Contacts of the helix formed by residues 114 - 130 (chain E) in PDB entry 5BMU
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 THR 114 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E TYR 4.4 7.6 - - - +
60E LEU* 3.0 24.2 - - - +
62E GLY 4.5 0.4 - - - +
67E GLU* 4.1 12.6 - - - +
71E VAL* 3.3 23.5 - - + +
109E THR* 3.6 25.8 - - - +
112E ASN* 3.8 4.5 - - + +
113E PHE* 1.3 80.9 - - - +
115E LEU* 1.3 64.6 + - - +
116E ALA* 3.4 14.0 - - - +
117E ASP* 3.1 28.3 + - - +
118E ILE* 3.6 7.9 + - - +
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Residues in contact with LEU 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LEU* 3.9 38.6 - - + -
48E ALA* 3.9 8.3 - - + -
49E ALA* 3.8 27.1 - - + +
52E VAL* 4.0 12.8 - - + -
60E LEU* 2.7 27.1 + - + +
61E LEU* 3.9 19.1 - - + -
71E VAL* 4.7 0.9 - - + -
75E LEU* 4.1 19.3 - - + -
114E THR* 1.3 68.0 - - - +
116E ALA* 1.3 65.2 + - - +
118E ILE* 3.5 12.9 + - + -
119E LEU* 2.9 33.6 + - + +
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Residues in contact with ALA 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E VAL* 4.3 15.9 - - - +
74E TRP* 4.0 19.7 - - + -
75E LEU* 4.1 13.2 - - - +
108E LEU* 3.7 23.1 - - + -
109E THR* 4.9 1.6 - - + -
114E THR* 3.4 14.5 + - - +
115E LEU* 1.3 75.5 - - - +
117E ASP* 1.3 52.7 + - - +
119E LEU* 3.1 3.7 + - - +
120E LEU* 2.6 36.9 + - - +
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Residues in contact with ASP 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E TYR* 3.6 22.0 - - - +
108E LEU* 3.1 28.0 + - - +
112E ASN 4.0 0.3 - - - +
113E PHE* 3.9 14.9 - - + -
114E THR* 3.1 33.4 + - - +
116E ALA* 1.3 71.9 - - - +
118E ILE* 1.3 59.0 + - - +
120E LEU 3.4 0.2 + - - -
121E TYR* 2.9 36.8 + - - +
145E TRP* 2.8 30.9 + - + -
149E ILE* 4.0 9.0 - - + -
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Residues in contact with ILE 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LEU* 3.8 27.4 - - + -
13E SER* 4.8 4.3 - - - +
14E LEU* 5.1 2.2 - - + -
60E LEU* 4.4 15.9 - - + -
113E PHE* 3.5 33.4 - - + -
114E THR 4.0 1.1 - - - +
115E LEU* 3.7 23.1 - - + +
117E ASP* 1.3 78.0 - - - +
119E LEU* 1.3 65.7 + - + +
121E TYR* 3.4 7.6 + - - +
122E TYR* 3.1 53.8 + - + +
149E ILE* 4.5 6.2 - - - +
155E ILE* 3.9 14.8 - - + -
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Residues in contact with LEU 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLU* 3.1 26.9 - - + +
10E LEU* 4.8 17.9 - - + -
44E LEU* 4.7 13.0 - - + -
45E THR* 4.0 27.4 - - + -
48E ALA* 4.6 12.1 - - + -
75E LEU* 4.3 16.6 - - + -
78E ARG* 3.2 25.5 + - + +
115E LEU* 2.9 21.3 + - + +
116E ALA* 3.7 3.6 - - - +
118E ILE* 1.3 76.6 - - + +
120E LEU* 1.3 64.4 + - - +
122E TYR* 3.1 11.4 + - + +
123E GLY 3.1 18.5 + - - -
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Residues in contact with LEU 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E TRP* 4.2 11.9 - - + +
77E TYR* 4.0 14.1 - - + -
78E ARG* 4.4 11.8 - - + +
82E VAL* 4.0 19.3 - - + -
98E LEU* 3.8 24.2 - - + -
108E LEU* 3.7 26.9 - - + -
116E ALA 2.6 20.1 + - - +
119E LEU* 1.3 72.8 - - - +
121E TYR* 1.3 56.2 + - - +
123E GLY 3.9 0.2 - - - -
124E LEU* 2.9 50.1 + - + +
145E TRP* 3.6 22.9 - - + -
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Residues in contact with TYR 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E ASP 2.9 18.5 + - - +
118E ILE 3.4 2.9 - - - +
120E LEU* 1.3 75.3 - - - +
122E TYR* 1.3 82.5 + + - +
124E LEU 3.8 0.3 - - - -
125E HIS* 3.1 38.5 + + - +
145E TRP* 3.6 9.1 - - + -
146E PHE* 3.5 40.6 - + - -
149E ILE* 3.7 19.3 - - + -
150E GLN* 3.4 23.2 - - + +
155E ILE* 3.7 31.6 - - + -
156E ARG* 3.4 30.9 - - - +
159E LEU* 4.1 3.9 - - + +
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Residues in contact with TYR 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 5.3 10.1 - - - +
6E GLU* 3.5 43.2 - - + +
