Contacts of the helix formed by residues 70 - 88 (chain B) in PDB entry 5A6C
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 ASP 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B TYR* 3.0 28.2 + - + +
68B LEU* 3.2 5.8 - - + +
69B HIS* 1.3 75.5 - - - +
71B TYR* 1.3 59.9 + - - +
72B ALA* 3.1 10.7 + - - +
73B LYS* 3.4 43.7 + - - +
74B ALA 3.2 15.8 + - - -
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Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PHE* 3.9 52.0 - + - -
69B HIS* 2.8 44.6 + + + -
70B ASP* 1.3 67.9 - - - +
72B ALA* 1.3 60.0 + - - +
74B ALA* 3.8 7.4 - - - -
75B LEU* 3.0 24.6 + - - +
104B THR* 3.4 12.0 - - + +
107B VAL* 3.6 35.4 - - + +
108B LEU* 3.9 27.7 - - + +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ASP* 3.1 9.8 - - - +
71B TYR* 1.3 74.3 - - - +
73B LYS* 1.3 67.3 + - + +
75B LEU* 3.1 8.5 + - - +
76B GLU* 3.0 29.4 + - - +
108B LEU* 5.1 5.9 - - - +
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU* 5.4 0.2 - - - +
65B TYR* 3.6 48.4 + - + +
70B ASP* 3.3 29.1 + - - +
72B ALA* 1.3 76.0 - - + +
74B ALA* 1.3 68.1 + - - +
76B GLU* 3.2 19.1 + - - +
77B TYR* 2.9 34.5 + - + +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLY* 3.5 27.5 - - - +
65B TYR* 3.7 4.2 - - - +
66B PHE* 3.7 22.0 - - + +
70B ASP 3.2 7.7 + - - +
71B TYR* 3.5 14.8 - - - +
73B LYS* 1.3 77.5 - - - +
75B LEU* 1.3 63.8 + - - +
77B TYR* 3.3 0.7 + - - -
78B HIS* 2.9 30.8 + - + -
104B THR* 4.2 11.2 - - + +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR 3.0 16.0 + - - +
72B ALA* 3.1 9.6 + - - +
74B ALA* 1.3 75.5 - - - +
76B GLU* 1.3 63.6 + - + +
78B HIS 3.4 0.2 + - - -
79B HIS* 2.9 25.3 + - + +
101B LEU* 3.5 30.6 - - + +
104B THR* 3.6 21.0 - - + +
105B LEU* 3.7 32.5 - - + -
108B LEU* 4.0 15.9 - - + -
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA* 3.0 19.5 + - - +
73B LYS* 3.5 21.1 - - - +
75B LEU* 1.3 77.0 - - + +
77B TYR* 1.3 61.4 + - + +
79B HIS* 2.9 23.1 + - - +
80B HIS* 2.9 32.4 + - + +
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Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU* 2.9 22.5 + - - -
44B VAL* 4.9 7.5 - - + +
58B TYR* 3.5 52.3 - + - +
61B LEU* 3.4 33.8 - - + +
62B GLY* 3.6 10.3 - - - +
65B TYR* 3.8 23.8 - + - -
73B LYS* 2.9 32.9 + - + +
76B GLU* 1.3 77.9 - - + +
78B HIS* 1.3 57.2 + - - +
80B HIS* 3.3 15.7 + + - +
81B ASP* 2.9 28.9 + - - +
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Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B SER* 3.6 26.2 + - - -
62B GLY* 3.4 11.0 + - - -
63B ASN* 3.1 30.4 + - - -
66B PHE* 5.2 2.8 - - - +
74B ALA* 2.9 24.7 + - + +
77B TYR* 1.3 75.6 - - - +
79B HIS* 1.3 56.8 + - - +
81B ASP* 3.4 7.9 + - - +
82B LEU* 2.9 27.7 + - - +
97B ALA* 4.1 6.4 + - - +
100B ASN* 3.3 37.7 + - + +
101B LEU* 3.6 24.6 - - + +
104B THR* 3.6 20.3 + - - -
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Residues in contact with HIS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 2.9 14.4 + - + +
76B GLU* 2.9 12.6 + - - +
78B HIS* 1.3 74.3 - - - +
80B HIS* 1.3 69.2 + - - +
82B LEU* 3.2 13.0 + - + +
83B THR* 2.8 47.8 + - - -
86B ARG* 6.1 0.8 + - - -
101B LEU* 3.9 21.7 - - + +
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Residues in contact with HIS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 3.9 30.3 - + + -
76B GLU* 2.9 31.8 + - + +
77B TYR* 3.7 25.8 - + - +
79B HIS* 1.3 83.7 + - - +
