Contacts of the helix formed by residues 81 - 92 (chain E) in PDB entry 5A15
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 LEU 81 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78E ASP* 3.1 30.0 + - + +
80E PHE* 1.3 74.2 - - + +
82E PHE* 1.3 64.5 + - - +
83E ARG 3.1 3.2 + - - -
84E TYR* 3.3 18.1 + - + -
85E ILE* 3.5 14.4 + - - +
100E PHE* 4.0 27.6 - - + -
102E GLU* 4.6 8.3 - - + +
105E ARG* 3.9 37.9 - - + +
106E LEU* 3.8 18.1 - - + +
109E GLU* 3.8 32.1 - - + +
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Residues in contact with PHE 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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29E LEU* 4.1 22.2 - - + -
31E VAL* 3.7 35.0 - - + -
36E TYR* 3.6 23.8 - + + -
43E LEU* 5.3 0.2 - - + -
51E LEU* 4.2 21.1 - - + -
75E ILE* 5.4 1.6 - - + -
78E ASP 3.4 6.1 + - - +
79E GLY 3.5 12.6 - - - +
80E PHE 3.2 1.0 - - - -
81E LEU* 1.3 77.4 - - - +
83E ARG* 1.3 58.1 - - - +
85E ILE* 3.2 13.0 + - + +
86E LEU* 2.8 50.2 + - + +
113E PHE* 3.5 44.0 - + + -
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Residues in contact with ARG 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ASP* 2.9 33.7 + - - +
80D PHE* 4.3 22.9 - - - +
81D LEU* 4.2 1.6 - - - +
102D GLU* 2.6 44.3 + - - -
105D ARG* 3.0 16.6 - - - +
36E TYR* 3.4 29.5 + - + +
80E PHE 3.3 15.8 + - - +
81E LEU 3.1 0.2 - - - -
82E PHE* 1.3 79.1 - - - +
84E TYR* 1.3 87.5 + - + +
86E LEU* 3.4 5.4 + - - +
87E ASP* 3.1 35.5 + - - +
90E ARG* 5.2 1.4 + - - +
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Residues in contact with TYR 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D GLU* 4.4 0.2 + - - -
105D ARG* 3.9 19.7 - - - -
80E PHE* 3.6 18.6 - - + -
81E LEU* 3.3 18.6 + - + +
82E PHE 3.2 0.2 - - - -
83E ARG* 1.3 105.9 + - - +
85E ILE* 1.3 65.5 + - - +
86E LEU 3.2 0.7 - - - -
87E ASP* 3.8 7.1 - - - +
88E TYR* 3.2 21.5 + - - +
94E VAL* 5.5 7.7 - - + +
95E VAL 4.8 1.8 - - - -
96E LEU* 4.3 11.4 - - + -
97E PRO* 3.4 38.5 - - + +
100E PHE* 4.2 24.7 - + - -
106E LEU* 4.2 19.2 - - + +
118E LEU* 5.2 1.4 - - - +
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Residues in contact with ILE 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E LEU* 4.9 1.3 - - + -
81E LEU 3.5 12.7 + - - +
82E PHE* 3.2 23.0 + - + +
84E TYR* 1.3 77.0 - - - +
86E LEU* 1.3 62.7 + - - +
88E TYR* 3.2 8.9 + - - +
89E LEU* 3.1 28.7 + - + +
106E LEU* 3.8 17.5 - - + -
109E GLU* 4.3 5.8 - - + -
110E ALA* 4.0 22.2 - - - +
113E PHE* 4.1 25.8 - - + -
115E LEU* 3.9 17.5 - - + -
118E LEU* 3.5 23.8 - - + -
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Residues in contact with LEU 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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36E TYR* 4.0 35.2 - - + -
37E PHE 4.4 4.9 - - - +
38E THR* 4.0 28.9 - - + +
42E THR* 4.4 6.1 - - + -
43E LEU* 4.9 0.9 - - + -
82E PHE* 2.8 31.7 + - + +
83E ARG 3.6 5.4 - - - +
85E ILE* 1.3 77.8 - - - +
87E ASP* 1.3 64.3 + - - +
89E LEU* 3.3 22.3 + - + +
90E ARG* 3.1 53.8 + - - +