9E LEU* 3.6 32.6 - - + +
10E LEU* 4.6 6.5 - - + -
13E SER* 2.6 28.8 + - - -
78E ARG* 4.1 1.6 - - - -
118E ILE* 3.1 40.8 + - + +
119E LEU* 3.1 5.5 + - + +
121E TYR* 1.3 87.4 - + - +
123E GLY* 1.3 61.5 + - - +
125E HIS* 3.8 13.5 + - - +
126E ARG* 4.8 3.3 + - - +
155E ILE* 3.1 25.1 + - + +
159E LEU* 3.6 23.1 - - + -
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Residues in contact with GLY 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ARG* 3.4 33.1 - - - +
82E VAL* 3.8 17.1 - - - +
119E LEU 3.1 9.1 + - - -
120E LEU 3.9 2.0 - - - -
122E TYR* 1.3 78.3 - - - +
124E LEU* 1.3 60.8 + - - +
125E HIS 3.4 0.6 + - - -
126E ARG* 4.1 11.8 + - - +
127E PHE* 3.9 12.8 - - - -
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Residues in contact with LEU 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E TYR* 5.9 1.1 - - + +
82E VAL* 4.1 18.4 - - + -
91E ILE* 5.4 7.0 - - + -
94E LEU* 5.9 7.2 - - + -
95E LEU* 4.6 16.8 - - + -
98E LEU* 3.8 29.2 - - + -
120E LEU* 2.9 42.3 + - + +
121E TYR 3.8 0.7 - - - -
123E GLY* 1.3 78.5 - - - +
125E HIS* 1.3 60.7 + - - +
126E ARG 3.6 0.9 - - - -
127E PHE* 3.4 14.6 + - + +
128E ILE* 3.0 37.4 + - + +
142E VAL* 5.0 2.7 - - + -
145E TRP* 4.2 9.6 - - + -
146E PHE* 4.0 6.7 - - + -
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Residues in contact with HIS 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E TYR* 3.1 32.0 + + - +
122E TYR* 3.9 11.2 - - - +
123E GLY 3.4 2.4 - - - -
124E LEU* 1.3 75.2 - - - +
126E ARG* 1.3 66.1 + - - +
127E PHE 3.1 0.2 + - - -
128E ILE* 3.2 1.7 + - - +
129E VAL* 3.0 46.7 + - + +
146E PHE* 3.8 24.2 - + - -
150E GLN* 5.8 0.2 - - - -
159E LEU* 3.8 27.5 - - + +
160E SER* 2.7 46.2 + - - -
162E VAL* 5.0 0.2 - - + -
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Residues in contact with ARG 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0E HIS* 3.6 59.7 - - + +
1E MET* 5.3 2.9 - - - +
82E VAL 4.1 7.9 + - - -
83E ASP* 5.3 4.2 + - - +
87E SER* 3.4 14.5 + - - -
122E TYR 4.8 3.0 + - - +
123E GLY 4.1 11.1 + - - +
125E HIS* 1.3 81.9 + - - +
127E PHE* 1.3 105.9 + - + +
129E VAL* 4.1 6.1 + - - +
130E ASP* 3.9 23.2 + - - +
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Residues in contact with PHE 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E VAL* 4.7 7.9 - - + -
87E SER* 3.6 20.4 - - - -
88E LYS* 4.7 12.6 - - + -
91E ILE* 3.7 47.1 - - + -
95E LEU* 5.9 0.4 - - + -
123E GLY 3.9 13.2 - - - -
124E LEU* 3.4 14.5 + - + +
125E HIS 3.1 0.8 - - - -
126E ARG* 1.3 126.4 - - + +
128E ILE* 1.3 67.6 + - + +
130E ASP* 3.5 12.4 + - - +
131E LEU* 3.0 23.4 + - + +
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Residues in contact with ILE 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E LEU* 4.2 23.8 - - + -
124E LEU* 3.0 25.4 + - + +
125E HIS 3.9 0.2 - - - +
127E PHE* 1.3 77.7 - - + +
129E VAL* 1.3 64.5 + - - +
130E ASP 3.2 1.8 - - - -
131E LEU* 3.1 42.3 + - + +
136E LYS* 4.2 7.2 - - + -
142E VAL* 4.4 11.2 - - + -
143E SER* 6.1 1.1 - - - -
146E PHE* 3.6 49.1 - - + -
162E VAL* 4.1 13.3 - - + +
164E PHE* 4.2 7.9 - - + -
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Residues in contact with VAL 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E HIS* 3.0 50.8 + - + +
126E ARG* 4.1 7.4 - - - +
128E ILE* 1.3 75.7 - - - +
130E ASP* 1.3 67.3 + - - +
131E LEU 3.5 5.5 + - - +
136E LYS* 4.8 4.5 + - - -
160E SER* 4.4 15.0 - - - +
162E VAL* 4.0 18.1 - - + +
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Residues in contact with ASP 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E ARG 3.9 13.6 + - - +
127E PHE* 3.5 11.5 + - - +
128E ILE 3.2 1.2 - - - -
129E VAL* 1.3 84.7 - - - +
131E LEU* 1.3 65.8 + - - +
132E THR* 3.6 4.0 + - - +
135E GLU* 5.1 0.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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