81B ASP* 1.3 57.9 + - - +
83B THR* 3.6 6.9 + - - -
84B LEU* 2.9 33.6 + - - +
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Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER* 2.6 38.4 + - - +
58B TYR* 3.9 14.5 - - + +
59B SER* 3.1 15.6 + - - +
77B TYR 2.9 13.8 + - - +
78B HIS* 3.4 12.5 + - - +
80B HIS* 1.3 76.1 - - - +
82B LEU* 1.3 57.0 + - - +
84B LEU* 3.5 4.5 - - - +
85B ALA* 2.9 29.6 + - - +
96B LYS* 2.7 33.2 + - - -
97B ALA* 3.3 10.3 - - - +
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B HIS 2.9 14.2 + - - +
79B HIS* 3.2 19.0 + - + +
81B ASP* 1.3 75.7 - - - +
83B THR* 1.3 63.0 + - - +
85B ALA* 3.5 2.0 - - - +
86B ARG* 3.0 52.9 + - - +
94B GLU* 3.6 40.8 - - + +
97B ALA* 3.6 10.6 - - + +
98B SER* 4.3 7.9 - - - +
101B LEU* 3.8 22.7 - - + -
117B CYS* 5.8 0.9 - - - -
120B ARG* 4.9 9.2 - - - +
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Residues in contact with THR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B HIS* 2.8 41.1 + - - -
80B HIS* 3.6 8.0 + - - -
82B LEU* 1.3 71.7 - - - +
84B LEU* 1.3 64.8 + - - +
86B ARG* 3.0 12.5 + - - +
87B THR* 2.9 34.2 + - + +
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Residues in contact with LEU 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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51B LEU* 3.7 39.9 - - + +
54B LEU* 3.8 19.3 - - + -
55B SER* 3.9 13.2 - - - +
58B TYR* 3.5 35.9 - - + -
80B HIS 2.9 15.0 + - - +
81B ASP* 3.5 5.4 - - - +
83B THR* 1.3 77.1 - - - +
85B ALA* 1.3 65.4 + - - +
87B THR* 3.1 21.3 + - + +
88B ILE* 3.2 18.9 + - + +
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Residues in contact with ALA 85 (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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55B SER* 4.9 4.8 + - - +
81B ASP* 2.9 24.0 + - - +
82B LEU* 3.5 4.9 - - - +
84B LEU* 1.3 73.0 - - - +
86B ARG* 1.3 63.2 + - - +
88B ILE* 3.5 5.6 - - - +
89B GLY 3.1 4.0 + - - -
90B ASP* 2.9 38.0 + - + +
93B GLY* 3.7 8.1 - - - +
94B GLU* 3.4 33.7 - - - +
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Residues in contact with ARG 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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79B HIS* 6.1 0.8 + - - -
82B LEU* 3.0 38.9 + - - +
83B THR* 3.3 11.4 - - - +
85B ALA* 1.3 73.4 - - - +
87B THR* 1.3 67.8 + - + +
89B GLY* 3.0 14.6 + - - -
90B ASP 5.0 0.2 - - - +
94B GLU* 2.8 32.8 + - + +
120B ARG* 3.2 27.7 - - - +
1388B SO4 2.7 29.0 + - - -
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Residues in contact with THR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 5.5 1.6 - - - +
83B THR* 2.9 31.9 + - + +
84B LEU* 3.1 13.9 + - + +
86B ARG* 1.3 76.1 - - - +
88B ILE* 1.3 70.4 + - - +
89B GLY* 2.8 6.8 + - - -
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Residues in contact with ILE 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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51B LEU* 4.0 54.1 - - + +
52B LYS* 4.3 9.4 - - + +
55B SER* 5.3 2.7 - - - -
84B LEU* 3.2 14.2 + - + +
85B ALA* 3.5 14.6 - - - +
87B THR* 1.3 87.6 + - - +
89B GLY* 1.3 59.9 + - - +
90B ASP* 3.8 20.8 - - + +
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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
------------------------------------------------------------
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