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Residues in contact with ASP 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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77D ARG* 5.6 2.3 + - - -
78D ASP* 4.5 6.8 + - - +
105D ARG* 2.5 42.9 + - - +
109D GLU* 4.6 7.7 - - - +
83E ARG* 3.1 24.6 + - - +
84E TYR* 4.0 6.3 - - - +
85E ILE 3.3 0.2 - - - -
86E LEU* 1.3 73.4 - - - +
88E TYR* 1.3 60.2 + - - +
90E ARG* 3.1 30.4 + - - +
91E ASP* 2.9 36.6 + - - +
93E GLN 4.1 3.9 - - - +
94E VAL* 6.5 0.2 - - - -
95E VAL 5.8 1.3 - - - +
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Residues in contact with TYR 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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46E ILE* 3.5 25.7 - - + +
84E TYR 3.2 13.9 + - - +
85E ILE 3.2 8.3 + - - +
87E ASP* 1.3 74.7 - - - +
89E LEU* 1.3 62.6 + - + +
92E ARG* 2.6 66.1 + - - -
93E GLN 3.5 20.3 + - - +
94E VAL* 3.9 6.7 - - + -
115E LEU* 4.1 14.9 - - + +
117E ASP* 3.6 24.3 + - - +
118E LEU* 3.7 50.7 + - + -
121E LEU* 4.2 13.9 - - + -
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Residues in contact with LEU 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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42E THR* 3.7 27.5 - - + +
43E LEU* 4.8 7.9 - - + +
45E SER* 3.9 22.1 + - - +
46E ILE* 3.5 30.3 - - + -
49E SER* 5.7 1.6 - - - +
51E LEU* 3.5 31.6 - - + -
82E PHE* 5.5 0.4 - - + -
85E ILE* 3.1 19.0 + - + +
86E LEU* 3.3 23.5 + - + +
88E TYR* 1.3 80.3 - - + +
90E ARG* 1.3 61.1 + - - +
92E ARG* 4.1 9.5 - - - +
115E LEU* 4.4 11.0 - - + -
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Residues in contact with ARG 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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32D GLY* 4.4 3.2 - - - -
76D ASP* 2.9 43.3 + - - +
77D ARG* 3.6 30.9 + - - +
78D ASP* 3.6 19.8 + - - +
36E TYR* 5.9 0.4 - - - -
37E PHE 3.4 12.1 + - - -
38E THR* 4.6 0.4 + - - -
42E THR* 4.4 11.7 - - + +
83E ARG* 5.2 1.6 + - - +
86E LEU* 3.1 47.0 + - - +
87E ASP* 3.1 32.1 + - - +
88E TYR 3.1 0.2 - - - -
89E LEU* 1.3 81.6 - - - +
91E ASP* 1.3 72.0 + - - +
92E ARG* 4.9 2.3 - - - +
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Residues in contact with ASP 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ARG* 2.6 37.7 + - - -
108D ARG* 3.1 43.0 + - - +
109D GLU* 5.0 0.3 - - - +
112D TYR* 4.9 0.7 - - - -
87E ASP* 2.9 21.5 + - - +
90E ARG* 1.3 75.5 - - - +
92E ARG* 1.3 73.6 + - - +
93E GLN* 3.7 22.0 - - + +
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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
----------------------------------------------------------
45E SER* 4.1 14.4 + - - -
46E ILE* 3.6 42.4 - - - +
88E TYR* 2.6 57.0 + - + -
89E LEU 4.1 11.4 - - - +
90E ARG 4.9 1.8 - - - +
91E ASP* 1.3 76.2 - - - +
93E GLN* 1.3 57.3 + - - +
117E ASP* 4.9 8.1 + - - -
121E LEU* 5.1 3.3 - - - +
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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