Contacts of the helix formed by residues 81 - 92 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78L ASP* 3.4 27.4 + - + +
79L GLY 3.4 0.4 - - - -
80L PHE* 1.3 73.5 - - + +
82L PHE* 1.3 65.4 + - - +
83L ARG 3.1 3.8 + - - -
84L TYR* 3.3 13.9 + - + -
85L ILE* 3.5 9.3 + - - +
100L PHE* 4.0 24.9 - - + -
102L GLU* 3.7 16.8 - - - +
105L ARG* 3.7 31.0 - - + +
106L LEU* 3.6 29.9 - - + +
109L GLU* 3.6 35.2 - - + +
83M ARG* 4.0 2.0 - - - +
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Residues in contact with PHE 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LEU* 3.9 26.9 - - + -
31L VAL* 3.6 41.3 - - + -
36L TYR* 3.6 22.2 - + + -
51L LEU* 4.5 13.9 - - + -
75L ILE* 4.9 2.9 - - + -
78L ASP 3.4 4.9 + - - +
79L GLY 3.6 12.6 - - - +
80L PHE 3.2 1.2 - - - -
81L LEU* 1.3 76.0 - - - +
83L ARG* 1.3 59.2 + - - +
85L ILE* 3.2 14.7 + - + +
86L LEU* 2.9 48.2 + - + +
109L GLU* 6.4 0.2 - - - -
113L PHE* 3.6 43.1 - + + -
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Residues in contact with ARG 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K ASP* 2.6 39.1 + - - +
80K PHE* 3.9 28.2 - - + +
81K LEU* 3.8 4.6 - - - +
102K GLU* 2.8 34.4 + - - -
105K ARG* 2.9 24.4 - - - +
36L TYR* 3.6 28.5 + - + +
80L PHE 3.5 15.1 + - - +
82L PHE* 1.3 78.9 - - - +
84L TYR* 1.3 79.1 + - + +
86L LEU* 3.6 5.3 + - - +
87L ASP* 3.3 32.6 + - - +
90L ARG* 5.3 0.5 + - - -
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Residues in contact with TYR 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K GLU* 4.3 0.5 + - - -
105K ARG* 4.2 28.0 - - - -
80L PHE 3.9 16.8 - - - -
81L LEU* 3.3 17.9 + - + +
82L PHE 3.2 0.2 - - - -
83L ARG* 1.3 94.8 + - + +
85L ILE* 1.3 65.6 + - - +
86L LEU 3.3 0.2 - - - -
87L ASP* 3.6 4.4 + - - +
88L TYR* 3.3 3.5 + - - +
94L VAL* 3.2 34.0 - - + +
95L VAL 4.8 4.7 - - - -
96L LEU* 5.1 5.4 - - + -
97L PRO* 3.5 36.6 - - + +
100L PHE* 3.6 33.7 - + - -
106L LEU* 3.8 25.1 - - + +
118L LEU* 5.1 1.3 - - - +
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Residues in contact with ILE 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L LEU* 5.0 0.7 - - + -
81L LEU 3.7 13.0 - - - +
82L PHE* 3.2 20.5 + - + +
84L TYR* 1.3 77.6 - - - +
86L LEU* 1.3 62.7 + - - +
88L TYR* 3.2 15.7 + - - +
89L LEU* 3.3 20.9 + - + +
106L LEU* 3.8 13.0 - - + -
109L GLU* 4.1 7.0 - - + -
110L ALA* 3.8 26.2 - - - +
113L PHE* 3.9 31.9 - - + -
115L LEU* 4.1 13.9 - - + -
118L LEU* 3.7 24.5 - - + -
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Residues in contact with LEU 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K GLY 5.8 0.2 - - - +
36L TYR* 3.9 36.1 - - + -
37L PHE 4.3 6.7 - - - +
38L THR* 3.8 29.2 - - + +
42L THR* 4.6 3.6 - - + -
43L LEU* 5.1 1.8 - - + -
82L PHE* 2.9 32.0 + - + +
