Contacts of the helix formed by residues 81 - 92 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ASP* 3.1 30.1 + - + +
79C GLY 3.3 0.4 - - - -
80C PHE* 1.3 74.2 - - + +
82C PHE* 1.3 65.4 + - - +
83C ARG 3.1 2.8 + - - -
84C TYR* 3.2 13.8 + - + +
85C ILE* 3.4 10.5 + - - +
100C PHE* 4.0 23.8 - - + -
102C GLU* 3.5 30.1 - - + +
105C ARG* 3.7 33.0 - - + +
106C LEU* 3.6 21.9 - - + +
109C GLU* 3.8 30.5 - - + +
83D ARG* 4.0 1.1 - - - +
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Residues in contact with PHE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LEU* 3.8 31.0 - - + -
31C VAL* 3.7 34.5 - - + -
36C TYR* 3.7 16.2 - + + -
43C LEU* 5.2 0.9 - - + -
51C LEU* 4.3 17.7 - - + -
75C ILE* 5.1 2.7 - - + -
77C ARG* 5.9 0.2 - - + -
78C ASP 3.5 5.0 + - - +
79C GLY 3.4 12.1 + - - +
80C PHE 3.2 1.0 - - - -
81C LEU* 1.3 76.4 - - - +
83C ARG* 1.3 55.1 + - - +
85C ILE* 3.6 20.0 - - + -
86C LEU* 2.8 54.3 + - + +
113C PHE* 3.8 39.3 - + - -
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Residues in contact with ARG 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASP* 2.7 42.8 + - - +
80B PHE* 4.0 25.5 - - + +
81B LEU* 3.9 4.0 - - - +
102B GLU* 2.8 43.6 + - - -
105B ARG* 3.8 9.6 - - - +
36C TYR* 3.4 29.3 + - + +
80C PHE 3.4 15.9 + - - +
82C PHE* 1.3 79.9 - - - +
84C TYR* 1.3 84.0 + - + +
86C LEU* 3.6 4.7 + - - +
87C ASP* 3.1 32.7 + - - +
90C ARG* 5.1 1.0 + - - -
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Residues in contact with TYR 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLU* 4.3 0.3 + - - -
105B ARG* 3.8 32.1 - - - -
80C PHE 3.9 16.6 - - - -
81C LEU* 3.2 15.1 + - + -
82C PHE 3.2 0.2 - - - -
83C ARG* 1.3 96.6 + - + +
85C ILE* 1.3 65.7 + - - +
86C LEU 3.3 0.2 - - - -
87C ASP* 3.8 4.3 - - - -
88C TYR* 3.2 19.1 + - - +
94C VAL* 3.7 19.5 - - + +
95C VAL 4.6 0.4 - - - -
96C LEU* 4.9 2.0 - - + -
97C PRO* 3.1 43.0 - - + +
100C PHE* 3.7 29.5 - + - -
106C LEU* 3.8 25.8 - - + -
118C LEU* 4.9 1.2 - - - +
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 4.7 1.3 - - + -
81C LEU 3.4 12.7 + - - +
82C PHE* 3.1 32.0 + - + +
84C TYR* 1.3 77.7 - - - +
86C LEU* 1.3 63.7 + - - +
88C TYR* 3.1 16.2 + - - +
89C LEU* 3.3 20.6 + - + +
106C LEU* 4.1 11.0 - - + -
109C GLU* 4.1 10.1 - - + +
110C ALA* 3.9 25.4 - - - +
113C PHE* 4.2 17.9 - - + -
115C LEU* 4.1 16.2 - - + -
118C LEU* 3.7 24.0 - - + -
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Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C TYR* 4.1 29.2 - - + -
37C PHE 4.0 11.9 - - - +
38C THR* 3.7 30.3 - - + +
42C THR* 4.2 10.3 - - + -
43C LEU* 4.9 1.3 - - + -
82C PHE* 2.8 30.8 + - + +
83C ARG* 3.8 5.4 - - - +
85C ILE* 1.3 79.5 - - - +
87C ASP* 1.3 62.4 + - - +
89C LEU* 3.3 14.8 + - + +
90C ARG* 3.2 57.4 + - - +
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Residues in contact with ASP 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ARG* 5.6 1.6 + - - -
78B ASP* 4.3 8.9 - - - +
105B ARG* 2.6 37.5 + - - +
109B GLU* 4.5 8.6 - - - +
83C ARG 3.1 18.1 + - - +
84C TYR* 3.9 8.1 - - - +
85C ILE 3.2 0.2 - - - -
86C LEU* 1.3 76.8 - - - +
88C TYR* 1.3 64.1 + - - +
90C ARG* 3.0 29.9 + - - +
91C ASP* 3.1 26.1 + - - +
93C GLN 3.4 9.4 - - - +
94C VAL* 4.5 10.1 - - + -
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Residues in contact with TYR 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ILE* 3.4 30.8 - - + +
84C TYR 3.2 8.1 + - - +
85C ILE 3.1 10.6 + - - +
87C ASP* 1.3 77.4 - - - +
89C LEU* 1.3 58.9 + - + +
92C ARG* 2.6 60.5 + - - +
93C GLN* 3.7 8.3 - - - -
94C VAL* 3.3 27.8 - - + +
115C LEU* 4.1 21.6 - - + +
117C ASP* 3.3 29.7 + - + +
118C LEU* 3.8 39.8 + - + -
121C LEU* 4.3 9.9 - - + -
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Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C THR* 3.5 35.7 - - + +
43C LEU* 4.8 6.3 - - + +
45C SER* 3.7 23.5 + - - +
46C ILE* 3.6 31.4 - - + +
49C SER* 5.7 1.1 - - - +
51C LEU* 3.7 29.6 - - + -
85C ILE* 3.3 17.2 + - + +
86C LEU* 3.3 17.7 + - + +
88C TYR* 1.3 79.5 - - + +
90C ARG* 1.3 62.6 + - - +
92C ARG* 4.3 8.2 + - - +
115C LEU* 4.3 15.0 - - + -
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Residues in contact with ARG 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLY* 4.3 3.2 + - - -
76B ASP* 2.8 43.6 + - - +
77B ARG* 3.6 31.3 + - - +
78B ASP* 3.5 19.4 + - - +
37C PHE 3.6 9.7 + - - -
42C THR* 4.2 11.7 - - + +
83C ARG 5.1 0.4 + - - -
86C LEU* 3.2 46.4 + - - +
87C ASP* 3.0 33.7 + - - +
88C TYR 3.2 0.6 - - - -
89C LEU* 1.3 81.1 - - - +
91C ASP* 1.3 71.0 + - - +
92C ARG* 5.2 1.7 - - - +
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Residues in contact with ASP 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ARG* 2.6 43.8 + - - -
108B ARG* 3.1 32.8 + - - +
112B TYR* 4.7 0.9 - - - -
87C ASP* 3.1 12.2 + - - +
90C ARG* 1.3 81.2 - - - +
92C ARG* 1.3 73.1 + - - +
93C GLN* 3.2 38.7 + - + +
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Residues in contact with ARG 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C SER* 3.1 31.5 + - - -
46C ILE* 3.9 28.2 - - - +
47C PRO* 5.5 1.2 - - - +
88C TYR* 2.6 49.9 + - + +
89C LEU 4.3 11.1 + - - +
90C ARG 3.6 1.8 - - - +
91C ASP* 1.3 75.3 - - - +
93C GLN* 1.3 57.4 + - - +
121C LEU* 4.9 3.8 - - - +
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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