Contacts of the helix formed by residues 73 - 90 (chain B) in PDB entry 1Q0K
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 GLU 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 2.9 37.3 - - - -
72B PRO* 1.3 79.8 - - - +
74B LEU* 1.3 55.1 + - - +
75B HIS 3.4 1.3 - - - -
76B THR* 3.2 10.2 + - - +
77B LEU* 2.8 41.6 + - + +
110B ILE* 4.2 12.4 - - + +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B PHE* 3.6 47.6 - - + -
67B HIS* 4.4 13.7 - - + +
68B PHE* 3.7 23.6 - - + -
71B TYR* 2.9 21.5 + - + +
72B PRO 3.5 0.2 - - - -
73B GLU* 1.3 81.8 - - - +
75B HIS* 1.3 63.3 + - - +
77B LEU* 4.1 9.9 - - + -
78B VAL* 2.9 45.7 + - + +
107B ILE* 5.1 2.7 - - + -
110B ILE* 4.1 24.0 - - + -
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Residues in contact with HIS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TRP* 3.0 29.5 + - - +
68B PHE* 3.4 52.6 - + + +
71B TYR 4.7 0.9 + - - -
72B PRO* 4.8 7.5 + - + +
73B GLU 3.4 0.6 - - - -
74B LEU* 1.3 76.9 - - - +
76B THR* 1.3 63.5 + - - +
78B VAL* 4.1 0.3 - - - -
79B ASN* 3.0 24.4 + - - +
59C TRP* 3.8 5.7 - - - -
75C HIS* 3.5 52.6 - + + +
76C THR* 4.3 13.4 + - - -
79C ASN* 4.2 7.6 - - + -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PRO 5.3 2.5 + - - -
73B GLU* 3.2 12.1 + - - -
75B HIS* 1.3 78.0 - - - +
77B LEU* 1.3 58.0 + - - +
79B ASN* 3.6 5.5 - - - +
80B GLU* 2.8 61.3 + - + +
68C PHE* 5.9 0.5 - - - +
69C GLU* 5.8 0.2 + - - -
75C HIS* 4.0 14.7 + - - -
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 2.8 28.5 + - + +
74B LEU* 3.6 8.3 - - + +
76B THR* 1.3 71.9 - - - +
78B VAL* 1.3 58.5 + - - +
80B GLU* 3.2 9.2 + - - +
81B ALA* 2.9 28.1 + - - +
103B TYR* 3.5 34.3 - - + +
106B GLN* 3.7 33.4 - - + +
107B ILE* 3.6 24.9 - - + +
110B ILE* 4.0 27.1 - - + -
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 4.0 22.4 - - + +
58B LEU* 6.4 0.4 - - + -
59B TRP* 3.8 25.8 - - + -
63B PHE* 4.8 5.2 - - + -
74B LEU* 2.9 40.7 + - + +
75B HIS 4.1 1.1 - - - +
77B LEU* 1.3 75.2 - - - +
79B ASN* 1.3 62.6 + - - +
81B ALA* 3.1 2.8 + - - +
82B VAL* 3.0 23.0 + - + +
107B ILE* 4.0 25.6 - - + -
59C TRP* 3.8 20.4 - - + -
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Residues in contact with ASN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS 3.0 19.7 + - - +
76B THR* 3.6 5.4 - - - +
78B VAL* 1.3 78.0 - - - +
80B GLU* 1.3 58.7 + - + +
82B VAL* 2.9 21.0 - - - +
83B LYS* 2.6 41.7 + - - +
59C TRP* 3.0 61.0 + - + +
60C SER* 4.1 0.8 - - - +
65C PRO* 5.6 1.9 - - - +
68C PHE* 3.7 15.5 - - - -
75C HIS* 4.0 4.9 - - + -
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B THR* 2.8 47.4 + - + +
77B LEU* 3.7 7.0 - - - +
79B ASN* 1.3 72.3 - - + +
81B ALA* 1.3 60.1 + - - +
83B LYS* 3.7 10.4 - - + +
84B ALA* 2.9 29.6 + - - +
103B TYR* 3.3 40.2 + - + +
65C PRO* 5.9 7.3 - - + +
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.8 13.7 - - + -
77B LEU 2.9 14.5 + - - +
78B VAL 3.1 9.2 + - - +
80B GLU* 1.3 78.6 - - - +
82B VAL* 1.3 61.8 + - - +
84B ALA* 3.1 6.1 + - - +
85B LEU* 3.1 23.6 + - - +
100B ALA* 4.8 2.1 - - - +
103B TYR* 3.7 24.6 - - + -
104B ILE* 4.9 1.7 - - + +
107B ILE* 3.7 22.4 - - + -
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LYS* 3.8 17.9 - - - +
55B LEU* 3.9 24.9 - - + -
56B ASP* 3.5 22.0 - - - +
78B VAL* 3.0 17.8 + - + +
79B ASN* 2.9 29.8 - - - +
81B ALA* 1.3 75.5 - - - +
83B LYS* 1.3 61.4 + - - +
85B LEU* 3.1 12.4 + - - +
86B SER* 3.0 23.1 + - - -
59C TRP* 4.1 3.4 - - + -
60C SER* 3.5 31.4 - - - -
