Contacts of the helix formed by residues 49 - 73 (chain O) in PDB entry 1I94
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 49 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650A G 3.5 22.9 - - - +
651A G 3.8 21.8 - - - +
43O LEU* 6.4 0.4 - - - -
46O HIS* 3.5 16.1 + - + +
47O LYS 3.5 2.6 - - - -
48O LYS* 1.3 71.8 - - - +
50O HIS* 1.3 64.2 + - - +
51O HIS 2.8 5.8 + - - -
52O SER* 3.0 23.8 + - - +
53O HIS* 3.1 9.8 + - - +
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Residues in contact with HIS 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A G 4.3 1.0 + - - -
711A A 5.0 5.8 + - - +
747A C 4.5 31.6 - - - +
748A G 5.5 2.2 - - - +
47O LYS 5.0 1.7 + - - -
48O LYS 2.8 14.7 + - - +
49O ASP* 1.3 70.4 - - - +
51O HIS* 1.3 65.9 + - - +
53O HIS* 3.0 23.3 + - + +
54O ARG* 3.1 5.7 + - - +
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Residues in contact with HIS 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A G 4.5 12.6 - - - +
650A G 4.3 27.8 + - - +
711A A 4.5 13.9 - - - +
712A A 6.1 0.2 - - - +
724A G 4.3 6.4 + - - +
49O ASP 2.8 1.4 + - - -
50O HIS* 1.3 76.0 - - - +
52O SER* 1.3 53.6 + - - +
54O ARG* 2.3 43.5 + - - +
55O GLY 3.4 1.0 + - - -
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Residues in contact with SER 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A G 4.7 2.3 - - - +
650A G 5.3 0.8 + - - -
723A U 3.0 35.2 - - - -
724A G 3.5 20.7 + - - +
39O LEU* 6.0 1.8 - - - +
43O LEU* 6.5 0.7 - - - -
49O ASP* 3.0 19.3 + - - +
51O HIS* 1.3 76.5 - - - +
53O HIS* 1.3 64.4 + - - +
54O ARG 2.7 1.7 + - - -
55O GLY* 3.0 11.3 + - - -
56O LEU* 3.0 11.4 + - - +
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Residues in contact with HIS 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43O LEU* 5.9 9.4 - - + -
49O ASP 3.1 6.8 + - - +
50O HIS* 3.0 23.3 + - + +
51O HIS 2.7 3.2 + - - -
52O SER* 1.3 75.2 - - - +
54O ARG* 1.3 60.1 + - - +
56O LEU* 3.2 20.3 - - - +
57O LEU* 3.5 7.1 + - - +
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Residues in contact with ARG 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A G 5.7 4.9 - - - +
563A U 5.8 1.9 - - - +
711A A 4.9 15.9 - - + +
724A G 5.0 1.8 - - - +
50O HIS 3.1 4.7 + - - +
51O HIS* 2.3 37.2 + - - +
53O HIS* 1.3 63.5 - - - +
55O GLY* 1.3 53.4 + - - +
56O LEU 2.9 4.0 - - - -
57O LEU* 2.7 30.8 + - - +
58O MET* 3.3 8.4 + - - +
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Residues in contact with GLY 55 (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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724A G 3.4 35.1 + - - -
725A G 4.1 10.4 + - - -
51O HIS 3.4 2.0 + - - -
52O SER 3.0 5.3 + - - -
54O ARG* 1.3 79.0 - - - +
56O LEU* 1.3 62.8 + - - +
58O MET* 3.3 15.8 + - - +
59O MET* 3.3 14.2 + - - +
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Residues in contact with LEU 56 (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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724A G 5.2 0.8 - - - -
36O ILE* 6.1 1.5 - - - +
39O LEU* 5.3 15.9 - - + -
40O SER* 6.2 1.3 - - - +
52O SER 3.0 10.0 + - - +
53O HIS* 3.2 18.6 - - - +
55O GLY* 1.3 78.3 - - - +
57O LEU* 1.3 52.5 + - - +
59O MET* 3.3 4.5 + - - +
60O VAL* 2.7 37.6 + - - +
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Residues in contact with LEU 57 (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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563A U 4.0 34.4 + - - +
53O HIS 3.5 6.7 + - - +
54O ARG* 2.7 18.0 + - - +
56O LEU* 1.3 73.2 - - - +
58O MET* 1.3 62.2 + - - +
60O VAL* 3.8 8.3 - - - +
61O GLY* 3.0 17.0 + - - -
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Residues in contact with MET 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A U 4.7 9.1 - - - +
564A G 4.3 8.7 + - - -
725A G 5.1 8.3 - - - +
54O ARG 3.3 6.3 + - - +
55O GLY* 3.6 13.2 - - - +
56O LEU 3.2 0.8 + - - -
57O LEU* 1.3 72.9 - - - +
59O MET* 1.3 56.5 - - - +
61O GLY* 2.8 4.3 + - - -
62O GLN* 2.2 41.6 + - + +
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Residues in contact with MET 59 (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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725A G 5.5 4.2 + - - +
32O LEU* 5.3 16.6 - - + +
35O ARG* 6.0 3.1 - - + -
36O ILE* 5.4 11.9 - - + +
55O GLY 3.3 8.0 + - - +
56O LEU* 3.6 8.7 - - - +
58O MET* 1.3 77.7 - - - +
60O VAL* 1.3 60.0 + - - +
62O GLN* 3.4 11.0 - - - +
63O ARG* 2.6 36.4 + - - +
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Residues in contact with VAL 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36O ILE* 5.8 4.9 - - - +
56O LEU 2.7 23.0 + - - +
57O LEU* 3.8 11.0 - - - +
59O MET* 1.3 76.0 - - - +
61O GLY* 1.3 60.2 + - - +
63O ARG* 4.2 3.7 - - - +
64O ARG* 3.4 19.4 + - - +
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Residues in contact with GLY 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A G 4.2 22.0 - - - -
57O LEU 3.0 12.3 + - - -
