Contacts of the helix formed by residues 75 - 88 (chain B) in PDB entry 5AJQ
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 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B VAL* 6.2 2.7 - - + -
76B GLU* 1.3 60.5 + - - +
77B ASP* 3.0 18.1 + - - +
78B TYR* 3.0 26.2 + - - +
79B ILE* 3.4 24.0 + - + +
101B TYR* 3.8 50.5 - - + -
106B LEU* 4.4 24.5 - - + +
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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
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75B LEU* 1.3 73.3 - - - +
77B ASP* 1.3 65.0 + - - +
78B TYR 3.3 0.2 - - - -
79B ILE* 3.7 29.3 + - + +
80B VAL* 4.4 9.9 + - - +
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Residues in contact with ASP 77 (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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75B LEU 3.0 11.2 + - - +
76B GLU* 1.3 79.4 - - - +
78B TYR* 1.3 59.2 + - + +
79B ILE 3.7 0.2 + - - -
80B VAL* 4.3 3.6 + - - +
180B ALA* 3.1 39.8 - - - +
181B LYS* 5.5 6.7 - - + -
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Residues in contact with TYR 78 (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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75B LEU* 3.0 7.9 + - - +
77B ASP* 1.3 76.1 - - + +
79B ILE* 1.3 64.0 + - - +
80B VAL 3.3 2.9 - - - -
81B GLU* 3.2 12.1 + - + +
82B ILE* 3.1 28.3 + - + +
106B LEU* 3.7 30.3 - - + -
108B ILE* 5.1 6.3 - - + -
180B ALA* 4.6 4.5 - - - -
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Residues in contact with ILE 79 (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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26B VAL* 4.6 20.9 - - + -
75B LEU* 3.4 22.3 + - + +
76B GLU* 3.7 29.8 + - + +
77B ASP 3.4 1.6 - - - -
78B TYR* 1.3 77.0 - - - +
80B VAL* 1.3 60.1 + - + +
82B ILE* 4.1 6.6 - - + +
83B GLU* 3.0 31.4 + - + +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU 4.6 10.1 - - - +
77B ASP 4.3 2.2 + - - +
78B TYR 3.3 0.8 - - - -
79B ILE* 1.3 78.7 - - + +
81B GLU* 1.3 58.2 + - - +
83B GLU* 3.8 5.1 - - - +
84B ILE* 3.0 42.2 + - + +
179B SER* 4.3 14.4 - - - +
180B ALA* 4.2 11.2 - - + +
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B TYR* 3.2 14.3 + - + +
80B VAL* 1.3 80.3 - - - +
82B ILE* 1.3 60.5 + - + +
84B ILE* 3.3 10.1 + - + +
85B LEU* 2.9 42.9 + - + +
108B ILE* 5.6 5.5 - - + +
175B ASP 3.3 20.9 - - - +
176B PHE* 3.0 32.8 - - + +
177B GLY* 3.1 18.8 - - - +
180B ALA* 3.3 21.0 - - + +
181B LYS* 5.2 1.4 - - - +
800B DB8 4.7 9.9 - - - +
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Residues in contact with ILE 82 (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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25B HIS* 4.7 9.6 - - + +
26B VAL* 4.2 22.2 - - + -
78B TYR* 3.1 24.5 + - + +
79B ILE* 4.1 6.7 - - + +
81B GLU* 1.3 79.1 - - + +
83B GLU* 1.3 61.1 + - - +
85B LEU* 3.5 6.6 + - + +
86B ALA* 2.9 28.8 + - - +
96B LEU* 3.7 21.2 - - + +
99B ALA* 3.8 15.5 - - + -
106B LEU* 4.2 18.2 - - + -
108B ILE* 4.1 35.9 - - + -
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Residues in contact with GLU 83 (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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25B HIS 5.9 4.9 - - - +
79B ILE* 3.0 22.8 + - + +
80B VAL* 3.8 6.1 - - - +
82B ILE* 1.3 74.7 - - - +
84B ILE* 1.3 56.4 + - - +
86B ALA* 4.4 4.3 - - - -
87B THR* 2.7 42.0 + - + +
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Residues in contact with ILE 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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80B VAL* 3.0 37.7 + - + +
81B GLU* 3.4 11.4 - - - +
82B ILE 3.3 0.2 - - - -
83B GLU* 1.3 75.1 - - - +
85B LEU* 1.3 66.7 + - - +
86B ALA 3.1 0.5 + - - -
87B THR* 3.1 6.3 + - - -
88B CYS* 2.9 45.7 + - - -
153B ILE* 3.9 39.3 - - + -
176B PHE* 4.0 25.6 - - + -
179B SER* 4.4 18.4 - - - +
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Residues in contact with LEU 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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81B GLU* 2.9 36.1 + - + +
82B ILE* 3.5 8.3 + - + +
84B ILE* 1.3 75.3 - - + +
86B ALA* 1.3 60.8 + - - +
88B CYS* 3.8 15.0 - - - +
93B ILE* 4.4 2.9 - - + -
94B VAL* 3.5 37.8 - - + +
95B LYS* 4.8 0.5 - - - -
96B LEU* 3.8 29.8 + - + +
108B ILE* 5.0 4.9 - - + -
110B ILE* 3.7 24.7 - - + -
175B ASP 5.8 3.4 - - - +
176B PHE* 3.8 30.5 - - + -
800B DB8 5.8 5.4 - - + -
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Residues in contact with ALA 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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25B HIS* 4.4 17.3 - - + -
82B ILE 2.9 20.0 + - - +
83B GLU* 3.7 6.1 - - - +
84B ILE 3.1 0.2 - - - -
85B LEU* 1.3 79.5 - - - +
87B THR* 1.3 66.7 + - + +
88B CYS 3.2 5.6 + - - +
89B ASP* 5.8 0.7 - - - +
96B LEU* 4.1 17.4 - - + +
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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
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83B GLU* 2.7 26.2 + - + +
84B ILE* 3.4 6.9 + - - -
86B ALA* 1.3 79.6 - - + +
88B CYS* 1.3 60.0 + - - +
89B ASP* 3.5 5.1 + - - +
147B PHE* 4.8 0.5 - - - -
151B LYS* 2.9 31.2 + - - -
153B ILE* 5.0 3.5 - - - +
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Residues in contact with CYS 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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84B ILE* 2.9 42.2 + - - +
85B LEU 3.8 12.0 - - - +
86B ALA 3.2 4.9 - - - +
87B THR* 1.3 75.9 - - - +
89B ASP* 1.3 60.3 + - - +
90B HIS 3.6 3.6 + - - +
93B ILE* 4.2 22.0 - - + +
94B VAL 5.2 3.1 - - - +
95B LYS* 5.6 3.6 - - - +
147B PHE* 3.9 18.4 - - + -
148B LEU* 3.8 23.3 - - - -
151B LYS* 5.2 0.7 - - - -
153B ILE* 4.0 11.0 - - - -
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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