Contacts of the helix formed by residues 71 - 87 (chain E) 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 PRO 71 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E ILE* 4.0 17.7 - - + -
69E LEU* 3.6 15.0 - - + +
70E VAL* 1.4 91.5 - - + +
72E SER* 1.3 65.5 + - - +
73E GLY 4.3 2.9 - - - +
74E ILE* 3.1 37.6 + - + +
75E VAL* 3.4 9.0 + - - +
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Residues in contact with SER 72 (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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69E LEU* 5.9 1.0 - - - +
70E VAL 3.5 3.1 + - - -
71E PRO* 1.3 71.9 - - - +
73E GLY* 1.3 58.3 + - - +
75E VAL* 3.2 11.6 + - - +
76E LEU* 2.8 31.5 + - - +
98E TYR* 4.5 4.0 + - - -
101E GLU* 5.8 1.1 - - - -
103E LYS* 5.8 2.3 - - - +
104E GLN* 3.8 39.0 - - - +
107E GLU* 5.6 6.1 - - - +
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Residues in contact with GLY 73 (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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71E PRO* 3.2 3.8 - - - +
72E SER* 1.3 81.4 + - - +
74E ILE* 1.3 62.3 + - - +
76E LEU* 3.8 8.2 - - - +
77E GLU* 3.1 27.5 + - - +
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Residues in contact with ILE 74 (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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151D LYS* 6.2 3.8 - - - +
56E ARG* 4.5 18.5 - - + +
59E LEU* 5.1 13.2 - - + -
60E ILE* 3.6 37.2 - - + -
63E ILE* 6.3 0.7 - - + -
70E VAL* 4.1 9.6 - - + -
71E PRO* 3.1 34.9 + - + +
73E GLY* 1.3 78.2 - - - +
75E VAL* 1.3 67.0 + - - +
77E GLU* 3.2 7.0 + - - +
78E LEU* 3.1 27.3 + - + +
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Residues in contact with VAL 75 (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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66D ARG 5.1 9.6 - - - +
67D GLY* 5.1 0.9 - - - -
42E THR* 3.6 37.0 - - + +
45E LEU* 4.5 5.3 - - + +
46E LEU* 5.0 14.6 - - + -
70E VAL* 4.1 21.3 - - + +
71E PRO 3.7 12.1 - - - +
72E SER* 3.2 12.2 + - - +
74E ILE* 1.3 75.6 - - - +
76E LEU* 1.3 63.3 + - - +
78E LEU* 3.3 11.8 + - + +
79E LEU* 3.0 22.3 + - + +
98E TYR* 4.2 13.5 - - + -
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Residues in contact with LEU 76 (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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72E SER 2.8 21.2 + - - +
73E GLY* 3.8 8.5 - - - +
75E VAL* 1.3 73.3 - - - +
77E GLU* 1.3 53.4 + - - +
79E LEU* 3.3 8.2 + - + +
80E LYS* 2.8 33.7 + - + +
98E TYR* 4.0 15.9 + - - +
107E GLU* 3.7 38.1 - - + +
108E PHE* 3.6 23.8 - - + -
111E ARG* 3.7 26.7 - - + +
112E ILE* 3.6 24.7 - - + -
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Residues in contact with GLU 77 (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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56E ARG* 3.5 24.2 - - - +
73E GLY 3.1 19.2 + - - +
74E ILE* 3.5 6.7 - - - +
76E LEU* 1.3 74.0 - - - +
78E LEU* 1.3 59.5 + - - +
80E LYS* 3.6 8.8 - - - +
81E GLU* 2.9 56.3 + - - +
111E ARG* 3.2 25.9 + - - +
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Residues in contact with LEU 78 (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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45E LEU* 3.7 27.6 - - + +
46E LEU* 4.1 26.7 - - + +
49E GLU* 3.6 42.0 - - + +
56E ARG* 3.6 22.2 - - - +
60E ILE* 4.3 8.3 - - + -
74E ILE* 3.1 21.9 + - + +
75E VAL* 3.3 12.1 + - + +
77E GLU* 1.3 75.2 - - - +
79E LEU* 1.3 63.2 + - - +
81E GLU* 3.4 8.8 + - - +
82E ALA* 3.1 23.6 + - - +
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Residues in contact with LEU 79 (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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40E LEU* 3.7 33.4 - - + -
42E THR* 6.0 0.7 - - + -