58O MET 2.8 5.6 + - - -
60O VAL* 1.3 74.6 - - - +
62O GLN* 1.3 55.8 + - - +
64O ARG* 3.2 6.9 + - - +
65O ARG* 2.8 36.3 + - - +
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Residues in contact with GLN 62 (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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564A G 4.6 1.6 + - - -
32O LEU* 6.1 2.0 - - + -
58O MET* 2.2 33.5 + - + +
59O MET* 2.9 14.3 + - - +
61O GLY 1.3 68.8 - - - +
63O ARG* 1.3 65.3 + - - +
65O ARG* 3.0 18.2 + - - +
66O LEU* 3.3 5.4 + - - +
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Residues in contact with ARG 63 (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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29O VAL* 5.1 14.5 - - + +
32O LEU* 4.6 20.9 - - + +
33O THR* 5.4 4.9 - - - +
59O MET* 2.6 19.6 + - - +
60O VAL* 4.2 3.1 - - - +
62O GLN* 1.3 70.7 - - - +
64O ARG* 1.3 65.7 + - - +
66O LEU* 2.9 21.2 + - - +
67O LEU* 3.1 10.3 + - - +
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Residues in contact with ARG 64 (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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60O VAL 3.4 14.6 + - - +
61O GLY* 3.2 11.8 + - - +
63O ARG* 1.3 78.1 - - - +
65O ARG* 1.3 64.8 + - - +
67O LEU* 3.0 12.2 + - - +
68O ARG* 2.9 20.9 + - - +
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Residues in contact with ARG 65 (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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737A C 4.6 3.1 + - - +
738A G 4.2 23.1 + - - +
61O GLY 2.8 15.7 + - - +
62O GLN* 3.0 12.3 + - - +
64O ARG* 1.3 72.9 - - - +
66O LEU* 1.3 63.6 + - - +
68O ARG* 2.9 19.2 + - - +
69O TYR* 3.0 12.5 + - - +
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Residues in contact with LEU 66 (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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737A C 4.8 4.9 - - - -
25O THR* 5.1 19.3 - - - +
28O GLN* 5.7 3.6 - - + -
29O VAL* 5.3 11.4 - - + +
62O GLN 3.3 4.4 + - - +
63O ARG* 2.9 17.1 + - - +
65O ARG* 1.3 73.4 - - - +
67O LEU* 1.3 54.0 + - - +
69O TYR* 2.8 10.1 + - - +
70O LEU* 2.7 37.9 + - - +
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Residues in contact with LEU 67 (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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63O ARG 3.1 6.3 + - - +
64O ARG* 3.0 13.6 + - - +
66O LEU* 1.3 79.2 - - - +
68O ARG* 1.3 53.6 + - - +
70O LEU* 4.3 6.5 - - - -
71O GLN* 2.6 38.3 + - - +
78O TYR* 5.5 0.2 - - - +
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Residues in contact with ARG 68 (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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64O ARG 2.9 10.2 + - - +
65O ARG* 2.9 14.6 + - - +
67O LEU* 1.3 77.4 - - - +
69O TYR* 1.3 60.0 + - - +
71O GLN* 3.8 6.9 - - - +
72O ARG* 3.4 20.3 + - - +
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Residues in contact with TYR 69 (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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737A C 3.6 36.8 - - + +
65O ARG 3.0 5.8 + - - +
66O LEU* 2.8 10.3 + - - +
68O ARG* 1.3 76.1 - - - +
70O LEU* 1.3 64.1 + - - +
72O ARG* 3.1 4.9 + - - +
73O GLU* 3.0 26.4 + - - +
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Residues in contact with LEU 70 (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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25O THR* 4.8 15.9 - - - -
66O LEU 2.7 19.5 + - - +
67O LEU* 3.9 6.3 - - - +
69O TYR* 1.3 73.2 - - - +
71O GLN* 1.3 62.5 + - - +
72O ARG 3.0 1.4 + - - -
73O GLU* 3.1 14.5 + - - +
74O ASP* 3.2 19.7 + - + +
77O ARG* 6.1 3.1 - - + -
78O TYR* 4.6 11.0 - - + +
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Residues in contact with GLN 71 (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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67O LEU 2.6 25.0 + - - +
68O ARG* 3.8 8.3 - - - +
70O LEU* 1.3 74.4 - - - +
72O ARG* 1.3 58.4 + - - +
75O PRO* 3.8 20.6 - - - +
78O TYR* 3.9 19.7 - - + +
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Residues in contact with ARG 72 (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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68O ARG 3.4 12.0 + - - +
69O TYR* 3.1 5.6 + - - +
70O LEU 3.1 0.6 - - - -
71O GLN* 1.3 79.5 - - - +
73O GLU* 1.3 58.9 + - - +
74O ASP 3.4 5.1 + - - -
75O PRO 5.1 0.5 - - - -
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Residues in contact with GLU 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A A 5.8 3.6 - - - +
69O TYR 3.0 16.1 + - - +
70O LEU* 3.1 4.7 + - - +
72O ARG* 1.3 76.8 - - + +
74O ASP* 1.3 64.8 + - - +
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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) + - + + + + + -
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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