Contacts of the helix formed by residues 81 - 92 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ASP* 2.9 24.0 + - + +
80B PHE* 1.3 73.4 - - - +
82B PHE* 1.3 63.3 + - - +
83B ARG 3.1 3.6 + - - -
84B TYR* 3.2 13.3 + - + -
85B ILE* 3.5 9.7 + - - +
100B PHE* 4.0 25.1 - - + -
102B GLU* 3.4 28.3 - - + +
105B ARG* 3.7 39.3 - - + +
106B LEU* 3.5 20.9 - - + +
109B GLU* 3.7 33.0 - - + +
83C ARG* 3.9 0.7 - - - +
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Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.1 24.2 - - + -
31B VAL* 3.7 27.6 - - + -
36B TYR* 3.7 28.0 - + + -
51B LEU* 4.2 16.6 - - + -
75B ILE* 5.2 1.8 - - + -
77B ARG* 5.9 0.2 - - + -
78B ASP 3.4 15.9 + - - +
79B GLY 3.8 7.6 - - - +
80B PHE 3.3 0.8 - - - -
81B LEU* 1.3 76.2 - - - +
83B ARG* 1.3 59.4 + - - +
85B ILE* 3.2 17.2 + - + +
86B LEU* 2.9 48.7 + - + +
89B LEU* 5.1 0.2 - - + -
113B PHE* 3.4 44.2 - + + -
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Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASP* 2.6 43.3 + - - +
80A PHE* 3.6 17.9 - - - +
81A LEU* 4.0 2.0 - - - +
102A GLU* 3.1 41.0 + - - -
105A ARG* 3.8 12.5 - - - +
36B TYR* 3.4 34.2 + - + +
80B PHE 3.5 11.7 - - - +
81B LEU 3.1 0.2 - - - -
82B PHE* 1.3 79.5 - - - +
84B TYR* 1.3 82.0 + - + +
86B LEU* 3.5 4.2 + - - +
87B ASP* 3.2 33.5 + - - +
90B ARG* 5.2 1.1 + - - +
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Residues in contact with TYR 84 (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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102A GLU* 4.4 0.5 + - - -
105A ARG* 3.9 28.3 - - - -
80B PHE 3.8 16.6 - - - -
81B LEU* 3.2 15.5 + - + +
82B PHE 3.2 0.2 - - - -
83B ARG* 1.3 98.6 + - + +
85B ILE* 1.3 66.1 + - - +
86B LEU 3.2 0.2 - - - -
87B ASP* 4.3 4.5 - - - +
88B TYR* 3.2 16.6 + - - +
94B VAL* 3.2 17.6 - - + +
95B VAL 4.9 1.6 - - - -
96B LEU* 5.1 6.1 - - + -
97B PRO* 3.3 38.2 - - + +
100B PHE* 3.6 35.6 - + - -
106B LEU* 3.8 26.1 - - + +
118B LEU* 4.9 0.9 - - - +
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 5.2 0.7 - - + -
81B LEU 3.5 11.8 + - - +
82B PHE* 3.2 23.5 + - + +
84B TYR* 1.3 76.6 - - - +
86B LEU* 1.3 63.4 + - - +
88B TYR* 3.1 9.4 + - - +
89B LEU* 3.0 28.7 + - + +
106B LEU* 4.0 12.1 - - + -
109B GLU* 4.2 5.6 - - + -
110B ALA* 3.8 26.5 - - - +
113B PHE* 4.0 26.2 - - + -
115B LEU* 3.7 19.5 - - + -
118B LEU* 3.5 24.7 - - + -
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Residues in contact with LEU 86 (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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36B TYR* 4.0 34.8 - - + -
37B PHE 4.4 0.9 - - - +
38B THR* 3.7 33.9 - - + +
42B THR* 4.3 4.7 - - + -
43B LEU* 5.0 0.4 - - + -
82B PHE* 2.9 30.4 + - + +
83B ARG* 3.6 6.1 - - - +
85B ILE* 1.3 79.1 - - - +
87B ASP* 1.3 60.3 + - - +
89B LEU* 3.2 23.5 + - + +
90B ARG* 3.0 61.2 + - - +
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 5.5 2.8 + - - -
78A ASP* 4.2 10.2 + - - +
105A ARG* 2.5 41.0 + - - +
109A GLU* 4.7 6.4 - - - +
83B ARG* 3.2 21.8 + - - +
84B TYR* 3.9 6.8 - - - +
85B ILE 3.3 0.2 - - - -
86B LEU* 1.3 73.4 - - - +
88B TYR* 1.3 60.9 + - - +
90B ARG* 3.3 28.5 + - - +
91B ASP* 3.0 30.9 + - - +
93B GLN 3.4 9.4 - - - +
94B VAL* 4.2 8.7 - - + -
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Residues in contact with TYR 88 (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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46B ILE* 3.5 28.3 - - + +
84B TYR 3.2 8.1 + - - +
85B ILE 3.1 9.3 + - - +
87B ASP* 1.3 75.4 - - - +
89B LEU* 1.3 63.0 + - - +
92B ARG* 2.5 67.0 + - + +
93B GLN* 3.7 7.2 - - - -
94B VAL* 3.4 16.1 - - + +
115B LEU* 4.1 25.7 - - + +
117B ASP* 3.3 28.7 + - + +
118B LEU* 3.8 44.7 + - + -
121B LEU* 4.1 8.5 - - + -
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Residues in contact with LEU 89 (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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42B THR* 3.7 33.5 - - + +
43B LEU* 4.7 6.7 - - + +
45B SER* 3.9 14.8 + - - +
46B ILE* 4.0 17.0 - - + -
49B SER* 5.8 1.6 - - - +
51B LEU* 3.6 32.3 - - + -
82B PHE* 5.1 0.7 - - + -
85B ILE* 3.0 21.8 + - + +
86B LEU* 3.2 27.8 + - + +
88B TYR* 1.3 78.1 - - + +
90B ARG* 1.3 62.0 + - - +
92B ARG* 4.4 10.4 + - - +
115B LEU* 4.0 33.2 - - + -
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Residues in contact with ARG 90 (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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32A GLY* 4.0 5.3 - - - -
76A ASP* 2.6 42.7 + - - +
77A ARG* 3.8 25.6 + - - +
78A ASP* 3.4 21.6 + - - +
36B TYR* 5.8 0.2 - - - -
37B PHE 3.6 12.5 + - - -
42B THR* 4.2 12.3 - - + +
83B ARG* 5.2 1.0 + - - +
86B LEU* 3.0 50.7 + - - +
87B ASP* 3.3 30.4 + - - +
88B TYR 3.1 0.2 - - - -
89B LEU* 1.3 81.1 - - - +
91B ASP* 1.3 73.9 + - - +
92B ARG* 4.7 6.6 + - - -
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Residues in contact with ASP 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 2.7 44.3 + - - -
108A ARG* 3.5 24.9 + - - +
112A TYR* 5.0 1.4 - - - -
87B ASP* 3.0 16.9 + - - +
90B ARG* 1.3 79.9 - - - +
92B ARG* 1.3 72.7 + - - +
93B GLN* 3.1 34.9 + - + +
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Residues in contact with ARG 92 (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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45B SER* 3.4 46.1 + - - -
46B ILE* 4.2 14.5 - - + +
88B TYR* 2.5 53.3 + - + +
89B LEU 4.4 9.4 + - - +
90B ARG 4.7 6.1 + - - -
91B ASP* 1.3 74.3 - - - +
93B GLN* 1.3 58.8 + - - +
121B LEU* 4.5 5.2 - - - +
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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