Contacts of the helix formed by residues 66 - 87 (chain O) in PDB entry 2HQT
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 THR 66 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O PHE* 3.9 9.0 - - - -
20O VAL* 5.0 8.7 - - + -
22O PHE* 4.4 17.0 - - + -
60O VAL* 3.8 5.7 - - - +
62O THR* 3.6 24.5 - - + +
64O TYR 3.6 10.1 - - - +
65O PRO* 1.3 79.4 - - - +
67O SER* 1.3 66.8 + - - +
68O THR* 2.8 26.0 + - - +
69O ASP* 2.8 21.2 + - - +
70O VAL* 3.1 11.8 + - - +
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Residues in contact with SER 67 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O VAL* 6.5 0.4 - - - -
10O PHE* 3.8 19.2 - - - -
11O GLU* 5.8 4.3 - - - -
66O THR* 1.3 75.5 - - - +
68O THR* 1.3 67.8 + - - +
70O VAL* 3.1 5.0 + - - +
71O HIS* 2.9 47.5 + - - -
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Residues in contact with THR 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22O PHE* 5.3 3.4 - - + -
30O ALA* 3.6 40.2 - - + +
33O TRP* 5.1 8.5 - - + -
37O LEU* 6.0 1.1 - - - -
59O ILE* 4.2 9.9 - - - +
60O VAL* 2.6 29.2 - - + +
66O THR* 2.8 12.4 + - - +
67O SER* 1.3 82.6 + - - +
69O ASP* 1.3 63.2 + - - +
71O HIS* 4.0 3.8 - - - -
72O VAL* 3.0 30.6 + - - +
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Residues in contact with ASP 69 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58O PHE* 3.5 19.5 - - - +
59O ILE* 2.8 37.9 + - - +
60O VAL 4.8 0.7 + - - -
62O THR* 4.4 1.9 + - - -
65O PRO* 3.5 3.3 - - + +
66O THR* 2.8 38.3 + - - +
68O THR* 1.3 78.3 + - - +
70O VAL* 1.3 58.0 + - - +
73O PHE* 2.9 32.4 + - - +
103O TRP* 2.8 23.0 + - - +
107O MET* 3.8 20.0 - - + -
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Residues in contact with VAL 70 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6O LEU* 4.0 22.0 - - + +
7O VAL* 3.8 28.0 - - + -
10O PHE* 3.4 38.8 - - + -
65O PRO* 5.5 0.2 - - + -
66O THR 3.6 11.0 - - - +
67O SER* 3.1 9.0 + - - +
69O ASP* 1.3 73.9 - - - +
71O HIS* 1.3 65.4 + - + +
73O PHE* 3.3 4.2 + - - +
74O GLU* 3.0 23.4 + - + +
107O MET* 4.1 18.2 - - + -
111O LEU* 4.3 9.9 - - + -
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Residues in contact with HIS 71 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O VAL* 3.8 31.6 - - + +
37O LEU* 3.5 32.1 - - + +
67O SER* 2.9 44.7 + - - +
68O THR* 4.1 2.9 - - - +
70O VAL* 1.3 79.1 - - + +
72O VAL* 1.3 64.2 + - - +
74O GLU* 3.5 20.1 + - - +
75O VAL* 3.7 5.0 + - - +
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Residues in contact with VAL 72 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O TRP* 3.9 29.4 - - + -
37O LEU* 3.9 24.9 - - + -
42O ILE* 4.1 12.6 - - + +
49O LEU* 3.8 27.4 - - + -
59O ILE* 3.6 25.6 - - + -
68O THR* 3.0 20.8 + - - +
71O HIS* 1.3 75.2 - - - +
73O PHE* 1.3 51.8 + - - +
75O VAL* 3.2 4.7 + - - +
76O ALA* 2.7 32.5 + - + +
103O TRP* 3.8 3.1 - - + -
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Residues in contact with PHE 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6O LEU* 4.0 20.9 - - + -
69O ASP 2.9 21.6 + - - +
70O VAL* 3.5 4.9 - - - +
71O HIS 3.3 0.2 - - - -
72O VAL* 1.3 77.1 - - - +
74O GLU* 1.3 58.5 + - - +
76O ALA 4.3 0.2 - - - +
77O LEU* 2.8 58.4 + - + +
103O TRP* 3.4 23.7 - + + -
104O ILE* 4.0 21.5 - - + -
107O MET* 3.5 24.2 - - + -
108O GLN* 3.6 30.1 - - + -
111O LEU* 4.0 22.4 - - + -
113O VAL* 4.1 12.1 - - + -
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Residues in contact with GLU 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4O SER* 2.5 41.0 + - - -
6O LEU* 3.3 40.5 + - + +
7O VAL* 3.7 9.2 - - - +
70O VAL* 3.0 19.2 + - + +
71O HIS* 3.6 14.1 + - - +
73O PHE* 1.3 76.4 - - - +
75O VAL* 1.3 61.7 + - + +
77O LEU* 5.3 0.6 - - - +
78O PRO* 3.2 21.7 - - - +
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Residues in contact with VAL 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O LEU* 4.0 24.9 - - + -
42O ILE* 3.0 38.1 - - + -
71O HIS 3.7 3.7 + - - +
72O VAL 3.2 5.9 + - - +
73O PHE 3.1 0.2 - - - -
74O GLU* 1.3 83.2 - - + +
76O ALA* 1.3 63.2 + - - +
77O LEU 3.4 0.4 - - - -
78O PRO* 3.6 6.6 - - - +
79O LEU* 3.5 21.6 + - + +
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Residues in contact with ALA 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O ILE* 4.8 5.8 - - + +
46O LEU* 4.4 4.9 - - + -
49O LEU* 4.3 14.4 - - + -