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Residues in contact with LYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASN* 2.6 47.7 + - - +
80B GLU* 3.8 9.9 - - + +
82B VAL* 1.3 78.2 - - - +
84B ALA* 1.3 57.0 + - - +
86B SER* 3.3 10.9 + - - -
87B ALA* 3.0 25.3 + - - +
59C TRP 3.7 1.0 + - - -
60C SER 3.0 25.4 + - - +
61C ASP 5.5 0.7 - - - -
63C PHE 3.0 28.7 + - - -
64C LYS* 4.2 10.1 - - - +
65C PRO* 4.1 26.9 - - + -
68C PHE* 4.4 0.8 - - - -
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU 2.9 14.4 + - - +
81B ALA 3.1 10.7 + - - +
83B LYS* 1.3 77.3 - - - +
85B LEU* 1.3 60.2 + - - +
87B ALA* 3.2 8.6 + - - +
88B ALA* 3.0 25.8 + - - +
96B THR 4.3 5.4 - - - +
99B LYS* 4.5 13.9 - - + +
100B ALA* 4.1 17.0 - - + +
103B TYR* 4.0 21.5 - - + -
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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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18B ALA* 4.3 12.8 - - + -
21B VAL* 5.1 4.5 - - + -
48B ALA* 4.1 13.2 - - + +
51B ALA* 3.7 20.4 - - + -
52B LYS* 3.5 43.5 - - + +
55B LEU* 3.7 26.0 - - + -
81B ALA 3.1 14.1 + - - +
82B VAL* 3.1 8.0 + - - +
84B ALA* 1.3 74.1 - - - +
86B SER* 1.3 66.5 + - - +
88B ALA* 3.2 9.7 + - + +
89B LYS* 3.1 23.7 + - - +
100B ALA* 3.7 21.1 - - + -
104B ILE* 5.0 2.2 - - + -
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Residues in contact with SER 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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39A ARG* 5.1 0.9 + - - -
52B LYS* 2.9 28.4 + - - +
82B VAL 3.0 8.8 + - - -
83B LYS* 3.3 14.9 - - - -
84B ALA 3.2 0.2 - - - -
85B LEU* 1.3 77.9 - - - +
87B ALA* 1.3 61.4 + - - +
89B LYS* 3.2 17.8 + - - +
90B ALA* 3.4 8.3 + - - +
3C ASP* 3.1 24.1 + - - +
60C SER 5.2 0.5 + - - -
61C ASP* 4.0 4.3 + - - -
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Residues in contact with ALA 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 LYS 3.0 13.1 + - - +
84B ALA* 3.2 12.3 + - - +
86B SER* 1.3 76.1 - - - +
88B ALA* 1.3 61.9 + - - +
90B ALA* 3.3 8.8 + - - +
91B SER* 3.3 24.0 + - - -
96B THR* 4.5 10.3 - - + -
99B LYS* 6.4 0.9 - - + -
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Residues in contact with ALA 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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21B VAL* 3.9 22.9 - - + -
25B GLN* 3.4 5.1 + - - +
44B LYS* 3.2 7.8 + - - +
48B ALA* 5.5 0.7 - - + -
84B ALA 3.0 13.5 + - - +
85B LEU* 3.4 16.8 - - + +
86B SER 3.1 0.2 - - - -
87B ALA* 1.3 75.2 - - - +
89B LYS* 1.3 64.2 + - - +
91B SER 3.0 18.7 - - - +
96B THR* 3.7 29.3 - - - +
97B GLY* 4.5 1.6 - - - -
100B ALA* 5.3 0.7 - - + -
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Residues in contact with LYS 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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39A ARG* 3.4 19.2 + - - +
44B LYS* 2.6 30.2 + - - +
45B GLU* 3.2 52.6 + - - +
48B ALA* 3.6 18.1 - - + +
49B GLU* 2.7 42.3 + - - +
52B LYS* 4.2 8.1 - - - +
85B LEU 3.1 11.8 + - - +
86B SER 3.2 6.9 + - - +
88B ALA* 1.3 75.8 - - - +
90B ALA* 1.3 58.3 + - - +
91B SER 3.1 0.4 + - - -
2C CYS 5.0 1.6 + - - -
3C ASP* 2.8 36.4 + - - +
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG* 3.5 30.1 - - - +
86B SER 3.4 6.9 + - - +
87B ALA* 3.3 9.7 + - - +
88B ALA 3.3 0.4 - - - -
89B LYS* 1.3 78.0 - - - +
91B SER* 1.3 58.8 + - - +
4C LEU 4.9 2.0 - - - +
5C PRO* 6.2 1.1 - - + -
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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