83L ARG* 3.7 6.1 - - - +
84L TYR 3.3 0.2 - - - -
85L ILE* 1.3 78.0 - - - +
87L ASP* 1.3 60.8 + - - +
89L LEU* 3.4 21.7 + - + +
90L ARG* 3.3 55.2 + - - +
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Residues in contact with ASP 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77K ARG* 5.3 1.0 - - - -
78K ASP* 4.1 9.3 + - - +
105K ARG* 2.2 37.0 + - - +
109K GLU* 4.5 7.1 - - - +
83L ARG 3.3 16.2 + - - +
84L TYR* 4.0 6.9 - - - +
85L ILE 3.3 0.4 - - - -
86L LEU* 1.3 74.6 - - - +
88L TYR* 1.3 61.4 + - - +
90L ARG* 2.8 33.1 + - - +
91L ASP* 2.9 33.7 + - - +
93L GLN 3.6 8.6 - - - +
94L VAL* 4.2 8.1 - - + -
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Residues in contact with TYR 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L ILE* 3.3 26.4 - - + +
84L TYR 3.3 5.5 + - - +
85L ILE 3.2 9.5 + - - +
87L ASP* 1.3 78.8 - - - +
89L LEU* 1.3 59.8 + - - +
92L ARG* 2.6 66.1 + - - -
93L GLN* 3.8 15.9 - - - -
94L VAL* 3.4 17.2 - - + +
115L LEU* 3.7 30.3 - - + +
117L ASP* 3.3 28.0 + - + +
118L LEU* 3.8 38.7 + - + -
121L LEU* 4.6 8.7 - - + -
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Residues in contact with LEU 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L THR* 3.6 25.6 - - + +
43L LEU* 4.8 7.6 - - + +
45L SER* 3.4 24.6 + - - +
46L ILE* 3.7 28.3 - - + -
49L SER* 5.5 2.2 - - - +
51L LEU* 3.4 33.4 - - + -
85L ILE* 3.3 16.7 + - + +
86L LEU* 3.6 22.9 - - + +
87L ASP 3.3 0.4 - - - -
88L TYR* 1.3 78.2 - - + +
90L ARG* 1.3 61.0 + - - +
92L ARG* 4.6 5.9 + - - -
115L LEU* 4.1 20.2 - - + -
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Residues in contact with ARG 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K GLY* 4.2 3.4 - - - -
76K ASP* 2.6 42.4 + - - +
77K ARG* 3.5 27.6 + - - +
78K ASP* 3.2 22.6 + - - +
37L PHE 3.8 8.9 + - - -
38L THR* 4.7 0.2 + - - -
42L THR* 4.0 15.3 - - + +
83L ARG 5.3 0.2 + - - -
86L LEU* 3.3 45.0 + - - +
87L ASP* 2.8 33.2 + - - +
88L TYR 3.1 0.6 - - - -
89L LEU* 1.3 80.9 - - - +
91L ASP* 1.3 71.6 + - - +
92L ARG* 5.2 1.4 - - - +
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Residues in contact with ASP 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77K ARG* 2.7 43.4 + - - -
108K ARG* 3.3 30.0 + - - +
112K TYR* 5.2 0.3 - - - -
87L ASP* 2.9 19.0 + - - +
90L ARG* 1.3 79.8 - - - +
92L ARG* 1.3 71.9 + - - +
93L GLN* 3.2 32.7 + - + +
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Residues in contact with ARG 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L SER* 5.0 6.9 + - - -
46L ILE* 4.1 34.0 - - - +
88L TYR* 2.6 58.7 + - + -
89L LEU 4.6 6.3 - - - +
90L ARG 5.2 1.6 - - - +
91L ASP* 1.3 75.2 - - - +
93L GLN* 1.3 58.3 + - - +
117L ASP* 4.0 18.4 + - - -
121L LEU* 5.1 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