72O VAL* 2.7 25.0 + - + +
73O PHE 4.2 1.3 - - - +
75O VAL* 1.3 74.8 - - - +
77O LEU* 1.3 63.2 + - - +
79O LEU* 3.3 3.3 + - - -
80O ILE* 2.5 45.0 + - + +
100O ILE* 5.0 0.9 - - + -
103O TRP* 4.3 18.2 - - + -
104O ILE* 4.7 0.9 - - + -
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Residues in contact with LEU 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O LEU* 5.4 6.3 - - + -
73O PHE* 2.8 44.2 + - + +
76O ALA* 1.3 77.6 - - - +
78O PRO* 1.3 67.3 - - + +
80O ILE* 3.8 1.2 - - - +
81O LYS* 2.9 43.6 + - + +
104O ILE* 4.1 16.6 - - + +
108O GLN* 3.9 19.5 - - - +
113O VAL* 4.3 13.9 - - + -
117O ASP* 3.9 15.5 - - + +
119O LEU* 3.9 19.1 - - + +
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Residues in contact with PRO 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74O GLU 3.2 24.2 - - - +
75O VAL* 3.6 11.4 - - - +
77O LEU* 1.3 100.8 - - + +
79O LEU* 1.3 54.7 + - - +
81O LYS* 3.6 9.4 - - + +
82O ASP* 3.0 39.4 + - - +
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Residues in contact with LEU 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O ILE* 3.0 35.0 - - + -
43O GLN* 3.8 39.3 - - + +
46O LEU* 4.1 15.7 - - + -
75O VAL* 3.5 12.6 + - + +
76O ALA* 3.3 7.3 + - - +
77O LEU 3.3 0.8 - - - -
78O PRO* 1.3 77.2 - - - +
80O ILE* 1.3 63.2 + - + +
82O ASP* 3.3 11.9 + - + +
83O LEU* 3.0 32.9 + - + +
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Residues in contact with ILE 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46O LEU* 3.8 28.9 - - + -
76O ALA* 2.5 44.4 + - + +
77O LEU 3.9 1.1 - - - +
79O LEU* 1.3 74.4 - - + +
81O LYS* 1.3 67.5 + - - +
83O LEU* 3.2 12.0 + - + +
84O VAL* 2.8 32.2 + - + +
93O THR* 6.1 0.2 - - + -
97O TYR* 5.3 11.2 - - + -
100O ILE* 4.1 12.3 - - + -
101O LEU* 3.8 13.5 - - + -
104O ILE* 3.9 16.2 - - + -
119O LEU* 3.8 25.8 - - + -
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Residues in contact with LYS 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77O LEU* 2.9 35.0 + - + +
78O PRO* 3.6 8.5 - - + +
80O ILE* 1.3 77.2 - - - +
82O ASP* 1.3 58.5 + - - +
84O VAL* 3.8 1.7 - - - +
85O ALA* 2.9 30.3 + - - +
116O THR 3.7 15.0 + - - -
117O ASP* 3.6 21.3 + - - +
118O LYS 3.2 24.2 + - - +
119O LEU* 4.0 22.9 - - + +
120O GLU 5.3 0.4 - - - +
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Residues in contact with ASP 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O PRO* 3.0 28.6 + - - +
79O LEU* 3.5 13.8 - - + +
81O LYS* 1.3 75.8 - - - +
83O LEU* 1.3 55.5 + - - +
85O ALA* 3.7 5.5 - - - +
86O SER* 2.8 40.1 + - - -
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Residues in contact with LEU 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O GLN* 4.2 20.0 - - - +
46O LEU* 3.7 29.6 - - + -
79O LEU* 3.0 18.3 + - + +
80O ILE* 3.6 13.2 - - + +
82O ASP* 1.3 77.0 - - + +
84O VAL* 1.3 63.3 + - - +
86O SER* 3.4 8.5 + - - +
87O SER* 3.0 25.5 + - - -
93O THR* 4.2 13.6 - - + +
97O TYR* 3.9 28.0 - - + +
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Residues in contact with VAL 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80O ILE* 2.8 33.2 + - + +
81O LYS 3.8 3.8 - - - +
83O LEU* 1.3 77.7 - - - +
85O ALA* 1.3 64.0 + - - +
87O SER* 3.2 19.7 + - - +
90O VAL* 3.9 21.3 - - + +
93O THR* 3.9 21.5 - - + -
94O TYR* 3.9 25.4 - - + +
101O LEU* 5.3 2.9 - - + -
119O LEU* 4.3 16.6 - - + -
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Residues in contact with ALA 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81O LYS 2.9 19.2 + - - +
82O ASP* 3.8 6.5 - - - +
84O VAL* 1.3 77.4 - - - +
86O SER* 1.3 60.4 + - - +
87O SER 3.6 3.3 + - - +
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Residues in contact with SER 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82O ASP 2.8 24.4 + - - -
83O LEU* 3.4 13.5 + - - +
85O ALA* 1.3 72.2 - - - +
87O SER* 1.3 62.2 + - - +
88O LYS* 3.4 12.6 + - - +
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Residues in contact with SER 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83O LEU 3.0 13.6 + - - -
84O VAL 3.2 14.3 + - - +
85O ALA 4.3 3.5 - - - +
86O SER* 1.3 77.5 - - - +
88O LYS* 1.3 60.8 + - - +
89O ASP 2.9 23.4 + - - -
90O VAL* 4.1 9.5 + - - +
92O SER* 4.8 0.2 + - - -
93O THR* 2.8 31.8 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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