1.6 + - - -
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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
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86B PHE* 5.9 2.5 - - + -
89B LEU* 5.0 11.7 - - + +
108B PHE* 2.8 35.8 + - + +
109B THR 3.9 0.4 - - - +
111B MSE 1.3 72.2 - - - +
113B GLU* 1.3 55.9 + - - +
115B GLY* 3.3 3.4 + - - -
116B MSE 3.0 34.5 + - + +
186B TRP* 3.6 27.8 - - + +
190B ILE* 6.0 1.3 - - + -
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Residues in contact with GLU 113 (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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109B THR 3.1 19.7 + - - +
110B ARG* 3.6 10.8 - - - +
111B MSE 3.3 0.4 - - - -
112B ALA* 1.3 72.8 - - - +
114B GLU* 1.3 61.1 + - + +
116B MSE 3.3 5.1 + - - +
117B ALA* 2.9 27.6 + - + +
121B PHE* 4.0 9.8 - - + -
186B TRP* 5.1 0.2 - - - -
199B PRO* 3.4 15.2 - - - +
202B LEU* 3.8 28.5 - - + +
203B HIS* 3.1 37.7 + - - -
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Residues in contact with GLU 114 (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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110B ARG* 3.1 39.6 + - + +
111B MSE 3.3 24.0 + - - +
113B GLU* 1.3 73.7 - - + +
115B GLY* 1.3 63.8 + - - +
117B ALA* 3.4 8.2 + - - +
118B ARG* 3.4 32.4 + - - +
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Residues in contact with GLY 115 (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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111B MSE 3.1 13.0 + - - -
112B ALA* 3.7 4.3 - - - -
113B GLU 3.3 0.2 - - - -
114B GLU* 1.3 74.4 - - - +
116B MSE 1.3 62.7 + - - +
118B ARG* 3.5 40.2 + - - +
119B HIS* 4.0 9.4 + - - -
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Residues in contact with MSE 116 (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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112B ALA* 3.0 18.5 + - - +
113B GLU 3.3 5.8 + - - +
115B GLY* 1.3 77.9 - - - +
117B ALA* 1.3 60.0 + - - +
119B HIS* 3.2 11.7 + - - +
121B PHE* 3.0 61.1 + - + +
123B ARG* 3.4 31.5 + - - +
124B GLY* 4.3 1.8 - - - -
186B TRP* 6.2 0.7 - - - -
190B ILE* 4.2 34.3 - - + -
193B ALA* 4.1 14.4 - - + -
194B LYS* 4.2 5.4 - - + +
202B LEU* 4.1 21.8 - - - -
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Residues in contact with ALA 117 (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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113B GLU* 2.9 18.3 + - + +
114B GLU* 3.8 9.4 - - - +
115B GLY 3.4 0.8 - - - -
116B MSE 1.3 71.7 - - - +
118B ARG* 1.3 63.2 + - - +
119B HIS 3.2 0.9 + - - -
120B GLY* 3.3 10.3 + - - -
121B PHE* 3.7 26.1 - - + -
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Residues in contact with ARG 118 (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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85B TYR* 5.7 2.4 + - - -
111B MSE 5.4 1.0 + - - -
114B GLU* 3.4 16.3 + - - +
115B GLY* 3.5 30.6 + - - +
116B MSE 3.2 0.2 - - - -
117B ALA* 1.3 76.9 - - - +
119B HIS* 1.3 84.9 + - + +
120B GLY 3.5 0.4 + - - -
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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