Contacts of the helix formed by residues 83 - 94 (chain E) in PDB entry 5BXD
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 MET 83 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D ARG* 3.6 17.7 - - - +
80E ASP* 3.0 19.5 + - - +
81E GLY 3.4 0.2 - - - -
82E GLN* 1.3 78.7 - - + +
84E PHE* 1.3 64.3 + - - +
85E ARG 3.1 3.1 - - - -
86E TYR* 3.0 36.3 + - + +
87E ILE* 3.5 11.6 + - - +
102E PHE* 4.1 4.0 - - - -
104E ASP* 3.6 34.3 - - + +
107E LEU* 3.5 21.3 - - + -
108E LEU* 3.8 33.6 - - + +
111E GLU* 3.8 19.7 - - + -
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Residues in contact with PHE 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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34E ILE* 4.3 17.7 - - + -
36E VAL* 3.7 29.8 - - + -
41E TYR* 3.6 35.7 - + + -
48E LEU* 4.9 0.4 - - + -
56E ILE* 4.1 24.5 - - + -
77E ILE* 4.2 6.5 - - + -
80E ASP 3.6 4.7 + - - +
81E GLY 3.8 2.9 - - - +
82E GLN 3.2 1.0 - - - -
83E MET* 1.3 78.0 - - - +
85E ARG* 1.3 57.2 + - - +
87E ILE* 3.1 16.6 + - + +
88E LEU* 2.8 57.8 + - + +
111E GLU* 6.3 0.2 - - - -
115E PHE* 3.8 37.5 - + - -
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Residues in contact with ARG 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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41E TYR* 3.2 28.9 + - + +
82E GLN 3.5 13.5 - - - +
84E PHE* 1.3 76.3 - - - +
86E TYR* 1.3 90.7 + - - +
88E LEU* 3.3 3.7 + - - +
89E ASN* 2.9 49.9 + - - +
92E ARG* 5.1 1.0 + - - +
97E LEU 5.2 0.8 + - - -
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Residues in contact with TYR 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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82E GLN 4.2 7.0 - - - -
83E MET* 3.0 37.9 + - + +
85E ARG* 1.3 99.3 + - - +
87E ILE* 1.3 65.5 + - - +
89E ASN* 4.0 5.9 - - - +
90E PHE* 3.0 23.9 + - - +
95E LYS 5.2 0.7 - - - +
96E LEU* 5.7 0.4 - - + -
97E LEU 3.1 31.3 + - - +
98E ILE* 3.7 17.5 - - + -
99E PRO* 4.2 9.9 - - + +
102E PHE* 3.8 30.4 - + - -
108E LEU* 3.8 19.1 - - + -
120E MET* 3.6 6.9 - - + +
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Residues in contact with ILE 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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56E ILE* 5.3 2.5 - - + -
83E MET 3.8 11.7 - - - +
84E PHE* 3.1 25.3 + - + +
86E TYR* 1.3 76.7 - - - +
88E LEU* 1.3 61.7 + - - +
90E PHE* 3.2 5.5 + - - +
91E LEU* 3.1 29.2 + - + +
108E LEU* 4.2 6.7 - - + -
111E GLU* 4.0 4.7 - - + -
112E ALA* 3.7 36.6 - - + +
115E PHE* 4.0 26.7 - - + -
117E LEU* 3.7 19.0 - - + +
120E MET* 3.9 19.5 - - + -
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Residues in contact with LEU 88 (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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34E ILE* 5.9 0.2 - - + -
41E TYR* 3.9 37.7 - - + -
42E THR 4.6 0.7 - - - +
43E SER* 3.7 22.7 - - - +
47E THR* 4.3 2.2 - - + -
48E LEU* 3.8 22.2 - - + -
84E PHE* 2.8 27.9 + - + +
85E ARG* 3.6 5.4 - - - +
87E ILE* 1.3 78.1 - - - +
89E ASN* 1.3 58.7 + - - +
91E LEU* 3.2 15.2 + - + +
92E ARG* 3.0 65.1 + - - +
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Residues in contact with ASN 89 (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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85E ARG* 2.9 53.4 + - - +
86E TYR* 4.0 7.0 - - - +
87E ILE 3.3 0.2 - - - -
88E LEU* 1.3 73.7 - - - +
90E PHE* 1.3 56.3 + - - +
92E ARG* 2.9 33.9 + - - +
93E THR* 2.7 41.2 + - + +
95E LYS 4.3 1.8 - - - +
97E LEU* 4.2 27.3 - - + +
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Residues in contact with PHE 90 (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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51E TYR* 3.5 41.8 - + - -
86E TYR 3.0 14.4 + - - +
87E ILE 3.5 7.0 - - - +
89E ASN* 1.3 76.4 - - - +
91E LEU* 1.3 62.7 + - - +
94E SER* 2.6 50.9 + - - -
95E LYS 3.5 25.2 + - - +
96E LEU* 4.3 1.6 - - - -
117E LEU* 4.2 17.0 - - + -
119E PRO* 3.8 13.7 - - + -
120E MET* 3.4 59.5 - - + -
123E GLU* 4.6 7.0 - - + -
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Residues in contact with LEU 91 (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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47E THR* 3.7 26.1 - - + +
48E LEU* 4.2 19.5 - - + +
50E LYS* 3.0 33.1 + - - +
51E TYR* 3.6 31.4 - - + +
56E ILE* 4.2 28.7 - - + -
84E PHE* 5.8 0.2 - - + -
87E ILE* 3.1 22.7 + - + +
88E LEU* 3.3 16.6 - - + +
90E PHE* 1.3 77.5 - - + +
92E ARG* 1.3 58.8 + - - +
94E SER 4.6 0.2 + - - -
117E LEU* 3.9 24.9 - - + -
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Residues in contact with ARG 92 (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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41E TYR* 6.0 0.6 - - - -
42E THR 3.2 24.7 + - - -
43E SER* 4.2 9.3 + - - +
47E THR* 3.6 20.3 + - + +
50E LYS* 2.9 19.9 + - - +
85E ARG* 5.1 1.0 + - - +
88E LEU* 3.0 45.4 + - - +
89E ASN* 2.9 33.4 + - - +
90E PHE 3.1 0.4 - - - -
91E LEU* 1.3 79.2 - - - +
93E THR* 1.3 64.8 + - + +
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Residues in contact with THR 93 (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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50E LYS* 5.6 0.2 - - - -
89E ASN* 2.7 21.8 + - + +
92E ARG* 1.3 86.0 - - + +
94E SER* 1.3 70.3 + - - +
95E LYS* 3.0 48.4 + - - +
97E LEU* 3.8 17.3 - - + +
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Residues in contact with SER 94 (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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50E LYS* 4.7 8.3 - - - +
51E TYR* 2.7 30.5 + - - -
90E PHE* 2.6 38.5 + - - -
92E ARG 3.8 0.4 - - - -
93E THR* 1.3 74.2 - - - +
95E LYS* 1.3 59.2 + - - +
123E GLU* 5.2 4.7 - - - +
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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