45E LEU* 3.7 22.3 - - + +
75E VAL* 3.0 13.5 + - + +
76E LEU* 3.4 10.3 - - + +
78E LEU* 1.3 74.4 - - - +
80E LYS* 1.3 64.5 + - - +
82E ALA* 3.3 3.6 + - - +
83E MET* 3.0 29.8 + - - +
95E ILE* 4.2 15.3 - - + -
98E TYR* 3.7 34.3 - - + -
108E PHE* 3.5 32.5 - - + -
112E ILE* 4.4 0.2 - - + -
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Residues in contact with LYS 80 (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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76E LEU* 2.8 21.2 + - + +
77E GLU* 3.3 18.1 + - - +
79E LEU* 1.3 72.5 - - - +
81E GLU* 1.3 57.3 + - - +
83E MET* 3.1 6.2 + - - +
84E VAL* 2.9 44.0 + - + +
111E ARG* 5.1 12.1 - - - +
112E ILE* 3.9 26.9 - - + +
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Residues in contact with GLU 81 (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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49E GLU* 5.0 0.5 - - - +
56E ARG* 2.9 41.0 + - - -
77E GLU* 2.9 35.4 + - - +
78E LEU* 3.7 13.2 - - - +
80E LYS* 1.3 71.9 - - + +
82E ALA* 1.3 61.6 + - - +
84E VAL* 3.3 13.4 - - + +
85E ALA* 2.9 30.9 + - - +
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Residues in contact with ALA 82 (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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40E LEU* 3.9 19.5 - - + -
45E LEU* 3.6 31.4 - - + -
48E GLU* 5.5 3.6 - - - +
78E LEU 3.1 5.2 + - - +
79E LEU 3.6 6.1 - - - +
81E GLU* 1.3 77.0 - - - +
83E MET* 1.3 57.2 + - - +
85E ALA* 3.5 5.8 + - - +
86E SER* 2.5 35.0 + - - +
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Residues in contact with MET 83 (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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9E ARG* 4.0 13.5 - - - -
13E ILE* 4.2 10.8 - - + -
40E LEU* 3.7 17.5 - - + -
79E LEU* 3.0 19.1 + - - +
80E LYS* 3.5 8.5 - - - +
82E ALA* 1.3 78.3 - - - +
84E VAL* 1.3 62.8 + - + +
86E SER 3.4 0.3 + - - -
87E LEU* 3.2 26.6 + - - +
93E PHE* 3.3 42.2 - - + -
95E ILE* 4.1 17.5 - - + -
108E PHE* 4.2 3.4 - - + -
112E ILE* 3.6 41.5 - - + -
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Residues in contact with VAL 84 (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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8E LEU* 6.5 1.1 - - + -
80E LYS* 2.9 27.9 + - + +
81E GLU* 3.3 18.4 - - + +
83E MET* 1.3 77.9 - - + +
85E ALA* 1.3 67.3 + - + +
86E SER 3.5 0.2 + - - -
87E LEU* 3.5 29.5 + - + +
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Residues in contact with ALA 85 (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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81E GLU 2.9 17.7 + - - +
82E ALA* 3.9 6.7 - - - +
83E MET 3.3 0.2 - - - -
84E VAL* 1.3 80.7 - - + +
86E SER* 1.3 58.7 + - - +
87E LEU 3.8 4.4 + - - +
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Residues in contact with SER 86 (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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38E THR* 3.6 26.7 - - - +
40E LEU* 5.5 0.3 - - - +
82E ALA* 2.5 25.2 + - - +
83E MET 3.4 0.6 + - - -
84E VAL 3.3 0.4 - - - -
85E ALA* 1.3 75.3 - - - +
87E LEU* 1.3 63.9 + - - +
89E ASP* 3.5 7.7 + - - -
90E THR* 3.3 26.5 + - - +
93E PHE* 3.8 17.7 - - - -
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Residues in contact with LEU 87 (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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8E LEU* 6.4 2.9 - - + -
9E ARG* 4.5 18.4 - - + -
11E CYS* 4.7 9.6 - - - -
83E MET 3.2 21.4 + - - +
84E VAL* 3.7 23.1 - - + +
85E ALA 3.4 7.3 - - - +
86E SER* 1.3 79.3 - - - +
88E GLY* 1.3 59.8 + - - +
89E ASP 3.3 0.8 + - - -
90E THR* 5.0 3.4 - - + -
93E PHE* 3.8 22.4 - - + -
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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